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PDBjͷσʔλ a member of Protein Data Bank Japan (PDBj) େࡕେനڀݚॴ দӜ ͷΊͷલ४උ 2008-06-11 ୈճ ຊനՊձ ϥϯνϣϯηϛφʔ

PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

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Page 1: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

PDBj

a member of

Protein Data Bank Japan (PDBj)

2008-06-11

Page 2: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

PDB

http://pdbdep.protein.osaka-u.ac.jp/adit/http://nmradit.protein.osaka-u.ac.jp/bmrb-adit/ (NMR)

http://pdbdep.protein.osaka-u.ac.jp/

http://pdbdep.protein.osaka-u.ac.jp/validate/

2008-06-11

http://pdbdep.protein.osaka-u.ac.jp/adit/
http://nmradit.protein.osaka-u.ac.jp/bmrb-adit/
http://pdbdep.protein.osaka-u.ac.jp/
http://pdbdep.protein.osaka-u.ac.jp/validate/
Page 3: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

PDB

http://pdbdep.protein.osaka-u.ac.jp/tutorial/http://bmrbdep.protein.osaka-u.ac.jp/manual_top.html (NMR)

http://pdbdep.protein.osaka-u.ac.jp/

wwPDB “Annotation Documentation” http://www.wwpfb.org/docs.html

Data Processing and Annotation Procedures Manualhttp://deposit.rcsb.org/depoinfo/download/dp.pdf

2008-06-11

http://pdbdep.protein.osaka-u.ac.jp/tutorial/
http://bmrbdep.protein.osaka-u.ac.jp/manual_top.html
http://pdbdep.protein.osaka-u.ac.jp/
http://www.wwpfb.org/docs.html
http://deposit.rcsb.org/depoinfo/download/dp.pdf
Page 4: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

24

4

2008-06-11

Page 5: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

2008-06-11

Page 6: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

?

Uniprot

/ ?

/?

2008-06-11

Page 7: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

?

wwPDB

referee

2008-06-11

Page 8: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

Uniprot ?

UniProt

http://www.pir.uniprot.org/

2008-06-11

http://www.pir.uniprot.org/
Page 9: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

Uniprot ?

EdmanEBI SPIN

DDBJ SAKURA, EMBL Webin, NCBI BankIt

http://www.ebi.ac.uk/swissprot/Submissions/spin/

http://sakura.ddbj.nig.ac.jp/http://www.ebi.ac.uk/embl/Submission/webin.htmlhttp://www.ncbi.nlm.nih.gov/BankIt/

2008-06-11

http://www.ebi.ac.uk/swissprot/Submissions/spin/
http://sakura.ddbj.nig.ac.jp/
http://www.ebi.ac.uk/embl/Submission/webin.html
http://www.ncbi.nlm.nih.gov/BankIt/
Page 10: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

/ ?

http://ligand-expo.rcsb.org/

PDB Ligand Expo

SMILES InChi

Ligand Expo

component identifier (3 )

2008-06-11

http://ligand-expo.rcsb.org/
Page 11: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

/ ?PDB

, ,

: ,

Ligand Expo “Sketch input and/or structure search options”

IUPAC

2008-06-11

Page 12: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

/?

chain ID

2008-06-11

Page 13: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

http://pdbdep.protein.osaka-u.ac.jp/validate/

close contact

3.5Å

Missing Residues/Atoms

Extra Atoms

Ramachandran revisited Φ/Ψ

2008-06-11

http://pdbdep.protein.osaka-u.ac.jp/validate/
Page 14: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

Ramachandran revisited Φ/ΨPhi/Psi-chology: Ramachandran revisitedG.J. Kleywegt and T.A. JonesStructure 4(12), 1395-1400 (1996)

1965 1996463 403463

Ramachandran Ramachandran revisited

3000Most favored,

Additional allowed,Generously allowed,

Disallowed

Inside coreOutside core

Gly, Pro Gly, Terminal

2008-06-11

Page 15: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

http://pdbdep.protein.osaka-u.ac.jp/adit/http://nmradit.protein.osaka-u.ac.jp/bmrb-adit/ (NMR)

XNMR

2008-06-11

http://pdbdep.protein.osaka-u.ac.jp/adit/
http://nmradit.protein.osaka-u.ac.jp/bmrb-adit/
Page 16: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

http://pdb-extract.rcsb.org/

CNS XPDB-extract deposit_mmcif.inp

(deposit.mmcif, deposit_sf.mmcif) PDB-extract xtal_pdbsubmission.inp

(xtal_pdbsubmission.deposit) SEQRES PDB

mmCIF

CCP4“NOHARVEST”

CCP4i “Data Harvesting” “Do not create harvest file”SCALA, MLPHARE, REFMAC5 CIF

2008-06-11

http://pdb-extract.rcsb.org/
Page 17: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

2008-06-11

http://pdbdep.protein.osaka-u.ac.jp/adit/http://nmradit.protein.osaka-u.ac.jp/bmrb-adit/ (NMR)

http://pdbdep.protein.osaka-u.ac.jp/adit/
http://nmradit.protein.osaka-u.ac.jp/bmrb-adit/
Page 18: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

PDBj

From: PDBj Annotator (XX) <[email protected]>Subject: structure of rcsbXXXXXX

Subject

2008-06-11

Page 19: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

(RELEASE NOW)(HOLD FOR RELEASE)

(X ) (NMR)(RELEASE NOW)

(HOLD FOR 8 WEEKS)(HOLD FOR 6 MONTHS)

(HOLD FOR 1 YEAR)(HOLD FOR PUBLICATION)

2008-06-11

Page 20: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

“HOLD FOR PUBLICATION”

(WITHDRAWN)

“HOLD FOR PUBLICATION”

2008-06-11

Page 21: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

PDBj

http://www.pdbj.org/pdbj_aditmail_j.html

2008-06-11

http://www.pdbj.org/pdbj_aditmail_j.html
Page 22: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

2008-06-11

Page 23: PDBj w à » J å - Protein Data Bank Japan - PDB Japan · $ B T w í ð Ä ò t x z c & t J å T w Ý ç t x z $ B T c X q ° ? º t & ô U § X From: PDBj Annotator (XX)

2008-06-11


U(t - T, x)

U(t - T, x)

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