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- PDB-1izl: Crystal Structure of Photosystem II -

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Basic information

Entry
Database: PDB / ID: 1izl
TitleCrystal Structure of Photosystem II
Components(Photosystem II: Subunit ...) x 14
KeywordsPHOTOSYNTHESIS / Photosynthetic reaction center / Core-antenna / Thermophilic cyanobacterium / Membrane protein complex / Electron transfer / Energy transfer
Function / homology
Function and homology information


cytochrome c-heme linkage / oxygen evolving activity / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding ...cytochrome c-heme linkage / oxygen evolving activity / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / respiratory electron transport chain / electron transfer activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II CP43 reaction centre protein superfamily / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein ...Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II CP43 reaction centre protein superfamily / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL A / : / PROTOPORPHYRIN IX CONTAINING FE / : / PHEOPHYTIN A / Chem-PLA / : / : / : ...BETA-CAROTENE / CHLOROPHYLL A / : / PROTOPORPHYRIN IX CONTAINING FE / : / PHEOPHYTIN A / Chem-PLA / : / : / : / Photosystem II extrinsic protein V / Photosystem II protein D1 / Cytochrome c-550 / Photosystem II D2 protein / Photosystem II CP43 reaction center protein / Cytochrome b559 subunit beta / Cytochrome b559 subunit alpha / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein K
Similarity search - Component
Biological speciesThermosynechococcus vulcanus (bacteria)
Thermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.7 Å
AuthorsKamiya, N. / Shen, J.-R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal structure of oxygen-evolving photosystem II from Thermosynechococcus vulcanus at 3.7-A resolution
Authors: Kamiya, N. / Shen, J.-R.
History
DepositionOct 4, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 28, 2012Group: Other
Revision 1.4Nov 20, 2019Group: Advisory / Database references / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle ...database_PDB_caveat / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_ref_seq
Item: _struct_ref_seq.db_align_end
Revision 2.0Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_chiral / struct_conn / struct_conn_type / struct_site
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photosystem II: Subunit PsbA
B: Photosystem II: Subunit PsbB
C: Photosystem II: Subunit PsbC
D: Photosystem II: Subunit PsbD
E: Photosystem II: Subunit PsbE
F: Photosystem II: Subunit PsbF
G: Photosystem II: Subunit PsbG
H: Photosystem II: Subunit PsbH
I: Photosystem II: Subunit PsbI
K: Photosystem II: Subunit PsbK
O: Photosystem II: Subunit PsbO
U: Photosystem II: Subunit PsbU
V: Photosystem II: Subunit PsbV
X: Photosystem II: Subunit PsbX
J: Photosystem II: Subunit PsbA
L: Photosystem II: Subunit PsbB
M: Photosystem II: Subunit PsbC
N: Photosystem II: Subunit PsbD
P: Photosystem II: Subunit PsbE
Q: Photosystem II: Subunit PsbF
R: Photosystem II: Subunit PsbG
S: Photosystem II: Subunit PsbH
T: Photosystem II: Subunit PsbI
W: Photosystem II: Subunit PsbK
Y: Photosystem II: Subunit PsbO
Z: Photosystem II: Subunit PsbU
0: Photosystem II: Subunit PsbV
1: Photosystem II: Subunit PsbX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)600,356122
Polymers527,69228
Non-polymers72,66394
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.377, 225.192, 308.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Photosystem II: Subunit ... , 14 types, 28 molecules AJBLCMDNEPFQGRHSITKWOYUZV0X1

#1: Protein Photosystem II: Subunit PsbA / / Photosystem Q(B) protein


Mass: 39792.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P51765
#2: Protein Photosystem II: Subunit PsbB / / photosystem II core light harvesting protein


Mass: 49478.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIQ1*PLUS
#3: Protein Photosystem II: Subunit PsbC / / photosystem II CP43 protein


Mass: 49868.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIF8*PLUS
#4: Protein Photosystem II: Subunit PsbD / / photosystem II reaction center D2 protein


Mass: 39388.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: GenBank: 22297998, UniProt: Q8CM25*PLUS
#5: Protein Photosystem II: Subunit PsbE / / cytochrome b559 alpha subunit


Mass: 9449.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: GenBank: 22299084, UniProt: Q8DIP0*PLUS
#6: Protein/peptide Photosystem II: Subunit PsbF / / cytochrome b559 beta subunit


Mass: 4936.704 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: GenBank: 22299085, UniProt: Q8DIN9*PLUS
#7: Protein Photosystem II: Subunit PsbG / / Coordinate model: Cα atoms only


Mass: 18741.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1
#8: Protein/peptide Photosystem II: Subunit PsbH /


Mass: 2826.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1
#9: Protein/peptide Photosystem II: Subunit PsbI /


Mass: 2230.741 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1
#10: Protein/peptide Photosystem II: Subunit PsbK / / Photosystem II reaction center protein K


Mass: 4101.911 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1K9
#11: Protein Photosystem II: Subunit PsbO /


Mass: 17464.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1
#12: Protein Photosystem II: Subunit PsbU /


Mass: 8273.189 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1
#13: Protein Photosystem II: Subunit PsbV / / Cytochrome c-550


Mass: 15148.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P56150, UniProt: P0A387*PLUS
#14: Protein/peptide Photosystem II: Subunit PsbX /


Mass: 2145.636 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1

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Non-polymers , 7 types, 94 molecules

#15: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#16: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 72 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#17: Chemical
ChemComp-PHO / PHEOPHYTIN A / Pheophytin


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#18: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#19: Chemical ChemComp-PLA / 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID / N-PYRIDOXYL-2-METHYLASPARTIC ACID-5-MONOPHOSPHATE


Mass: 378.272 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N2O9P
#20: Chemical ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56
#21: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Details

Sequence detailsCHAIN B, L: THE DEPOSITOR KNOWS THE SEQUENCE. GENBANK NP_682320 (ACCESSION CODE 22299073) BUT THEY ...CHAIN B, L: THE DEPOSITOR KNOWS THE SEQUENCE. GENBANK NP_682320 (ACCESSION CODE 22299073) BUT THEY COULD NOT ASSIGN THE RESIDUES 259-344 AND 345-402. THE RESIUDES 1001-1048 AND 1049-1106 (ONLY THE ALPHA CARBONS) ARE CERTAINLY PART OF RESIDUES 259-344 AND 345-402. BUT THEY DO NOT KNOW WHETHER THESE PART IS CORRECT DIRECTION. MET GLY LEU PRO TRP TYR ARG VAL HIS THR VAL LEU ILE ASN ASP PRO GLY ARG LEU ILE ALA ALA HIS LEU MET HIS THR ALA LEU VAL ALA GLY TRP ALA GLY SER MET ALA LEU TYR GLU LEU ALA THR PHE ASP PRO SER ASP PRO VAL LEU ASN PRO MET TRP ARG GLN GLY MET PHE VAL LEU PRO PHE MET ALA ARG LEU GLY VAL THR GLY SER TRP SER GLY TRP SER ILE THR GLY GLU THR GLY ILE ASP PRO GLY PHE TRP SER PHE GLU GLY VAL ALA LEU ALA HIS ILE VAL LEU SER GLY LEU LEU PHE LEU ALA ALA CYS TRP HIS TRP VAL TYR TRP ASP LEU GLU LEU PHE ARG ASP PRO ARG THR GLY GLU PRO ALA LEU ASP LEU PRO LYS MET PHE GLY ILE HIS LEU PHE LEU ALA GLY LEU LEU CYS PHE GLY PHE GLY ALA PHE HIS LEU THR GLY LEU PHE GLY PRO GLY MET TRP VAL SER ASP PRO TYR GLY LEU THR GLY SER VAL GLN PRO VAL ALA PRO GLU TRP GLY PRO ASP GLY PHE ASN PRO TYR ASN PRO GLY GLY VAL VAL ALA HIS HIS ILE ALA ALA GLY ILE VAL GLY ILE ILE ALA GLY LEU PHE HIS ILE LEU VAL ARG PRO PRO GLN ARG LEU TYR LYS ALA LEU ARG MET GLY ASN ILE GLU THR VAL LEU SER SER SER ILE ALA ALA VAL PHE PHE ALA ALA PHE VAL VAL ALA GLY THR MET TRP TYR GLY SER ALA THR THR PRO ILE GLU LEU PHE GLY PRO THR ARG TYR GLN TRP ASP SER SER TYR PHE GLN GLN GLU ILE ASN ARG ARG VAL GLN ALA SER LEU ALA SER GLY ALA THR LEU GLU GLU ALA TRP SER ALA ILE PRO GLU LYS LEU ALA PHE TYR ASP TYR ILE GLY ASN ASN PRO ALA LYS GLY GLY LEU PHE ARG THR GLY PRO MET ASN LYS GLY ASP GLY ILE ALA GLN ALA TRP LYS GLY HIS ALA VAL PHE ARG ASN LYS GLU GLY GLU GLU LEU PHE VAL ARG ARG MET PRO ALA PHE PHE GLU SER PHE PRO VAL ILE LEU THR ASP LYS ASN GLY VAL VAL LYS ALA ASP ILE PRO PHE ARG ARG ALA GLU SER LYS TYR SER PHE GLU GLN GLN GLY VAL THR VAL SER PHE TYR GLY GLY GLU LEU ASN GLY GLN THR PHE THR ASP PRO PRO THR VAL LYS SER TYR ALA ARG LYS ALA ILE PHE GLY GLU ILE PHE GLU PHE ASP THR GLU THR LEU ASN SER ASP GLY ILE PHE ARG THR SER PRO ARG GLY TRP PHE THR PHE ALA HIS ALA VAL PHE ALA LEU LEU PHE PHE PHE GLY HIS ILE TRP HIS GLY ALA ARG THR LEU PHE ARG ASP VAL PHE SER GLY ILE ASP PRO GLU LEU SER PRO GLU GLN VAL GLU TRP GLY PHE TYR GLN LYS VAL GLY ASP VAL THR THR ARG ARG LYS GLU ALA VAL CHAIN C, M:THE DEPOSITOR KNOWS THE SEQUENCE. GENBANK NP_682421 (ACCESSION CODE 22299174) BUT THEY COULD NOT ASSIGN THE RESIDUES 299-375. THE RESIUDES 1001-1077 (ONLY THE ALPHA CARBONS) ARE CERTAINLY PART OF RESIDUES 299-375. BUT THEY DO NOT KNOW WHETHER THIS PART IS CORRECT DIRECTION. MET LYS THR LEU SER SER GLN LYS ARG TYR SER PRO VAL VAL THR LEU SER SER ASN SER ILE PHE ALA THR ASN ARG ASP GLN GLU SER SER GLY PHE ALA TRP TRP ALA GLY ASN ALA ARG LEU ILE ASN LEU SER GLY LYS LEU LEU GLY ALA HIS VAL ALA HIS ALA GLY LEU ILE VAL PHE TRP ALA GLY ALA MET THR LEU PHE GLU LEU ALA HIS PHE ILE PRO GLU LYS PRO MET TYR GLU GLN GLY LEU ILE LEU ILE PRO HIS ILE ALA THR LEU GLY TRP GLY VAL GLY PRO GLY GLY GLU VAL VAL ASP THR PHE PRO PHE PHE VAL VAL GLY VAL VAL HIS LEU ILE SER SER ALA VAL LEU GLY PHE GLY GLY VAL TYR HIS ALA ILE ARG GLY PRO GLU THR LEU GLU GLU TYR SER SER PHE PHE GLY TYR ASP TRP LYS ASP LYS ASN LYS MET THR THR ILE LEU GLY PHE HIS LEU ILE VAL LEU GLY ILE GLY ALA LEU LEU LEU VAL ALA LYS ALA MET PHE PHE GLY GLY LEU TYR ASP THR TRP ALA PRO GLY GLY GLY ASP VAL ARG VAL ILE THR ASN PRO THR LEU ASP PRO ARG VAL ILE PHE GLY TYR LEU LEU LYS SER PRO PHE GLY GLY GLU GLY TRP ILE VAL SER VAL ASN ASN LEU GLU ASP VAL VAL GLY GLY HIS ILE TRP ILE GLY LEU ILE CYS ILE ALA GLY GLY ILE TRP HIS ILE LEU THR THR PRO PHE GLY TRP ALA ARG ARG ALA PHE ILE TRP SER GLY GLU ALA TYR LEU SER TYR SER LEU GLY ALA LEU SER MET MET GLY PHE ILE ALA THR CYS PHE VAL TRP PHE ASN ASN THR VAL TYR PRO SER GLU PHE TYR GLY PRO THR GLY PRO GLU ALA SER GLN ALA GLN ALA MET THR PHE LEU ILE ARG ASP GLN LYS LEU GLY ALA ASN VAL GLY SER ALA GLN GLY PRO THR GLY LEU GLY LYS TYR LEU MET ARG SER PRO THR GLY GLU ILE ILE PHE GLY GLY GLU THR MET ARG PHE TRP ASP PHE ARG GLY PRO TRP LEU GLU PRO LEU ARG GLY PRO ASN GLY LEU ASP LEU ASN LYS ILE LYS ASN ASP ILE GLN PRO TRP GLN GLU ARG ARG ALA ALA GLU TYR MET THR HIS ALA PRO LEU GLY SER LEU ASN SER VAL GLY GLY VAL ALA THR GLU ILE ASN SER VAL ASN PHE VAL SER PRO ARG SER TRP LEU ALA THR SER HIS PHE VAL LEU ALA PHE PHE PHE LEU VAL GLY HIS LEU TRP HIS ALA GLY ARG ALA ARG ALA ALA ALA ALA GLY PHE GLU LYS GLY ILE ASP ARG GLU SER GLU PRO VAL LEU SER MET PRO SER LEU ASP CHAIN G, R:THE AUTHOR COULD NOT DECIDE THE SEQUENCE. CHAIN H, S: THE DEPOSITORS KNOW THE SEQUENCE. BUT THEY DON'T KNOW IF THE FIRST RESIDUE OF THE CHAIN REALLY IS THE FIRST OF THE SEQUENCE. MET ALA ARG ARG THR TRP LEU GLY ASP ILE LEU ARG PRO LEU ASN SER GLU TYR GLY LYS VAL ALA PRO GLY TRP GLY THR THR PRO LEU MET ALA VAL PHE MET GLY LEU PHE LEU VAL PHE LEU LEU ILE ILE LEU GLU ILE TYR ASN SER THR LEU ILE LEU ASP GLY VAL ASN VAL SER TRP LYS ALA LEU GLY CHAIN I, T:THE DEPOSITORS KNOW THE SEQUENCE. BUT THEY DON'T KNOW IF THE FIRST RESIDUE OF THE CHAIN REALLY IS THE FIRST OF THE SEQUENCE. MET GLU THR LEU LYS ILE THR VAL TYR ILE VAL VAL THR PHE PHE VAL LEU LEU PHE VAL PHE GLY PHE LEU SER GLY ASP PRO ALA ARG ASN PRO LYS ARG LYS ASP LEU GLU CHAIN O, Y:THE DEPOSITORS KNOW THE SEQUENCE. CHAIN O INCLUDES THREE POLYPEPTIDES. RESIDUES 1-9, 10-175 AND 176-205. CHAIN Y INCLUDES FOUR POLYPEPTIDES. RESIDUES 1-37, 43-65, 67-168 AND 176-205. BUT THEY DON'T KNOW THE PART OF THE SEQUENCE WHERE EACH OF THESE PARTS CORRESPONDS TO. ALA LYS GLN THR LEU THR TYR ASP ASP ILE VAL GLY THR GLY LEU ALA ASN LYS CYS PRO THR LEU ASP ASP THR ALA ARG GLY ALA TYR PRO ILE ASP SER SER GLN THR TYR ARG ILE ALA ARG LEU CYS LEU GLN PRO THR THR PHE LEU VAL LYS GLU GLU PRO LYS ASN LYS ARG GLN GLU ALA GLU PHE VAL PRO THR LYS LEU VAL THR ARG GLU THR THR SER LEU ASP GLN ILE GLN GLY GLU LEU LYS VAL ASN SER ASP GLY SER LEU THR PHE VAL GLU GLU ASP GLY ILE ASP PHE GLN PRO VAL THR VAL GLN MET ALA GLY GLY GLU ARG ILE PRO LEU LEU PHE THR VAL LYS ASN LEU VAL ALA SER THR GLN PRO ASN VAL THR SER ILE THR THR SER THR ASP PHE LYS GLY GLU PHE ASN VAL PRO SER TYR ARG THR ALA ASN PHE LEU ASP PRO LYS GLY ARG GLY LEU ALA SER GLY TYR ASP SER ALA ILE ALA LEU PRO GLN ALA LYS GLU GLU GLU LEU ALA ARG ALA ASN VAL LYS ARG PHE SER LEU THR LYS GLY GLN ILE SER LEU ASN VAL ALA LYS VAL ASP GLY ARG THR GLY GLU ILE ALA GLY THR PHE GLU SER GLU GLN LEU SER ASP ASP ASP MET GLY ALA HIS GLU PRO HIS GLU VAL LYS ILE GLN GLY VAL PHE TYR ALA SER ILE GLU PRO ALA CHAIN U, Z:THE DEPOSITORS KNOW THE SEQUENCE. BUT THEY DON'T KNOW IF THE FIRST RESIDUE OF THE CHAIN REALLY IS THE FIRST OF THE SEQUENCE. ALA THR ALA SER THR GLU GLU GLU LEU VAL ASN VAL VAL ASP GLU LYS LEU GLY THR ALA TYR GLY GLU LYS ILE ASP LEU ASN ASN THR ASN ILE ALA ALA PHE ILE GLN TYR ARG GLY LEU TYR PRO THR LEU ALA LYS LEU ILE VAL LYS ASN ALA PRO TYR GLU SER VAL GLU ASP VAL LEU ASN ILE PRO GLY LEU THR GLU ARG GLN LYS GLN ILE LEU ARG GLU ASN LEU GLU HIS PHE THR VAL THR GLU VAL GLU THR ALA LEU VAL GLU GLY GLY ASP ARG TYR ASN ASN GLY LEU TYR LYS CHAIN X, 1:THE DEPOSITORS KNOW THE SEQUENCE. BUT THEY DON'T KNOW IF THE FIRST RESIDUE OF THE CHAIN REALLY IS THE FIRST OF THE SEQUENCE. MET ILE GLN SER ALA SER SER LEU LEU LEU THR ILE THR PRO SER LEU LYS GLY PHE PHE ILE GLY LEU LEU SER GLY ALA VAL VAL LEU GLY LEU THR PHE ALA VAL LEU ILE ALA ILE SER GLN ILE ASP LYS VAL GLN ARG SER LEU

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 100

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Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 71.12 %
Crystal growTemperature: 293 K / Method: microdialysis / pH: 6.5
Details: PEG 1450, MES, calcium chloride, magnesium sulfate, dodecyl maltoside, pH 6.5, MICRODIALYSIS, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Details: Shen, J.R., (2000) Biochemistry, 39, 14739.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
14-5 mg/mlprotein11
220 mM11MgSO4
38 mM11CaCl2
46-7 %PEG145012
540 mM12MgSO4
620 mM12CaCl2
720 mMMES12pH6.5
820 mM12NaCl
90.02 %n-dodecyl beta-D-maltoside12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 21, 2001 / Details: KB mirrors
RadiationMonochromator: Rotated Inclined Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→25 Å / Num. all: 94859 / % possible obs: 98 % / Redundancy: 12 % / Rmerge(I) obs: 0.071
Reflection shellResolution: 3.7→3.9 Å / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2.8 / Num. unique all: 94859 / % possible all: 95
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 94859
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CCP4(SCALA)data scaling
RefinementResolution: 3.7→25 Å / Cor.coef. Fo:Fc: 0.485 / SU B: 246.899 / SU ML: 2.608 / Isotropic thermal model: 1.02 / ESU R: 1.006
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: the missing atom list was suppressed. each unkown atom has C, CA, N, O atom only.
RfactorNum. reflection% reflection
Rwork0.53045 --
obs0.53045 96299 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.095 Å2
Baniso -1Baniso -2Baniso -3
1-6.11 Å20 Å20 Å2
2--0.88 Å20 Å2
3----6.99 Å2
Refinement stepCycle: LAST / Resolution: 3.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19964 0 2840 0 22804
LS refinement shellResolution: 3.7→3.794 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.57 6812
Refinement
*PLUS
Rfactor Rwork: 0.53
Solvent computation
*PLUS
Displacement parameters
*PLUS

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