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- PDB-1qzv: Crystal structure of plant photosystem I -

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Database: PDB / ID: 1qzv
TitleCrystal structure of plant photosystem I
Components
  • (PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT ...) x 4
  • (PLANT PHOTOSYSTEM I: SUBUNIT ...) x 12
KeywordsPHOTOSYNTHESIS / PLANT PHOTOSYNTHETIC REACTION CENTER / PERIPHERAL ANTENNA / LIGHT-HARVESTING SYSTEM / PLANT MEMBRANE PROTEIN COMPLEX
Function / homologyCHLOROPHYLL A / PHYLLOQUINONE / IRON/SULFUR CLUSTER
Function and homology information
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 4.44 Å
AuthorsBen-Shem, A. / Frolow, F. / Nelson, N.
CitationJournal: Nature / Year: 2003
Title: Crystal structure of plant photosystem I.
Authors: Ben-Shem, A. / Frolow, F. / Nelson, N.
History
DepositionSep 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 25, 2012Group: Non-polymer description
Revision 2.0Feb 14, 2024Group: 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_site
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE AND NOMENCLATURE: THE NUMBERING OF RESIDUES IN CHAINS A,B,C,D,E,F,I,J,K,L IS DERIVED FROM ... SEQUENCE AND NOMENCLATURE: THE NUMBERING OF RESIDUES IN CHAINS A,B,C,D,E,F,I,J,K,L IS DERIVED FROM PAIR-WISE ALIGNMENT BETWEEN THE SEQUENCE IN HIGHER PLANTS AND THAT IN CYANOBACTERIA (SYNECHOCOCCUS ELONGATUS) AND FROM COMPARISON OF THE PLANT STRUCTURE TO THE CYANOBACTERIAL STRUCTURE (PDB CODE 1JB0). SINCE THE RESULTS FROM SUCH A PROCEDURE MIGHT NOT BE EXACT, RESIDUE TYPE IN MOST CASES IS DESIGNATED AS UNKNOWN (UNK). IN CHAIN D RESIDUES D1-D22 CORRESPOND TO AN ADDITIONAL N-TERMINAL DOMAIN THAT HAS NO PARALLEL IN CYANOBACTERIA. DUE TO DISCONTINUITY IN THE MAP AND THE MODEL (NEXT RESIDUE IS D31) THE POSSIBILITY EXISTS THAT THE DIRECTION OF THIS SEGMENT IS ACTUALLY D22 -> D1. NUMBERING OF RESIDUES IN CHAINS H AND G SHOULD BE REGARDED AS SPECULATIVE. MOST SECONDARY STRUCTURE PREDICTING PROGRAMS SUGGEST THAT THE TRANSMEMBRANE HELIX OF CHAIN H IS LOCATED TOWARDS THE C-TERMINUS OF THIS CHAIN. THIS SUGGESTION WAS ADOPTED HERE. SUBUNIT G HAS TWO TRANSMEMBRANe HELICES - ONE TOWARDS THE N-TERMINUS AND THE OTHER TOWARDS THE C-TERMINUS. OUR CHOICE REGARDING WHICH OF THE TWO OBSERVED HELICES SHOULD BE ASSIGNED TO THE N-TERMINUS AND WHICH TO THE C-TERMINUS IS ARBITRARY. NUMBERING OF RESIDUES IN THE FOUR LHCI SUBUNITS IS BASED ON MULTIPLE SEQUENCE ALIGNMENT OF SEVERAL LHCI AND LHCII PROTEINS (SEE MELKOZERNOV AND BLANKENSHIP 2003). WE IDENTIFIED IN THE MODEL AND IN THE ALIGNMENT THE RESIDUES THAT SEEM TO BE THE LIGANDS OF CHLOROPHYLLS A1,A2,A3,A4,A5,A6,B3,B5,B6 (LABELING AS IN LHCII). THESE ANCHOR POINTS DETERMINED RESIDUE NUMBERING OF HELICES A,B,C,D AND THEIR CONTINUATIONS IN ALL LHCI SUBUNITS. AS FOR RESIDUE NUMBERS IN LOOPS THAT ARE NOT CONNECTED TO THE HELICES IN THE MODEL (DISCONTINUITIES)- THESE ARE SPECULATIVE. IN LHCA3 ONLY, THE TRANSMEMBRANE HELIX CLOSEST TO HELIX C IS NOT THE LONGEST OF THE TWO TILTED TRANSMEMBRANE HELICES (LABELING AS IN KUHLBRANDT ET AL. 1994). THIS MIGHT INDICATE THAT IN LHCA3 THE HELIX CLOSEST TO HELIX C IS NOT THE FIRST HELIX (FROM THE N-TERMINUS) BUT THE THIRD ONE. THE ELECTRON DENSITY MAP IS NOT CONCLUSIVE HERE BUT SEEMS TO SUGGEST THAT THIS MIGHT BE THE CASE. IF THIS IS TRUE, AND LHCA3 FOLDS DIFFERENTLY, THEN THE NUMBERING OF RESIDUES IN LHCA3 MUST CHANGE ACCORDINGLY. C-ALPHA ATOMS ONLY WERE SUBMITTED FOR THIS MODEL. CHLOROPHYLL NOTATION: REACTION CENTER CHLOROPHYLLS - FOLLOW THE NOTATION OF THE CYANOBACTERIAL STRUCTURE PDB CODE 1JB0 (NO CHAIN I.D.) "GAP" CHLOROPHYLLS (SEE BEN-SHEM ET AL. NATURE 426 630-635) - NO CHAIN I.D., RESIDUE NUMBERS 4001-4010. THESE DO NOT INCLUDE "LINKER" CHLOROPHYLLS. LHCI CHLOROPHYLLS - CHAIN I.D. 1,2,3,4 CORRESPONDING TO LHCA1-4. RESIDUE NUMBERS 1011-1017 IDENTIFY CHLOROPHYLLS AT POSITIONS SIMILAR TO A1-A7 IN LHCII. RESIDUE NUMBERS 1021-1026 IDENTIFY CHLOROPHYLLS AT POSITIONS SIMILAR TO B1-B6 IN LHCII, RESIDUE NUMBERS 1031-1033 IDENTIFY "LINKER" CHLOROPHYLLS. RESIDUE NUMBER 1041 IDENTIFY ONE CHLOROPHYLL IN LHCA3 WHICH IS IN A POSITION BETWEEN A3 AND B3. CHLOROPHYLLS WITH CHAIN I.D. 7,8,9,0 ARE THE SYMMETRY EQUIVALENTS OF CHLOROPHYLLS WITH CHAIN I.D. 1,2,3,4. CHLOROPHYLLS NUMBERED 5011-5901 ARE THE SYMMETRY EQUIVALENTS OF CHLOROPHYLLS NUMBERED 1011-1901. CHLOROPHYLLS NUMBERED 8001-8010 ARE THE SYMMETRY EQUIVALENTS OF CHLOROPHYLLS NUMBERED 4001-4010. PQN 6001 AND 6002 ARE THE SYMMETRY EQUIVALENTS OF PQN 2001 AND 2002. FS4 MOLECULES 7001-7003 ARE THE SYMMETRY EQUIVALENTS OF FS4 MOLECULES 3001-3003.
Remark 600HETEROGEN ATOMS C11, C12, C13, C14, C15, C16, C17, C18, C19, C20, C21, C22, C23, C24, C25, C26, ...HETEROGEN ATOMS C11, C12, C13, C14, C15, C16, C17, C18, C19, C20, C21, C22, C23, C24, C25, C26, C27, C28, C29, AND C30 FOR LIGAND PQN ARE MISSING IN THE COORDINATES. ATOMS CMA, CAA, CBA, CGA, O1A, O2A, CMB, CAB, CBB, CMC, CAC, CBC, CMD, CAD, OBD, CBD, CGD, O1D, O2D, CED, C1, C2, C3, C4, C5, C6, C7, C8, C9, C10, C11, C12, C13, C14, C15, C16, C17, C18, C19, AND C20 FOR LIGAND CLA ARE MISSING IN THE COORDINATES. CHLOROPHYLLS WERE MODELLED BY PORPHYRINS.
Remark 400 COMPOUND THE ASYMMETRIC UNIT CONTAINS 2 MONOMERS. EACH MONOMER IS A BIOLOGICAL UNIT. MONOMER ONE ... COMPOUND THE ASYMMETRIC UNIT CONTAINS 2 MONOMERS. EACH MONOMER IS A BIOLOGICAL UNIT. MONOMER ONE CONSISTS OF CHAINS A-L AND 1-4. MONOMER TWO CONSISTS OF CHAINS P-Z AND 5-0. CHAIN IDS P-Z AND 5-0 ARE FOR THE CHAIN ID ASSIGNMENT IN THE PDB FILE ONLY AND ARE NOT SUPPOSED TO IMPLY THEY ARE SUBUNITS THAT ARE NOT PART OF THE FIRST MONOMER. THE CHAINS ARE RELATED BY NCS IN THE FOLLOWING WAY: CHAIN P IS THE NCS PARTNER OF CHAIN A. CHAIN Q IS THE NCS PARTNER OF CHAIN B. CHAIN R IS THE NCS PARTNER OF CHAIN C. CHAIN S IS THE NCS PARTNER OF CHAIN D. CHAIN T IS THE NCS PARTNER OF CHAIN E. CHAIN U IS THE NCS PARTNER OF CHAIN F. CHAIN V IS THE NCS PARTNER OF CHAIN G. CHAIN W IS THE NCS PARTNER OF CHAIN H. CHAIN Y IS THE NCS PARTNER OF CHAIN I. CHAIN Z IS THE NCS PARTNER OF CHAIN J. CHAIN 5 IS THE NCS PARTNER OF CHAIN K. CHAIN 6 IS THE NCS PARTNER OF CHAIN L. CHAIN 7 IS THE NCS PARTNER OF CHAIN 1. CHAIN 8 IS THE NCS PARTNER OF CHAIN 2. CHAIN 9 IS THE NCS PARTNER OF CHAIN 3. CHAIN 0 IS THE NCS PARTNER OF CHAIN 4.
Remark 295 NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE ... NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG ATOMS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. CHAIN IDENTIFIERS GIVEN AS "?" REFER TO CHAINS FOR WHICH ATOMS ARE NOT FOUND IN THIS ENTRY. APPLIED TO TRANSFORMED TO TRANSFORM CHAIN RESIDUES CHAIN RESIDUES RMSD SSS M 1 A 29 .. 758 P 29 .. 758 0.000 WHERE SSS -> COLUMNS 8-10 OF MTRIX RECORDS REMARK: THE RMSD IS 0.00 IN ALL TRANSFORMED CHAINS. THEY WERE ALL GENERATED AUTOMATICALLY BY EXACTLY THE SAME TRANSFORMATION, FROM THE FIRST MONOMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLANT PHOTOSYSTEM I: SUBUNIT PSAA
B: PLANT PHOTOSYSTEM I: SUBUNIT PSAB
C: PLANT PHOTOSYSTEM I: SUBUNIT PSAC
D: PLANT PHOTOSYSTEM I: SUBUNIT PSAD
E: PLANT PHOTOSYSTEM I: SUBUNIT PSAE
F: PLANT PHOTOSYSTEM I: SUBUNIT PSAF
G: PLANT PHOTOSYSTEM I: SUBUNIT PSAG
H: PLANT PHOTOSYSTEM I: SUBUNIT PSAH
I: PLANT PHOTOSYSTEM I: SUBUNIT PSAI
J: PLANT PHOTOSYSTEM I: SUBUNIT PSAJ
K: PLANT PHOTOSYSTEM I: SUBUNIT PSAK
L: PLANT PHOTOSYSTEM I: SUBUNIT PSAL
1: PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA1
2: PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA2
3: PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA3
4: PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA4
P: PLANT PHOTOSYSTEM I: SUBUNIT PSAA
Q: PLANT PHOTOSYSTEM I: SUBUNIT PSAB
R: PLANT PHOTOSYSTEM I: SUBUNIT PSAC
S: PLANT PHOTOSYSTEM I: SUBUNIT PSAD
T: PLANT PHOTOSYSTEM I: SUBUNIT PSAE
U: PLANT PHOTOSYSTEM I: SUBUNIT PSAF
V: PLANT PHOTOSYSTEM I: SUBUNIT PSAG
W: PLANT PHOTOSYSTEM I: SUBUNIT PSAH
Y: PLANT PHOTOSYSTEM I: SUBUNIT PSAI
Z: PLANT PHOTOSYSTEM I: SUBUNIT PSAJ
5: PLANT PHOTOSYSTEM I: SUBUNIT PSAK
6: PLANT PHOTOSYSTEM I: SUBUNIT PSAL
7: PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA1
8: PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA2
9: PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA3
0: PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)771,331376
Polymers468,99332
Non-polymers302,338344
Water0
1
A: PLANT PHOTOSYSTEM I: SUBUNIT PSAA
B: PLANT PHOTOSYSTEM I: SUBUNIT PSAB
C: PLANT PHOTOSYSTEM I: SUBUNIT PSAC
D: PLANT PHOTOSYSTEM I: SUBUNIT PSAD
E: PLANT PHOTOSYSTEM I: SUBUNIT PSAE
F: PLANT PHOTOSYSTEM I: SUBUNIT PSAF
G: PLANT PHOTOSYSTEM I: SUBUNIT PSAG
H: PLANT PHOTOSYSTEM I: SUBUNIT PSAH
I: PLANT PHOTOSYSTEM I: SUBUNIT PSAI
J: PLANT PHOTOSYSTEM I: SUBUNIT PSAJ
K: PLANT PHOTOSYSTEM I: SUBUNIT PSAK
L: PLANT PHOTOSYSTEM I: SUBUNIT PSAL
1: PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA1
2: PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA2
3: PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA3
4: PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)385,665188
Polymers234,49716
Non-polymers151,169172
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
P: PLANT PHOTOSYSTEM I: SUBUNIT PSAA
Q: PLANT PHOTOSYSTEM I: SUBUNIT PSAB
R: PLANT PHOTOSYSTEM I: SUBUNIT PSAC
S: PLANT PHOTOSYSTEM I: SUBUNIT PSAD
T: PLANT PHOTOSYSTEM I: SUBUNIT PSAE
U: PLANT PHOTOSYSTEM I: SUBUNIT PSAF
V: PLANT PHOTOSYSTEM I: SUBUNIT PSAG
W: PLANT PHOTOSYSTEM I: SUBUNIT PSAH
Y: PLANT PHOTOSYSTEM I: SUBUNIT PSAI
Z: PLANT PHOTOSYSTEM I: SUBUNIT PSAJ
5: PLANT PHOTOSYSTEM I: SUBUNIT PSAK
6: PLANT PHOTOSYSTEM I: SUBUNIT PSAL
7: PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA1
8: PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA2
9: PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA3
0: PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)385,665188
Polymers234,49716
Non-polymers151,169172
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.283, 190.376, 220.253
Angle α, β, γ (deg.)90.00, 90.48, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.82712, -0.02534, 0.56146), (0.06053, 0.99719, -0.04416), (-0.55876, 0.07051, 0.82633)
Vector: 28.31186, 1.07145, -88.9968)

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Components

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PLANT PHOTOSYSTEM I: SUBUNIT ... , 12 types, 24 molecules APBQCRDSETFUGVHWIYJZK5L6

#1: Protein PLANT PHOTOSYSTEM I: SUBUNIT PSAA / / Coordinate model: Cα atoms only


Mass: 61804.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Cellular location: Thylakoid MembraneThylakoid / Strain: ALASKA
#2: Protein PLANT PHOTOSYSTEM I: SUBUNIT PSAB / / Coordinate model: Cα atoms only


Mass: 62314.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Cellular location: Thylakoid MembraneThylakoid / Strain: ALASKA
#3: Protein PLANT PHOTOSYSTEM I: SUBUNIT PSAC / / Coordinate model: Cα atoms only


Mass: 6826.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Cellular location: Thylakoid MembraneThylakoid / Strain: ALASKA
#4: Protein PLANT PHOTOSYSTEM I: SUBUNIT PSAD / / Coordinate model: Cα atoms only


Mass: 13124.170 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Cellular location: Thylakoid MembraneThylakoid / Strain: ALASKA
#5: Protein PLANT PHOTOSYSTEM I: SUBUNIT PSAE / / Coordinate model: Cα atoms only


Mass: 5464.728 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Cellular location: Thylakoid MembraneThylakoid / Strain: ALASKA
#6: Protein PLANT PHOTOSYSTEM I: SUBUNIT PSAF / / Coordinate model: Cα atoms only


Mass: 13804.815 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Cellular location: Thylakoid MembraneThylakoid / Strain: ALASKA
#7: Protein PLANT PHOTOSYSTEM I: SUBUNIT PSAG / / Coordinate model: Cα atoms only


Mass: 6315.777 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Cellular location: Thylakoid MembraneThylakoid / Strain: ALASKA
#8: Protein PLANT PHOTOSYSTEM I: SUBUNIT PSAH / / Coordinate model: Cα atoms only


Mass: 4443.468 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Cellular location: Thylakoid MembraneThylakoid / Strain: ALASKA
#9: Protein/peptide PLANT PHOTOSYSTEM I: SUBUNIT PSAI / / Coordinate model: Cα atoms only


Mass: 2571.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Cellular location: Thylakoid MembraneThylakoid / Strain: ALASKA
#10: Protein/peptide PLANT PHOTOSYSTEM I: SUBUNIT PSAJ / / Coordinate model: Cα atoms only


Mass: 3507.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Cellular location: Thylakoid MembraneThylakoid / Strain: ALASKA
#11: Protein/peptide PLANT PHOTOSYSTEM I: SUBUNIT PSAK / / Coordinate model: Cα atoms only


Mass: 3592.419 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Cellular location: Thylakoid MembraneThylakoid / Strain: ALASKA
#12: Protein PLANT PHOTOSYSTEM I: SUBUNIT PSAL / / Coordinate model: Cα atoms only


Mass: 11507.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Cellular location: Thylakoid MembraneThylakoid / Strain: ALASKA

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PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT ... , 4 types, 8 molecules 17283940

#13: Protein PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA1 / Coordinate model: Cα atoms only


Mass: 9294.448 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Cellular location: Thylakoid MembraneThylakoid / Strain: ALASKA
#14: Protein PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA2 / Coordinate model: Cα atoms only


Mass: 9805.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Cellular location: Thylakoid MembraneThylakoid / Strain: ALASKA
#15: Protein PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA3 / Coordinate model: Cα atoms only


Mass: 9975.288 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Cellular location: Thylakoid MembraneThylakoid / Strain: ALASKA
#16: Protein PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA4 / Coordinate model: Cα atoms only


Mass: 10145.497 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Cellular location: Thylakoid MembraneThylakoid / Strain: ALASKA

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Non-polymers , 3 types, 344 molecules

#17: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 334 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#18: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H46O2
#19: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: Ben-Shem, A., Nelson, N., Frolow, F. (2003) Acta Crystallogr D. 59:1824-7. PEG 6000, AMMONIUM CITRATE, PEG 400, MES, BIS-TRIS, DODECYL-THIO-MALTOSIDE, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: Ben-Shem, A., (2003) Acta Cryst., D59, 1824.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlprotein1drop
222.5 mMMES-bis-tris1reservoirpH6.6
30.5 %(v/v)PEG4001reservoir
48.1 mMammonium citrate1reservoir
55.6-6.4 %(w/v)PEG60001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-110.933
SYNCHROTRONESRF ID14-420.939
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 1, 2002
ADSC QUANTUM 42CCDJun 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9331
20.9391
ReflectionResolution: 4.44→50 Å / Num. all: 92318 / Num. obs: 92318 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 18.8
Reflection shellResolution: 4.44→4.52 Å / Redundancy: 7 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.05 / Num. unique all: 4562 / Rsym value: 0.86 / % possible all: 99.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMAC5refinement
RefinementMethod to determine structure: MIR / Resolution: 4.44→50 Å / σ(F): 0 / Stereochemistry target values: REFMAC MONOMER LIBRARY
Details: RIGID BODY REFINEMENT, BULK SOLVENT CORRECTION AND TLS REFINEMENT (OF CORE REGION).
RfactorNum. reflection% reflectionSelection details
Rfree0.42 4600 -RANDOM
Rwork0.41 ---
obs0.41 92318 99.6 %-
all-92318 --
Refinement stepCycle: LAST / Resolution: 4.44→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5488 0 8450 0 13938

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