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- PDB-1eys: CRYSTAL STRUCTURE OF PHOTOSYNTHETIC REACTION CENTER FROM A THERMO... -

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Basic information

Entry
Database: PDB / ID: 1eys
TitleCRYSTAL STRUCTURE OF PHOTOSYNTHETIC REACTION CENTER FROM A THERMOPHILIC BACTERIUM, THERMOCHROMATIUM TEPIDUM
Components(PHOTOSYNTHETIC REACTION ...) x 4
KeywordsELECTRON TRANSPORT / MEMBRANE PROTEIN COMPLEX
Function / homology
Function and homology information


plasma membrane light-harvesting complex / photosynthesis, light reaction / membrane
Similarity search - Function
Photosynthetic Reaction Center, subunit C; domain 2 / Photosynthetic Reaction Center, subunit C, domain 2 / Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal ...Photosynthetic Reaction Center, subunit C; domain 2 / Photosynthetic Reaction Center, subunit C, domain 2 / Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel-like superfamily / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / SPIRILLOXANTHIN / : / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE 8 / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / H subunit of photosynthetic reaction center complex
Similarity search - Component
Biological speciesThermochromatium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsNogi, T. / Fathir, I. / Kobayashi, M. / Nozawa, T. / Miki, K.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: thermostability and electron transfer.
Authors: Nogi, T. / Fathir, I. / Kobayashi, M. / Nozawa, T. / Miki, K.
#1: Journal: FEBS Lett. / Year: 1994
Title: Preliminary X-ray Crystallographic Studies of Photosynthetic Reaction Center from a Thermophilic Sulfur Bacterium, Chromatium tepidum
Authors: Katayama, N. / Kobayashi, M. / Motojima, F. / Inaka, K. / Nozawa, T. / Miki, K.
History
DepositionMay 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: PHOTOSYNTHETIC REACTION CENTER
L: PHOTOSYNTHETIC REACTION CENTER
M: PHOTOSYNTHETIC REACTION CENTER
H: PHOTOSYNTHETIC REACTION CENTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,84925
Polymers136,9134
Non-polymers11,93621
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47460 Å2
ΔGint-365 kcal/mol
Surface area41500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.299, 196.596, 84.163
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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PHOTOSYNTHETIC REACTION ... , 4 types, 4 molecules CLMH

#1: Protein PHOTOSYNTHETIC REACTION CENTER


Mass: 40880.738 Da / Num. of mol.: 1 / Fragment: CYTOCHROME SUBUNIT / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria)
#2: Protein PHOTOSYNTHETIC REACTION CENTER


Mass: 31417.588 Da / Num. of mol.: 1 / Fragment: L SUBUNIT / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria)
#3: Protein PHOTOSYNTHETIC REACTION CENTER


Mass: 36328.285 Da / Num. of mol.: 1 / Fragment: M SUBUNIT / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria)
#4: Protein PHOTOSYNTHETIC REACTION CENTER


Mass: 28286.398 Da / Num. of mol.: 1 / Fragment: H SUBUNIT / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: Q93RD8

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Sugars , 1 types, 6 molecules

#6: Sugar
ChemComp-BGL / 2-O-octyl-beta-D-glucopyranose / 2-O-octyl-beta-D-glucose / 2-O-octyl-D-glucose / 2-O-octyl-glucose


Type: D-saccharide, beta linking / Mass: 292.369 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-D-Glcp2octylIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 9 types, 203 molecules

#5: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#7: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#8: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6
#9: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#10: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#11: Chemical ChemComp-MQ8 / MENAQUINONE 8 / 2-METHYL-3-(3,7,11,15,19,23,27,31-OCTAMETHYL-DOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL)-[1,4]NAPTHOQUINONE


Mass: 717.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H72O2
#12: Chemical ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H60O2
#13: Chemical ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.02 Å3/Da / Density % sol: 69.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG4000, sodium chloride, phosphate, beta-octyl-glucopyranoside, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion
Details: Kobayashi, M., (1993) Bull. Chem. Soc. Jpn., 66, 3834.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-20 mg/mlprotein1drop
20.36 M1dropNaCl
315 mMphosphate1reservoir
40.6 M1reservoirNaCl
61.0 mMEDTA1reservoir
51reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.708
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 25, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.708 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 110923 / Num. obs: 103031 / % possible obs: 92.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.6
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.362 / Num. unique all: 6548 / % possible all: 78.6
Reflection
*PLUS
Num. obs: 110923 / Num. measured all: 508729
Reflection shell
*PLUS
% possible obs: 78.6 % / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→10 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.287 4785 RANDOM
Rwork0.231 --
all0.234 95278 -
obs0.234 95278 -
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9009 0 847 188 10044
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.89
X-RAY DIFFRACTIONx_torsion_deg22.9
X-RAY DIFFRACTIONx_torsion_impr_deg0.87
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.87
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rfactor Rfree: 0.312 / Rfactor Rwork: 0.302

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