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- PDB-5v8k: Homodimeric reaction center of H. modesticaldum -

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Basic information

Entry
Database: PDB / ID: 5v8k
TitleHomodimeric reaction center of H. modesticaldum
Components
  • p800 reaction center core protein
  • proteinsubunit pshX
KeywordsPHOTOSYNTHESIS / reaction center / homodimeric
Function / homology
Function and homology information


thylakoid / photosynthesis / membrane => GO:0016020
Similarity search - Function
Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein
Similarity search - Domain/homology
8(1)-OH-Chlorophyll aF / 4,4'-Diaponeurosporene / Chem-DGG / Bacteriochlorophyll g' / Bacteriochlorophyll g / IRON/SULFUR CLUSTER / Uncharacterized protein / p800 reaction center core protein
Similarity search - Component
Biological speciesHeliobacterium modesticaldum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.2 Å
AuthorsGisriel, C. / Sarrou, I. / Ferlez, B. / Golbeck, J. / Redding, K.E. / Fromme, R.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
Citation
Journal: Science / Year: 2017
Title: Structure of a symmetric photosynthetic reaction center-photosystem.
Authors: Gisriel, C. / Sarrou, I. / Ferlez, B. / Golbeck, J.H. / Redding, K.E. / Fromme, R.
#1: Journal: Nature / Year: 2001
Title: Three-dimensional structure of cyanobacterial photosystem I at 2.5 A resolution.
Authors: Jordan, P. / Fromme, P. / Witt, H.T. / Klukas, O. / Saenger, W. / Krauss, N.
#2: Journal: J. Mol. Biol. / Year: 1984
Title: X-ray structure analysis of a membrane protein complex. Electron density map at 3 A resolution and a model of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis.
Authors: Deisenhofer, J. / Epp, O. / Miki, K. / Huber, R. / Michel, H.
#3: Journal: Science / Year: 2003
Title: Crystal structure of the RC-LH1 core complex from Rhodopseudomonas palustris.
Authors: Roszak, A.W. / Howard, T.D. / Southall, J. / Gardiner, A.T. / Law, C.J. / Isaacs, N.W. / Cogdell, R.J.
#4: Journal: Photosyn. Res. / Year: 2012
Title: Purification of the photosynthetic reaction center from Heliobacterium modesticaldum.
Authors: Sarrou, I. / Khan, Z. / Cowgill, J. / Lin, S. / Brune, D. / Romberger, S. / Golbeck, J.H. / Redding, K.E.
History
DepositionMar 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Experimental preparation / Structure summary
Category: citation / entity ...citation / entity / exptl_crystal / exptl_crystal_grow / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _entity.pdbx_description / _exptl_crystal.density_percent_sol / _exptl_crystal_grow.pdbx_details / _struct.pdbx_descriptor
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: p800 reaction center core protein
B: proteinsubunit pshX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,89740
Polymers69,9742
Non-polymers27,92338
Water4,306239
1
A: p800 reaction center core protein
B: proteinsubunit pshX
hetero molecules

A: p800 reaction center core protein
B: proteinsubunit pshX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,79580
Polymers139,9484
Non-polymers55,84776
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area25610 Å2
ΔGint-221 kcal/mol
Surface area48360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.358, 89.714, 111.637
Angle α, β, γ (deg.)90.00, 108.15, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1280-

HOH

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Components

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Protein / Protein/peptide / Sugars , 3 types, 4 molecules AB

#1: Protein p800 reaction center core protein


Mass: 66920.359 Da / Num. of mol.: 1 / Fragment: reaction center protein / Source method: isolated from a natural source / Source: (natural) Heliobacterium modesticaldum (bacteria) / References: UniProt: Q1MX24
#2: Protein/peptide proteinsubunit pshX


Mass: 3053.593 Da / Num. of mol.: 1 / Fragment: UNP residues 13-37 / Source method: isolated from a natural source
Source: (natural) Heliobacterium modesticaldum (strain ATCC 51547 / Ice1) (bacteria)
Strain: ATCC 51547 / Ice1 / References: UniProt: B0TAT4
#9: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 8 types, 275 molecules

#3: Chemical ChemComp-GB0 / Bacteriochlorophyll g'


Mass: 819.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C50H58MgN4O5
#4: Chemical...
ChemComp-GBF / Bacteriochlorophyll g


Mass: 819.324 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C50H58MgN4O5
#5: Chemical ChemComp-AOH / 8(1)-OH-Chlorophyll aF


Mass: 837.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H60MgN4O6
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#7: Chemical ChemComp-DGG / 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL


Mass: 734.981 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H75O10P
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-C4D / 4,4'-Diaponeurosporene / (4E,6E,8E,10E,12E,14E,16E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,4,6,8,10,12,14,16,18,22-decaene


Mass: 402.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H42
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

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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: 4.47 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 298 K / Method: evaporation
Details: 0.3 mM HbRC, 100 mM Tris-HCl (ph 8.2), 600 mM NH4Cl, 0.02 % b-DDM, up to 1% n-heptyl-b-D-glucopyranoside, up to 20 % PEG 500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0088 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0088 Å / Relative weight: 1
ReflectionResolution: 2.2→29.1 Å / Num. obs: 61415 / % possible obs: 98 % / Redundancy: 1.9 % / Biso Wilson estimate: 41.31 Å2 / Net I/σ(I): 16.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.48 / % possible all: 89

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXDEV_2450refinement
Aimlessdata scaling
BUCCANEERmodel building
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
SHELXEmodel building
RefinementResolution: 2.2→29.08 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.67 / Details: MOLECULAR REPLACEMENT FROM 1JB0 DERIVED MODELS
RfactorNum. reflection% reflection
Rfree0.191 2936 4.78 %
Rwork0.158 --
obs0.16 61363 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 54.04 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4898 0 1821 239 6958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127120
X-RAY DIFFRACTIONf_angle_d1.5710091
X-RAY DIFFRACTIONf_dihedral_angle_d18.0733767
X-RAY DIFFRACTIONf_chiral_restr0.066880
X-RAY DIFFRACTIONf_plane_restr0.0091077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2007-2.23680.33841310.2922259X-RAY DIFFRACTION81
2.2368-2.27540.27731440.23542658X-RAY DIFFRACTION94
2.2754-2.31670.24471470.21372735X-RAY DIFFRACTION98
2.3167-2.36130.23271200.19142817X-RAY DIFFRACTION100
2.3613-2.40940.24781220.18842855X-RAY DIFFRACTION100
2.4094-2.46180.21581360.16962814X-RAY DIFFRACTION100
2.4618-2.5190.20061230.15932836X-RAY DIFFRACTION100
2.519-2.5820.19471570.15232815X-RAY DIFFRACTION100
2.582-2.65180.19511410.14832865X-RAY DIFFRACTION100
2.6518-2.72970.19861530.1382775X-RAY DIFFRACTION100
2.7297-2.81780.17281380.13722824X-RAY DIFFRACTION100
2.8178-2.91840.17991350.14122818X-RAY DIFFRACTION100
2.9184-3.03510.19971360.13962832X-RAY DIFFRACTION100
3.0351-3.17310.18311640.14142821X-RAY DIFFRACTION100
3.1731-3.34020.17441190.13842851X-RAY DIFFRACTION100
3.3402-3.54910.16441430.1382826X-RAY DIFFRACTION100
3.5491-3.82260.15441480.13622809X-RAY DIFFRACTION99
3.8226-4.20620.15781170.1392829X-RAY DIFFRACTION99
4.2062-4.81250.15631510.14572798X-RAY DIFFRACTION98
4.8125-6.05420.20381600.17242783X-RAY DIFFRACTION98
6.0542-29.08420.22671510.19482807X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.10530.17560.1690.95840.11111.23880.1389-0.2022-0.24750.3145-0.0744-0.3470.17040.3106-0.04350.4059-0.0931-0.10750.52120.08660.5014158.681380.876625.5174
21.2159-0.29310.28291.0322-0.0071.74260.2388-0.576-0.10020.7349-0.2531-0.04510.06930.0832-0.03340.6847-0.2218-0.05570.67180.10020.3697145.977682.239939.4001
31.33120.1540.22721.3081-0.10451.3470.1776-0.28180.09150.2027-0.17460.0165-0.12630.0860.00370.3588-0.09950.00630.4160.01810.3427143.24789.303922.7282
41.18970.0468-0.00642.1293-0.53261.5870.1317-0.4052-0.34830.4002-0.1521-0.08310.2944-0.1192-0.09350.4583-0.14620.01040.54520.07440.4621121.694870.7321.8092
51.1163-0.10050.10880.93120.07911.26170.1433-0.1425-0.08670.1437-0.11060.01790.0696-0.0388-0.03440.281-0.05060.00850.31120.02170.3346131.79782.18679.7714
61.58520.2550.012.0580.00031.31080.26470.1979-0.0495-0.1923-0.0367-0.34520.08940.4244-0.02240.80880.04720.01951.1862-0.06361.2321159.980386.6846-3.365
71.1055-0.3614-1.59651.85560.86272.90330.1938-0.0726-0.23370.137-0.1283-0.22040.31370.2908-0.04551.02110.0964-0.08710.97570.08860.973152.397668.79780.8115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 9 THROUGH 145 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 146 THROUGH 232 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 233 THROUGH 299 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 300 THROUGH 352 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 353 THROUGH 608 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 13 THROUGH 31 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 32 THROUGH 37 )

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