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- PDB-1dv3: PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN TH... -

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Basic information

Entry
Database: PDB / ID: 1dv3
TitlePHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-SEPARATED D+QAQB-STATE WITH THE PROTON TRANSFER INHIBITOR CD2+
Components(PHOTOSYNTHETIC REACTION CENTER REACTION ...) x 3
KeywordsPHOTOSYNTHESIS / Bacterial Photosynthesis / Rhodobacter sphaeroides / Metal Ion Binding / Cation Binding / Proton Transfer / Integral Membrane Protein
Function / homology
Function and homology information


: / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / : / membrane => GO:0016020 / metal ion binding
Similarity search - Function
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, M subunit / Photosynthetic reaction centre, H subunit, N-terminal ...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, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / : / UBIQUINONE-10 / Reaction center protein M chain / Reaction center protein L chain / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain / Reaction center protein H chain
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsAxelrod, H.L. / Abresch, E.C. / Paddock, M.L. / Okamura, M.Y. / Feher, G.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Determination of the binding sites of the proton transfer inhibitors Cd2+ and Zn2+ in bacterial reaction centers.
Authors: Axelrod, H.L. / Abresch, E.C. / Paddock, M.L. / Okamura, M.Y. / Feher, G.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Identification of the Proton Pathway in Bacterial Reaction Centers: Inhibition of Proton Transfer by Binding of Zn2+ or Cd2+
Authors: Paddock, M.L. / Graige, M.S. / Feher, G. / Okamura, M.Y.
#2: Journal: Photosynth.Res. / Year: 1998
Title: Identification of proton transfer pathways in the X-ray crystal structure of the bacterial reaction center from Rhodobacter sphaeroides
Authors: Abresch, E.C. / Paddock, M.L. / Stowell, M.H.B. / McPhillips, T.M. / Axelrod, H.L. / Soltis, S.M. / Rees, D.C. / Okamura, M.Y. / Feher, G.
#3: Journal: Science / Year: 1997
Title: Light-Induced Structural Changes in Photosynthetic Reaction Center: Implications for Mechanism of Electron-Proton Transfer
Authors: Stowell, M.H. / McPhillips, T.M. / Rees, D.C. / Soltis, S.M. / Abresch, E. / Feher, G.
History
DepositionJan 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 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 / struct_ref_seq_dif / struct_site
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_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.pdbx_dist_value / _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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
L: PHOTOSYNTHETIC REACTION CENTER REACTION CENTER
M: PHOTOSYNTHETIC REACTION CENTER REACTION CENTER
H: PHOTOSYNTHETIC REACTION CENTER REACTION CENTER
R: PHOTOSYNTHETIC REACTION CENTER REACTION CENTER
S: PHOTOSYNTHETIC REACTION CENTER REACTION CENTER
T: PHOTOSYNTHETIC REACTION CENTER REACTION CENTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,84730
Polymers187,6796
Non-polymers15,16824
Water7,314406
1
L: PHOTOSYNTHETIC REACTION CENTER REACTION CENTER
M: PHOTOSYNTHETIC REACTION CENTER REACTION CENTER
H: PHOTOSYNTHETIC REACTION CENTER REACTION CENTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,65316
Polymers93,8393
Non-polymers7,81413
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31290 Å2
ΔGint-233 kcal/mol
Surface area30050 Å2
MethodPISA
2
R: PHOTOSYNTHETIC REACTION CENTER REACTION CENTER
S: PHOTOSYNTHETIC REACTION CENTER REACTION CENTER
T: PHOTOSYNTHETIC REACTION CENTER REACTION CENTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,19414
Polymers93,8393
Non-polymers7,35511
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29510 Å2
ΔGint-232 kcal/mol
Surface area30560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.250, 141.250, 275.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a monomer composed of chain L, chain M, chain H, and bound cofactors

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Components

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PHOTOSYNTHETIC REACTION CENTER REACTION ... , 3 types, 6 molecules LRMSHT

#1: Protein PHOTOSYNTHETIC REACTION CENTER REACTION CENTER


Mass: 31346.389 Da / Num. of mol.: 2 / Fragment: L CHAIN / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: P02954, UniProt: P0C0Y8*PLUS
#2: Protein PHOTOSYNTHETIC REACTION CENTER REACTION CENTER


Mass: 34355.520 Da / Num. of mol.: 2 / Fragment: M CHAIN / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: P02953, UniProt: P0C0Y9*PLUS
#3: Protein PHOTOSYNTHETIC REACTION CENTER REACTION CENTER


Mass: 28137.398 Da / Num. of mol.: 2 / Fragment: H CHAIN / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: P11846, UniProt: P0C0Y7*PLUS

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Non-polymers , 8 types, 430 molecules

#4: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


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


Mass: 889.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H76N4O6
#6: Chemical
ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C59H90O4
#7: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#10: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 3.66 Å3/Da / Density % sol: 66.36 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 4000, heptanetriol, TRIS-HCL, LDAO detergent, sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 mMTris-Cl1drop
36.0 %PEG40001drop
40.4 %ampiphiles benzamidine hydrochloride1drop
52.5 %heptane triol1drop
632 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.49→27.8 Å / Num. all: 94618 / Num. obs: 91189 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 49.14 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.2
Reflection shellResolution: 2.49→2.56 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.33 / Num. unique all: 5527 / % possible all: 78.3
Reflection
*PLUS
Num. obs: 12363 / Num. measured all: 91189
Reflection shell
*PLUS
% possible obs: 78.3 %

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementResolution: 2.5→27.8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
Details: Bulk solvent correction applied during the refinement. Refinement was carried out with a maximum likelihood target function and non-crystallographic symmetry restraints.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 4391 -The test set was the same subset of reflections used for the refinement of PDB entry 1aij
Rwork0.226 ---
all0.227 96784 --
obs0.227 87765 95.2 %-
Refinement stepCycle: LAST / Resolution: 2.5→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12982 0 883 406 14271
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_d1.65
X-RAY DIFFRACTIONc_torsion_deg21.26
X-RAY DIFFRACTIONc_torsion_impr_deg1.03
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.65

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