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- PDB-1hh7: REFINED CRYSTAL STRUCTURE OF CYTOCHROME C2 FROM RHODOPSEUDOMONAS ... -

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Basic information

Entry
Database: PDB / ID: 1hh7
TitleREFINED CRYSTAL STRUCTURE OF CYTOCHROME C2 FROM RHODOPSEUDOMONAS PALUSTRIS AT 1.4 ANGSTROM RESOLUTION
ComponentsCYTOCHROME C2
KeywordsELECTRON TRANSPORT / ELECTRON CARRIER / HEME PROTEIN
Function / homology
Function and homology information


photosynthesis / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / 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
HEME C / AMMONIA / Cytochrome c2
Similarity search - Component
Biological speciesRHODOPSEUDOMONAS PALUSTRIS (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGarau, G. / Geremia, S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary X-Ray Analysis of Two Ph-Dependent Forms of Cytochrome C2 from Rhodopseudomonas Palustris
Authors: Garau, G. / Geremia, S. / Randaccio, L. / Vaccari, L. / Viezzoli, M.S.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Refined Crystal Structure of Ferrocytochrome C2 from Rhodopseudomonas Viridis at 1.6 A Resolution
Authors: Sogabe, S. / Miki, K.
#2: Journal: Nature / Year: 1979
Title: Cytochrome C2 Sequence Variation Among the Recognised Species of Purple Nonsulphur Photosynthetic Bacteria
Authors: Ambler, R.P. / Daniel, M. / Hermoso, J. / Meyer, T.E. / Bartsch, R.G. / Kamen, M.D.
History
DepositionDec 21, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Mar 11, 2020Group: Advisory / Polymer sequence / Category: database_PDB_caveat / entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0155
Polymers12,1871
Non-polymers8284
Water4,486249
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.670, 64.670, 68.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2041-

HOH

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Components

#1: Protein CYTOCHROME C2


Mass: 12186.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) RHODOPSEUDOMONAS PALUSTRIS (phototrophic) / Strain: 42 OL / References: UniProt: P00091
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NH3 / AMMONIA


Mass: 17.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPCA 1: GLN 1 HAS BEEN CYCLIZED TO PYRROLIDONE CARBOXYLIC ACID

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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: 3.18 Å3/Da / Density % sol: 61.3 %
Crystal growpH: 9 / Details: 60% AMMONIUM SULPHATE, 0.1 M TRIS PH 9.0
Crystal grow
*PLUS
Temperature: 291 K / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.67 mMprotein1drop9.0mg/ml
2200 mMphosphate1drop
361 %satammonium sulfate1reservoir
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 23, 1999 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→56 Å / Num. obs: 31246 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 12 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 5.9
Reflection shellResolution: 1.4→1.47 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 5.9 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 56 Å / Observed criterion σ(I): 0 / Num. measured all: 394132
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameClassification
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C2C

2c2c


Resolution: 1.4→56 Å / Num. parameters: 4681 / Num. restraintsaints: 3727 / Cross valid method: FREE R-VALUE / σ(F): 0
Details: ANISOTROPIC REFINEMENT FOR IRON AND ALL SULFUR ATOMS CHEMICALLY EQUIVALENT BONDS AND ANGLE DISTANCES IN HEME RESTRAINED TO BE EQUAL WITHOUT TARGET VALUES. NO GEOMETRIC OR ADP RESTRAINTS APPLIED TO IRON ATOM.
RfactorNum. reflection% reflectionSelection details
obs0.1508 -99.8 %-
Rfree-1669 5 %RANDOM
all-31246 --
Refine analyzeNum. disordered residues: 1
Refinement stepCycle: LAST / Resolution: 1.4→56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms855 0 54 249 1158
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.034
X-RAY DIFFRACTIONs_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.068
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.035
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELX / Version: VERSION 97-1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_plane_restr0.034
X-RAY DIFFRACTIONx_chiral_restr0.069

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