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- PDB-1cxy: STRUCTURE AND CHARACTERIZATION OF ECTOTHIORHODOSPIRA VACUOLATA CY... -

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Basic information

Entry
Database: PDB / ID: 1cxy
TitleSTRUCTURE AND CHARACTERIZATION OF ECTOTHIORHODOSPIRA VACUOLATA CYTOCHROME B558, A PROKARYOTIC HOMOLOGUE OF CYTOCHROME B5
ComponentsCYTOCHROME B5
KeywordsELECTRON TRANSPORT / HELIX / BETA-STRAND
Function / homology
Function and homology information


intracellular membrane-bounded organelle / heme binding / membrane / metal ion binding
Similarity search - Function
: / Flavocytochrome B2; Chain A, domain 1 / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / Roll / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Soluble cytochrome b558
Similarity search - Component
Biological speciesEctothiorhodospira shaposhnikovii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsKostanjevecki, V. / Leys, D. / Van Driessche, G. / Meyer, T.E. / Cusanovich, M.A. / Fischer, U. / Guisez, Y. / Van Beeumen, J.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Structure and characterization of Ectothiorhodospira vacuolata cytochrome b(558), a prokaryotic homologue of cytochrome b(5).
Authors: Kostanjevecki, V. / Leys, D. / Van Driessche, G. / Meyer, T.E. / Cusanovich, M.A. / Fischer, U. / Guisez, Y. / Van Beeumen, J.
History
DepositionAug 31, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_seq_id / _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 B5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7232
Polymers10,1061
Non-polymers6161
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.406, 46.406, 91.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CYTOCHROME B5


Mass: 10106.286 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ectothiorhodospira shaposhnikovii (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P82291
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
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: 2.82 Å3/Da / Density % sol: 56.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: MES, NACL, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 63.8 %
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMTris/Cl1drop
34 M1reservoirNaCl
40.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.65→15 Å / Num. all: 92730 / Num. obs: 14370 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.45 % / Biso Wilson estimate: 23.13 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 19.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.318 / % possible all: 99.7
Reflection
*PLUS
Num. measured all: 92730 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementResolution: 1.65→12 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: USE MAXIMUM LIKELIHOOD PROCEDURE
RfactorNum. reflection% reflectionSelection details
Rfree0.22 711 -RANDOM
Rwork0.199 ---
all0.186 14226 --
obs0.186 14226 99.7 %-
Refinement stepCycle: LAST / Resolution: 1.65→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms639 0 43 166 848
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.25

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