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- PDB-1vyd: Crystal structure of cytochrome C2 mutant G95E -

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Basic information

Entry
Database: PDB / ID: 1vyd
TitleCrystal structure of cytochrome C2 mutant G95E
ComponentsCYTOCHROME C2
KeywordsELECTRON TRANSPORT / REDOX
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-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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c2
Similarity search - Component
Biological speciesRHODOBACTER CAPSULATUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDumortier, C. / Fitch, J. / Van Petegem, F. / Vermeulen, W. / Meyer, T.E. / Van Beeumen, J.J. / Cusanovich, M.A.
CitationJournal: Biochemistry / Year: 2004
Title: Protein Dynamics in the Region of the Sixth Ligand Methionine Revealed by Studies of Imidazole Binding to Rhodobacter Capsulatus Cytochrome C2 Hinge Mutants.
Authors: Dumortier, C. / Fitch, J. / Van Petegem, F. / Vermeulen, W. / Meyer, T.E. / Van Beeumen, J.J. / Cusanovich, M.A.
History
DepositionApr 27, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2004Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jun 13, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 C2
B: CYTOCHROME C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9494
Polymers24,7162
Non-polymers1,2332
Water1,47782
1
A: CYTOCHROME C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9752
Polymers12,3581
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CYTOCHROME C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9752
Polymers12,3581
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)100.230, 100.230, 162.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.26323, -0.45915, -0.84846), (-0.40994, -0.74289, 0.5292), (-0.8733, 0.48712, 0.00733)
Vector: 59.40797, 98.56004, 0.79309)

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Components

#1: Protein CYTOCHROME C2


Mass: 12358.074 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00094
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION GLY 116 GLU

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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: 3.17 Å3/Da / Density % sol: 61.21 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: ROTATING ANODE / Type: NONIUS / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. obs: 12459 / % possible obs: 88 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.27

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD TYPE CYTOCHROME C2

Resolution: 2.3→10 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.242 -5 %RANDOM
Rwork0.198 ---
obs-12459 88 %-
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 86 82 1904

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