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- PDB-1cc5: CRYSTAL STRUCTURE OF AZOTOBACTER CYTOCHROME C5 AT 2.5 ANGSTROMS R... -

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Basic information

Entry
Database: PDB / ID: 1cc5
TitleCRYSTAL STRUCTURE OF AZOTOBACTER CYTOCHROME C5 AT 2.5 ANGSTROMS RESOLUTION
ComponentsCYTOCHROME C5
KeywordsELECTRON TRANSPORT (HEME PROTEIN)
Function / homology
Function and homology information


electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c, class IE / Cytochrome C oxidase, cbb3-type, subunit III / 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 c5
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsStout, C.D. / Carter, D.C.
Citation
Journal: J.Mol.Biol. / Year: 1985
Title: Crystal structure of Azotobacter cytochrome c5 at 2.5 A resolution.
Authors: Carter, D.C. / Melis, K.A. / O'Donnell, S.E. / Burgess, B.K. / Furey Jr., W.R. / Wang, B.C. / Stout, C.D.
#1: Journal: J.Mol.Biol. / Year: 1978
Title: Preliminary Crystallographic Data for Azotobacter Cytochrome C5
Authors: Stout, C.D.
History
DepositionAug 10, 1984Processing site: BNL
Revision 1.0Oct 29, 1984Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 13, 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.pdbx_leaving_atom_flag / _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
A: CYTOCHROME C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8052
Polymers8,1881
Non-polymers6161
Water00
1
A: CYTOCHROME C5
hetero molecules

A: CYTOCHROME C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6094
Polymers16,3762
Non-polymers1,2332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)45.730, 37.560, 42.550
Angle α, β, γ (deg.)90.00, 111.30, 90.00
Int Tables number5
Space group name H-MC121
DetailsIN THIS SPACE GROUP, THE CYTOCHROME MOLECULE OCCUPIES A CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY SITE. TO GENERATE THE DIMER THE FOLLOWING TRANSFORMATION SHOULD BE APPLIED TO THE COORDINATES GIVEN BELOW -1.0 0.0 0.0 -.36325 0.0 1.0 0.0 0.0 0.0 0.0 -1.0 .93169 IN THE FRACTIONAL COORDINATE FRAME THE SYMMETRY TRANSFORMATION IS GIVEN BY -1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 -1.0 1.0

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Components

#1: Protein CYTOCHROME C5


Mass: 8188.235 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / References: UniProt: P11732
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal grow
*PLUS
pH: 6.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
20.4 Mpotassium phosphate1drop
31.2 Mammonium sulfate1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. measured all: 11526

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Processing

RefinementResolution: 2.5→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.29 -
obs-1938
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms568 0 43 0 611
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.018
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d0.04
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 10.1 Å2
Refine LS restraints
*PLUS
Type: o_planar_d / Dev ideal: 0.019
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.7 Å / Num. reflection obs: 336 / Rfactor obs: 0.258

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