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- PDB-1jaf: CRYSTAL STRUCTURE OF CYTOCHROME C' FROM RHODOCYCLUS GELATINOSUS A... -

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Basic information

Entry
Database: PDB / ID: 1jaf
TitleCRYSTAL STRUCTURE OF CYTOCHROME C' FROM RHODOCYCLUS GELATINOSUS AT 2.5 ANGSTOMS RESOLUTION
ComponentsCYTOCHROME C'
KeywordsELECTRON TRANSPORT / HEME PROTEIN / CYTOCHROME C'
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c prime, subgroup / Cytochrome c, class II / Cytochrome c prime / Cytochrome C' / Cytochrome c class II profile. / Cytochrome c/b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c'
Similarity search - Component
Biological speciesRubrivivax gelatinosus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsArcher, M. / Banci, L. / Dikaya, E. / Romao, M.J.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 1997
Title: Crystal Structure of Cytochrome C' from Rhodocyclus Gelatinosus and Comparison with Other Cytochromes C'
Authors: Archer, M. / Banci, L. / Dikaya, E. / Romao, M.J.
#1: Journal: Biochemistry / Year: 1993
Title: One-and Two-Dimensional NMR Characterization of Oxidized and Reduced Cytochrome C' from Rhodocyclus Gelatinosus
Authors: Bertini, I. / Gori, G. / Luchinat, C. / Vila, A.J.
History
DepositionJun 24, 1997Processing site: BNL
Revision 1.0Jan 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C'
B: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8394
Polymers26,6062
Non-polymers1,2332
Water99155
1
A: CYTOCHROME C'
B: CYTOCHROME C'
hetero molecules

A: CYTOCHROME C'
B: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6788
Polymers53,2124
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+5/31
Unit cell
Length a, b, c (Å)70.180, 70.180, 126.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein CYTOCHROME C'


Mass: 13303.056 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rubrivivax gelatinosus (bacteria) / References: UniProt: P00142
#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.: 55 / 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: 3.5 Å3/Da / Density % sol: 60 %
Crystal growpH: 6
Details: 55% SATURATED (NH4)2SO4, 50 MM (NH4)2HPO4, 1 M NACL, pH 6.
Crystal grow
*PLUS
Temperature: 277 K / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
155 %satammonium sulfate11
250 mMammonium phosphate11
31 M11NaCl
410-20 mg/mlprotein12
550 mMammonium phosphate12

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceType: BRUKER NONIUS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→27.4 Å / Num. obs: 13010 / % possible obs: 99.3 % / Redundancy: 7.4 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.7
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 2.4 / % possible all: 98.7
Reflection
*PLUS
Num. measured all: 96234 / Rmerge(I) obs: 0.112
Reflection shell
*PLUS
% possible obs: 98.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CYTOCHROME C' FROM ALCALIGENES SP (PDB ENTRY 1CGO)

1cgo


Resolution: 2.5→27.4 Å / Cross valid method: FREE R / σ(F): 2
Details: BULK SOLVENT CORRECTION USED (KSOL=0.33, SOLRAD=0.25 A, B=50 A**2).
RfactorNum. reflection% reflection
Rfree0.221 988 7.5 %
Rwork0.179 --
obs0.179 12807 99.3 %
Displacement parametersBiso mean: 34.3 Å2
Refinement stepCycle: LAST / Resolution: 2.5→27.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1876 0 43 56 1975
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.403
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.33
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.327
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection% reflection
Rfree0.351 112 -
Rwork0.325 1156 -
obs--98.7 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.334
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.327

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