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- PDB-4o1w: Crystal Structure of Colwellia psychrerythraea cytochrome c -

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Basic information

Entry
Database: PDB / ID: 4o1w
TitleCrystal Structure of Colwellia psychrerythraea cytochrome c
ComponentsCytochrome c552
KeywordsELECTRON TRANSPORT / cytochrome c
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
: / 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 / DI(HYDROXYETHYL)ETHER / Cytochrome c552
Similarity search - Component
Biological speciesColwellia psychrerythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHarvilla, P.B. / Wolcott, H.N. / Magyar, J.S. / Shapiro, L.S.
CitationJournal: Metallomics / Year: 2014
Title: The structure of ferricytochrome c552 from the psychrophilic marine bacterium Colwellia psychrerythraea 34H.
Authors: Harvilla, P.B. / Wolcott, H.N. / Magyar, J.S.
History
DepositionDec 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2Jun 18, 2014Group: Database references
Revision 2.0Mar 10, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c552
B: Cytochrome c552
C: Cytochrome c552
D: Cytochrome c552
E: Cytochrome c552
F: Cytochrome c552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,36615
Polymers49,3476
Non-polymers4,0199
Water3,675204
1
A: Cytochrome c552
D: Cytochrome c552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7825
Polymers16,4492
Non-polymers1,3333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-60 kcal/mol
Surface area7420 Å2
MethodPISA
2
B: Cytochrome c552
C: Cytochrome c552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7925
Polymers16,4492
Non-polymers1,3433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-44 kcal/mol
Surface area7560 Å2
MethodPISA
3
E: Cytochrome c552
F: Cytochrome c552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7925
Polymers16,4492
Non-polymers1,3433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-46 kcal/mol
Surface area7700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.280, 45.043, 87.574
Angle α, β, γ (deg.)90.00, 90.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Cytochrome c552


Mass: 8224.474 Da / Num. of mol.: 6 / Fragment: UNP residues 22-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea (bacteria) / Strain: 34H / ATCC BAA-681 / Gene: CPS_0313 / Production host: Escherichia coli (E. coli) / References: UniProt: Q48A34
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 30% PEG 4000, 0.2M lithium sulfate, 50mM Tris, 5% trehalose, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9795
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 12, 2012
RadiationMonochromator: BENT SINGLE SI(III) CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→19.95 Å / Num. obs: 34186 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 23.62 Å2
Reflection shellResolution: 2→19.95 Å / % possible all: 92.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CNO

1cno


Resolution: 2→19.95 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 1720 5.04 %
Rwork0.17 --
obs0.172 34128 98.6 %
all-34496 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3375 0 277 204 3856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173777
X-RAY DIFFRACTIONf_angle_d1.5275171
X-RAY DIFFRACTIONf_dihedral_angle_d16.8841325
X-RAY DIFFRACTIONf_chiral_restr0.075503
X-RAY DIFFRACTIONf_plane_restr0.009649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0018-2.06060.21831010.16642525X-RAY DIFFRACTION92
2.0606-2.1270.22631460.16642664X-RAY DIFFRACTION98
2.127-2.2030.2251150.16782699X-RAY DIFFRACTION99
2.203-2.29110.23541440.17252698X-RAY DIFFRACTION99
2.2911-2.39520.2631520.18452674X-RAY DIFFRACTION99
2.3952-2.52120.24971460.19472695X-RAY DIFFRACTION99
2.5212-2.67880.24641360.19032695X-RAY DIFFRACTION99
2.6788-2.88510.25511560.19672705X-RAY DIFFRACTION100
2.8851-3.17440.26491620.20142736X-RAY DIFFRACTION100
3.1744-3.63130.21821560.1712746X-RAY DIFFRACTION100
3.6313-4.5660.17631550.13672736X-RAY DIFFRACTION100
4.566-19.94620.16731510.1542835X-RAY DIFFRACTION100

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