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- PDB-2cth: CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH -

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Basic information

Entry
Database: PDB / ID: 2cth
TitleCYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH
ComponentsCYTOCHROME C3
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


anaerobic respiration / electron transfer activity / periplasmic space / heme binding / metal ion binding
Similarity search - Function
Class III cytochrome C / Class III cytochrome C family / Cytochrome c, class III / Cytochrome C3 / Cytochrome C3 / Multiheme cytochrome c family profile. / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c3
Similarity search - Component
Biological speciesDesulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsSimoes, P. / Matias, P.M. / Morais, J. / Wilson, K. / Dauter, Z. / Carrondo, M.A.
Citation
Journal: Inorg.Chim.Acta. / Year: 1998
Title: Refinement of the Three-Dimensional Structures of Cytochromes C3 from Desulfovibrio Vulgaris Hildenborough at 1.67 Angstrom Resolution and from Desulfovibrio Desulfuricans Atcc 27774 at 1.6 Angstrom Resolution
Authors: Simoes, P. / Matias, P.M. / Morais, J. / Wilson, K. / Dauter, Z. / Carrondo, M.A.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Structure Analysis of Cytochrome C3 from Desulfovibrio Vulgaris Hildenborough at 1.9 A Resolution
Authors: Matias, P.M. / Frazao, C. / Morais, J. / Coll, M. / Carrondo, M.A.
History
DepositionJun 18, 1997Processing site: BNL
SupersessionDec 24, 1997ID: 1CTH
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C3
B: CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,30710
Polymers23,3752
Non-polymers4,9328
Water2,234124
1
A: CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1535
Polymers11,6871
Non-polymers2,4664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1535
Polymers11,6871
Non-polymers2,4664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.300, 77.300, 77.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein CYTOCHROME C3


Mass: 11687.463 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria)
Species: Desulfovibrio vulgaris / Strain: HILDENBOROUGH / References: UniProt: P00131
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growpH: 5.5
Details: PROTEIN WAS CRYSTALLIZED FROM 75% (V/V) ETHANOL AND 0.05 M SODIUM ACETATE (PH 5.5)

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1993 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.67→25.3 Å / Num. obs: 28861 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 8.1
Reflection shellResolution: 1.67→1.71 Å / Redundancy: 4 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.265 / % possible all: 89.6

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Processing

Software
NameVersionClassification
SHELXL-93model building
SHELXL-93refinement
MOSFLMdata reduction
CCP4(ROTAVATA)data scaling
SHELXL-93phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CDV

2cdv


Resolution: 1.67→8 Å / Num. parameters: 8266 / Num. restraintsaints: 30043 / Cross valid method: FREE R-VALUE / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2857 10 %EVERY 10TH
all0.161 28861 --
obs0.153 ---
Refinement stepCycle: LAST / Resolution: 1.67→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 344 124 2432
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.03
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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