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- PDB-2bq4: Crystal structure of type I cytochrome c3 from Desulfovibrio africanus -

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Basic information

Entry
Database: PDB / ID: 2bq4
TitleCrystal structure of type I cytochrome c3 from Desulfovibrio africanus
ComponentsBASIC CYTOCHROME C3
KeywordsELECTRON TRANSPORT / BASIC CYTOCHROME C3 / ELECTRON TRANSFER / SULFATE REDUCING BACTERIA / SAD / HEME / IRON
Function / homology
Function and homology information


anaerobic respiration / periplasmic space / electron transfer activity / 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
HEME C / Basic cytochrome c3
Similarity search - Component
Biological speciesDESULFOVIBRIO AFRICANUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.68 Å
AuthorsCzjzek, M. / Pieulle, L. / Morelli, X. / Guerlesquin, F. / Hatchikian, E.C.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The Type I / Type II Cytochrome C(3) Complex: An Electron Transfer Link in the Hydrogen-Sulfate Reduction Pathway.
Authors: Pieulle, L. / Morelli, X. / Gallice, P. / Lojou, E. / Barbier, P. / Czjzek, M. / Bianco, P. / Guerlesquin, F. / Hatchikian, E.C.
History
DepositionApr 27, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,15712
Polymers25,1292
Non-polymers5,02810
Water5,098283
1
A: BASIC CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0786
Polymers12,5641
Non-polymers2,5145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BASIC CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0786
Polymers12,5641
Non-polymers2,5145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)100.900, 46.300, 54.816
Angle α, β, γ (deg.)90.00, 118.97, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 120
2116B1 - 120

NCS oper: (Code: given
Matrix: (0.999442, 0.031835, -0.010076), (-0.030947, 0.996428, 0.078568), (0.012541, -0.078213, 0.996858)
Vector: -0.38652, -0.55287, 0.66256)

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Components

#1: Protein BASIC CYTOCHROME C3 / CYTOCHROME C3


Mass: 12564.343 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: FOUR C-TYPE HEME-GROUPS COVALENTLY LINKED BY CYSTEINE RESIDUES
Source: (natural) DESULFOVIBRIO AFRICANUS (bacteria) / References: UniProt: P94691
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growDetails: 3.2M NAH2PO4/K2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 31, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.68→48.22 Å / Num. obs: 106337 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.2
Reflection shellResolution: 1.68→1.75 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 11.3 / % possible all: 71.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.68→48.22 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.9 / SU B: 1.854 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1237 5.1 %RANDOM
Rwork0.2 ---
obs0.202 22893 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-0.15 Å2
2--0.09 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.68→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1717 0 346 283 2346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212159
X-RAY DIFFRACTIONr_bond_other_d0.0020.021730
X-RAY DIFFRACTIONr_angle_refined_deg1.3792.4123022
X-RAY DIFFRACTIONr_angle_other_deg0.99134059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2365227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1510.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022299
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02311
X-RAY DIFFRACTIONr_nbd_refined0.3430.2596
X-RAY DIFFRACTIONr_nbd_other0.2170.22103
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.2955
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2171
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2970.251
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5881.51141
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10621822
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.48731018
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2934.51200
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1889 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.435
loose thermal1.9510
LS refinement shellResolution: 1.68→1.72 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.24 70
Rwork0.197 1220

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