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- PDB-1qn2: cytochrome cH from Methylobacterium extorquens -

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Basic information

Entry
Database: PDB / ID: 1qn2
Titlecytochrome cH from Methylobacterium extorquens
ComponentsCYTOCHROME CH
KeywordsCYTOCHROME / CYTOCHROME C / ELECTRON TRANSPORT
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / 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
Biological speciesMETHYLOBACTERIUM EXTORQUENS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsRead, J. / Gill, R. / Dales, S.L. / Cooper, J.B. / Wood, S.P. / Anthony, C.
CitationJournal: Protein Sci. / Year: 1999
Title: The Molecular Structure of an Unusual Cytochrome C2 Determined at 2.0A; the Cytochrome cH from Methylobacterium Extorquens
Authors: Read, J. / Gill, R. / Dales, S.L. / Cooper, J.B. / Wood, S.P. / Anthony, C.
History
DepositionOct 13, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 30, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _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 CH
B: CYTOCHROME CH
C: CYTOCHROME CH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3956
Polymers31,5393
Non-polymers1,8563
Water3,171176
1
A: CYTOCHROME CH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1322
Polymers10,5131
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CYTOCHROME CH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1322
Polymers10,5131
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: CYTOCHROME CH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1322
Polymers10,5131
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)33.760, 57.570, 50.950
Angle α, β, γ (deg.)67.81, 89.33, 74.40
Int Tables number1
Space group name H-MP1

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Components

#1: Protein CYTOCHROME CH


Mass: 10513.021 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) METHYLOBACTERIUM EXTORQUENS (bacteria) / References: UniProt: Q7SIA4*PLUS
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.79 Å3/Da / Density % sol: 40 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: HANGING DROP VAPOUR DIFFUSION, 10 MG/ML PROTEIN, 18% PEG 1500, 50 MM TRIS-HCL, PH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
218 %PEG15001reservoir
350 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF NONIUS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1997
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 16999 / % possible obs: 94.4 % / Redundancy: 2.25 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.3
Reflection shellResolution: 2.01→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 6.3 / % possible all: 71.5
Reflection shell
*PLUS
% possible obs: 71.5 %

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Processing

Software
NameClassification
CCP4refinement
MOSFLMdata reduction
Agrovatadata scaling
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C2C

2c2c


Resolution: 2.01→30 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.222 -5 %RANDOM
Rwork0.161 ---
obs-16999 94.4 %-
Displacement parametersBiso mean: 31.4 Å2
Refinement stepCycle: LAST / Resolution: 2.01→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 129 176 2453
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d0.018
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.009
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.007
X-RAY DIFFRACTIONp_chiral_restr0.011
X-RAY DIFFRACTIONp_singtor_nbd0.028
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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