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- PDB-2xm4: Cytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124E v... -

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Basic information

Entry
Database: PDB / ID: 2xm4
TitleCytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124E variant
ComponentsCYTOCHROME C'
KeywordsELECTRON TRANSPORT
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
HEME C / Cytochrome c'
Similarity search - Component
Biological speciesACHROMOBACTER XYLOSOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsHough, M.A. / Antonyuk, S.V. / Hasnain, S.S.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Distal-to-Proximal No Conversion in Hemoproteins: The Role of the Proximal Pocket.
Authors: Hough, M.A. / Antonyuk, S.V. / Barbieri, S. / Rustage, N. / Mckay, A.L. / Servid, A.E. / Eady, R.R. / Andrew, C.R. / Hasnain, S.S.
History
DepositionJul 23, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Mar 11, 2020Group: Other / Polymer sequence / Category: entity_poly / pdbx_database_status
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf
Revision 2.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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 C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2222
Polymers13,6031
Non-polymers6191
Water4,576254
1
A: CYTOCHROME C'
hetero molecules

A: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4444
Polymers27,2072
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3540 Å2
ΔGint-52.9 kcal/mol
Surface area13230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.463, 53.463, 180.813
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2040-

HOH

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Components

#1: Protein CYTOCHROME C'


Mass: 13603.362 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACHROMOBACTER XYLOSOXIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00138
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 124 TO GLU
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: 2.74 Å3/Da / Density % sol: 55.14 % / Description: NONE
Crystal growpH: 7.4 / Details: AMMONIUM SULPHATE, HEPES PH7.5, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.1→46 Å / Num. obs: 61966 / % possible obs: 97.8 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.6
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3 / % possible all: 88.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→46.3 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.721 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.16988 3139 5.1 %RANDOM
Rwork0.14496 ---
obs0.14623 58504 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.205 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å20 Å2
2---0.08 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.1→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 43 254 1253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221198
X-RAY DIFFRACTIONr_bond_other_d0.0020.02815
X-RAY DIFFRACTIONr_angle_refined_deg1.8652.0721659
X-RAY DIFFRACTIONr_angle_other_deg1.00132012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9935167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.65625.28353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49915203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.326156
X-RAY DIFFRACTIONr_chiral_restr0.1060.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211412
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02232
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7171.5730
X-RAY DIFFRACTIONr_mcbond_other0.5361.5292
X-RAY DIFFRACTIONr_mcangle_it2.62121177
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3823468
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6334.5468
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.38832013
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 216 -
Rwork0.298 3751 -
obs--86.5 %

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