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- PDB-7zrx: F61V Cytochrome c prime beta from Methylococcus capsulatus (Bath)... -

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Basic information

Entry
Database: PDB / ID: 7zrx
TitleF61V Cytochrome c prime beta from Methylococcus capsulatus (Bath) Chemically Reduced Ferrous State
ComponentsCytochrome c
KeywordsOXIDOREDUCTASE / Cytochrome c prime / Beta-sheet
Function / homologyCytochrome P460 / Cytochrome P460 superfamily / Cytochrome P460 / metal ion binding / HEME C / Cytochrome c
Function and homology information
Biological speciesMethylococcus capsulatus str. Bath (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsAdams, H.R. / Hough, M.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2023
Title: A heme pocket aromatic quadrupole modulates gas binding to cytochrome c'-beta : Implications for NO sensors.
Authors: Adams, H.R. / Svistunenko, D.A. / Wilson, M.T. / Fujii, S. / Strange, R.W. / Hardy, Z.A. / Vazquez, P.A. / Dabritz, T. / Streblow, G.J. / Andrew, C.R. / Hough, M.A.
History
DepositionMay 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1978
Polymers34,6452
Non-polymers1,5526
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-95 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.537, 105.537, 105.537
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-201-

ZN

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Components

#1: Protein Cytochrome c


Mass: 17322.607 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus str. Bath (bacteria)
Gene: ccp, MCA2394 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G1UBD5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.8 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2 microlitres of 15 mg/ml protein in 0.1 M HEPES buffer, pH 7.5, mixed with with an equivalent volume of reservoir solution containing 0.01 M ZnSO4, 30% PEG 550 (v/v) and 0.1 M MES, pH 6.5. ...Details: 2 microlitres of 15 mg/ml protein in 0.1 M HEPES buffer, pH 7.5, mixed with with an equivalent volume of reservoir solution containing 0.01 M ZnSO4, 30% PEG 550 (v/v) and 0.1 M MES, pH 6.5. Cryoprotection in ML plus 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 20, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.04→47.2 Å / Num. obs: 24699 / % possible obs: 97.9 % / Redundancy: 2.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.036 / Rrim(I) all: 0.062 / Net I/σ(I): 8.7 / Num. measured all: 65229 / Scaling rejects: 62
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.5 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.04-2.090.67431117060.6220.4850.8321.391.6
9.12-47.20.0327853150.9950.0230.0423.397.6

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HIH

6hih


Resolution: 2.04→47.2 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.21 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 1220 4.9 %RANDOM
Rwork0.184 ---
obs0.1855 23455 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 128.77 Å2 / Biso mean: 45.046 Å2 / Biso min: 31.74 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.04→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 100 107 2306
Biso mean--47.94 54.63 -
Num. residues----272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132330
X-RAY DIFFRACTIONr_bond_other_d0.0020.0182045
X-RAY DIFFRACTIONr_angle_refined_deg2.2791.723187
X-RAY DIFFRACTIONr_angle_other_deg1.3871.6284697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5855286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96621.339127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17815331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6581516
X-RAY DIFFRACTIONr_chiral_restr0.1420.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022985
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02590
LS refinement shellResolution: 2.04→2.091 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.295 112 -
Rwork0.286 1576 -
obs--91.19 %

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