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- PDB-7zvz: Cytochrome c prime beta from Methylococcus capsulatus (Bath): Che... -

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Basic information

Entry
Database: PDB / ID: 7zvz
TitleCytochrome c prime beta from Methylococcus capsulatus (Bath): Chemically Reduced Ferrous Form
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: 1.68 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 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 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

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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)36,3208
Polymers34,7412
Non-polymers1,5796
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-65 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.560, 105.560, 105.560
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-202-

ZN

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Components

#1: Protein Cytochrome c /


Mass: 17370.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus str. Bath (bacteria)
Strain: ATCC 33009 / NCIMB 11132 / Bath / Gene: ccp, MCA2394 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G1UBD5
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 15 mg/ml protein mixed with 10 mM ZnSO4, 35% PEG 550, 100 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.68→43.09 Å / Num. obs: 44860 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.018 / Rrim(I) all: 0.048 / Net I/σ(I): 24.2 / Num. measured all: 299156
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.68-1.726.81.3152246832980.5510.5411.4241.5100
7.51-43.096.30.02235625630.9990.0090.024101.199.4

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HIH

6hih


Resolution: 1.68→37.35 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.124 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 2216 4.9 %RANDOM
Rwork0.1921 ---
obs0.1937 42598 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.56 Å2 / Biso mean: 31.401 Å2 / Biso min: 17.92 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.68→37.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 105 119 2368
Biso mean--34.5 39.65 -
Num. residues----272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132373
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182126
X-RAY DIFFRACTIONr_angle_refined_deg2.3221.7123230
X-RAY DIFFRACTIONr_angle_other_deg1.4171.6334891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8945288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.19521.791134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38915360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0631516
X-RAY DIFFRACTIONr_chiral_restr0.0870.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022792
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02600
LS refinement shellResolution: 1.68→1.724 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 185 -
Rwork0.293 3096 -
all-3281 -
obs--99.94 %

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