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

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Basic information

Entry
Database: PDB / ID: 7zqz
TitleF61V Cytochrome c prime beta from Methylococcus capsulatus (Bath): NO complex
ComponentsCytochrome c
KeywordsOXIDOREDUCTASE / NO bound / Cytochrome c prime / Beta-sheet
Function / homologyCytochrome P460 / Cytochrome P460 superfamily / Cytochrome P460 / metal ion binding / HEME C / NITRIC OXIDE / DI(HYDROXYETHYL)ETHER / 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 3, 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 6, 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)36,40411
Polymers34,6452
Non-polymers1,7599
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-67 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.236, 106.236, 106.236
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

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 6 types, 186 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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, 35% 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, 35% 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: 1.68→33.59 Å / Num. obs: 45336 / % possible obs: 99.3 % / Redundancy: 3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.028 / Rrim(I) all: 0.05 / Net I/σ(I): 11.7 / Num. measured all: 137210 / Scaling rejects: 137
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
1.68-1.722.90.758979333300.5790.5110.9191.199.5
7.51-33.5930.02616245500.9980.0170.03139.598.1

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HIH

6hih


Resolution: 1.68→33.59 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.131 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 2318 5.1 %RANDOM
Rwork0.1779 ---
obs0.1792 42969 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.34 Å2 / Biso mean: 31.457 Å2 / Biso min: 20.91 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.68→33.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 117 177 2393
Biso mean--35.54 40.74 -
Num. residues----272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132347
X-RAY DIFFRACTIONr_bond_other_d0.0020.0182071
X-RAY DIFFRACTIONr_angle_refined_deg1.8591.7123187
X-RAY DIFFRACTIONr_angle_other_deg1.4861.6264741
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.165287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.421.25128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33915333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8161517
X-RAY DIFFRACTIONr_chiral_restr0.0880.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023004
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02603
LS refinement shellResolution: 1.68→1.724 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 196 -
Rwork0.286 3114 -
all-3310 -
obs--99.34 %

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