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- PDB-8gar: Nitrosomonas europaea Cytochrome P460 Arg44Ala -

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Basic information

Entry
Database: PDB / ID: 8gar
TitleNitrosomonas europaea Cytochrome P460 Arg44Ala
ComponentsCytochrome P460
KeywordsMETAL BINDING PROTEIN / Cytochrome / Heme protein
Function / homologyCytochrome P460 / Cytochrome P460 superfamily / Cytochrome P460 / metal ion binding / ACETATE ION / HEME C / Cytochrome P460
Function and homology information
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsBollmeyer, M.M. / Lancaster, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM124908 United States
Citation
Journal: J.Am.Chem.Soc. / Year: 2023
Title: Cytochrome P460 Cofactor Maturation Proceeds via Peroxide-Dependent Post-translational Modification.
Authors: Bollmeyer, M.M. / Coleman, R.E. / Majer, S.H. / Ferrao, S.D. / Lancaster, K.M.
History
DepositionFeb 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 P460
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9153
Polymers21,2371
Non-polymers6782
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.111, 53.111, 125.894
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-354-

HOH

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Components

#1: Protein Cytochrome P460


Mass: 21236.994 Da / Num. of mol.: 1 / Mutation: R44A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Gene: cyp / Production host: Escherichia coli (E. coli) / References: UniProt: Q50927
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 3000, calcium acetate, sodium cacodylate, MOP buffer

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→46.0157 Å / Num. obs: 30693 / % possible obs: 99.68 % / Redundancy: 19.8 % / Biso Wilson estimate: 25.3002206217 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.05202 / Rrim(I) all: 0.05344 / Net I/σ(I): 32.17
Reflection shellResolution: 1.55→1.605 Å / Redundancy: 20.2 % / Rmerge(I) obs: 1.518 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 3014 / CC1/2: 0.916 / CC star: 0.978 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→46.0157 Å / SU ML: 0.185834184717 / Cross valid method: FREE R-VALUE / σ(F): 1.34973758215 / Phase error: 22.6285976111
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.201100991811 1453 4.74728003398 %
Rwork0.165058650345 29154 -
obs0.166847748623 30607 99.6775874422 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.5325967268 Å2
Refinement stepCycle: LAST / Resolution: 1.55→46.0157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 0 140 1380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01009126312481288
X-RAY DIFFRACTIONf_angle_d0.9914228665651757
X-RAY DIFFRACTIONf_chiral_restr0.05549551118182
X-RAY DIFFRACTIONf_plane_restr0.00718127157384222
X-RAY DIFFRACTIONf_dihedral_angle_d13.9480520189732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.60520.2982357289821500.2560236856232849X-RAY DIFFRACTION99.502322495
1.6052-1.66950.2772855807241310.2007765269972871X-RAY DIFFRACTION99.601857996
1.6695-1.74550.2298372747691450.1689744847452836X-RAY DIFFRACTION99.2673992674
1.7455-1.83750.1817699368051260.1411016695582905X-RAY DIFFRACTION99.4748933377
1.8375-1.95270.1776534515391350.1305810139072889X-RAY DIFFRACTION99.801980198
1.9527-2.10340.2092930745811510.1359250039992890X-RAY DIFFRACTION99.5417348609
2.1034-2.31510.1960959117331440.1378216749492913X-RAY DIFFRACTION99.7064579256
2.3151-2.65010.174845794221240.1476656372742956X-RAY DIFFRACTION99.9675430055
2.6501-3.33870.1904046869471660.1738337655792947X-RAY DIFFRACTION99.9678869621
3.3387-46.01570.2058851938521810.1769998460613098X-RAY DIFFRACTION99.9695121951

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