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- PDB-9hrk: Cytochrome P460 from Methyloccocus capsulatus in the ferrous stat... -

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Basic information

Entry
Database: PDB / ID: 9hrk
TitleCytochrome P460 from Methyloccocus capsulatus in the ferrous state (single crosslink from Lys)
ComponentsCytochrome P460
KeywordsOXIDOREDUCTASE / Hydroxylamine / Nitrous Oxide / Ferrous
Function / homologyCytochrome P460 / Cytochrome P460 superfamily / Cytochrome P460 / metal ion binding / HEME C / Cytochrome P460
Function and homology information
Biological speciesMethylococcus capsulatus str. Bath (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsPfalzgraf, H.E. / Adams, H.R. / Jaho, S. / Hough, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V01577X/1 United Kingdom
CitationJournal: Chem Sci / Year: 2025
Title: Double crossed? Structural and computational studies of an unusually crosslinked haem in Methylococcus capsulatus cytochrome P460.
Authors: Pfalzgraf, H.E. / Rao, A.G. / Sen, K. / Adams, H.R. / Edwards, M. / Lu, Y. / Yong, C. / Jaho, S. / Tosha, T. / Sugimoto, H. / Horrell, S. / Beilsten-Edmands, J. / Owen, R.L. / Andrew, C.R. / ...Authors: Pfalzgraf, H.E. / Rao, A.G. / Sen, K. / Adams, H.R. / Edwards, M. / Lu, Y. / Yong, C. / Jaho, S. / Tosha, T. / Sugimoto, H. / Horrell, S. / Beilsten-Edmands, J. / Owen, R.L. / Andrew, C.R. / Worrall, J.A.R. / Tews, I. / Mulholland, A.J. / Hough, M.A. / Keal, T.W.
History
DepositionDec 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P460
B: Cytochrome P460
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6566
Polymers31,2272
Non-polymers1,4294
Water7,278404
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-81 kcal/mol
Surface area12660 Å2
Unit cell
Length a, b, c (Å)46.380, 80.441, 84.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome P460


Mass: 15613.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus str. Bath (bacteria)
Gene: MCA0524 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G1UBD9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.51 Å3/Da / Density % sol: 51.1 % / Description: Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2 uL of 7 mg/mL protein with 2 uL precipitant 1.9 M ammonium sulfate, 100 mM Tris-HCl pH 8.0 Cryoprotectant 1.0 M sodium malonate final, soak 100 mM sodium hydrosulfite final

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6199 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 24, 2024 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 1.33→58.34 Å / Num. obs: 73519 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.052 / Rrim(I) all: 0.133 / Net I/σ(I): 8.9
Reflection shellResolution: 1.33→1.35 Å / % possible obs: 99 % / Redundancy: 4.2 % / Rmerge(I) obs: 2.112 / Num. measured all: 15083 / Num. unique obs: 3594 / CC1/2: 0.228 / Rpim(I) all: 1.133 / Rrim(I) all: 2.407 / Net I/σ(I) obs: 0.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
DIALS3.18.1data scaling
DIALS3.18.1data reduction
REFMAC5.8.0425phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→58.34 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.796 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Used riding hydrogens during refinement Used MEH restraints for heme
RfactorNum. reflection% reflectionSelection details
Rfree0.19976 3735 5.1 %RANDOM
Rwork0.1562 ---
obs0.1584 69671 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.131 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å2-0 Å20 Å2
2---2.23 Å2-0 Å2
3---2 Å2
Refinement stepCycle: 1 / Resolution: 1.33→58.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 96 404 2700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132651
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162408
X-RAY DIFFRACTIONr_angle_refined_deg2.0741.8983680
X-RAY DIFFRACTIONr_angle_other_deg0.631.7925593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4125358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.849511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40110424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023327
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02585
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_it3.8531.6841253
X-RAY DIFFRACTIONr_mcbond_other3.841.6841253
X-RAY DIFFRACTIONr_mcangle_it5.7843.0341592
X-RAY DIFFRACTIONr_mcangle_other5.7863.0351593
X-RAY DIFFRACTIONr_scbond_it4.6971.851398
X-RAY DIFFRACTIONr_scbond_other4.6971.851397
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7463.3072060
X-RAY DIFFRACTIONr_long_range_B_refined16.29321.283212
X-RAY DIFFRACTIONr_long_range_B_other13.58919.133079
X-RAY DIFFRACTIONr_rigid_bond_restr3.05535059
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.33→1.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 263 -
Rwork0.352 5041 -
obs--98.22 %

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