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- PDB-9hs6: Cytochrome P460 from Methyloccocus capsulatus (double crosslink f... -

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Basic information

Entry
Database: PDB / ID: 9hs6
TitleCytochrome P460 from Methyloccocus capsulatus (double crosslink from Lys), aged
ComponentsCytochrome P460
KeywordsOXIDOREDUCTASE / Hydroxylamine / Nitrous Oxide / Ferrous / double-crosslinked unsaturated lysine
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: 1.77 Å
AuthorsPfalzgraf, H.E. / Adams, H.R. / Mikolajek, H. / Sanchez-Weatherby, J. / Sandy, J. / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,7688
Polymers31,2272
Non-polymers1,5416
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-129 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.701, 80.468, 84.612
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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 618.503 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C34H34FeN4O4
Source: (gene. exp.) Methylococcus capsulatus str. Bath (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.55 Å3/Da / Density % sol: 51.77 % / Description: Hexagon x rectangle x rhombus
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 nL protein at 7 mg/mL with 100 nL of precipitant (2.05 M ammonium sulfate, 100 mM Tris-HCl pH 8.0)

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Sep 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.77→58.32 Å / Num. obs: 31820 / % possible obs: 99.31 % / Redundancy: 66.5 % / CC1/2: 0.982 / Rpim(I) all: 0.1479 / Net I/σ(I): 15.88
Reflection shellResolution: 1.77→1.833 Å / Mean I/σ(I) obs: 0.54 / Num. unique obs: 3124 / CC1/2: 0.285

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
DIALS3.16.1data scaling
DIALS3.16.1data reduction
REFMAC5.8.0419phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→58.32 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.377 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 0.3 weight given to X-ray term
RfactorNum. reflection% reflectionSelection details
Rfree0.19437 1498 4.7 %RANDOM
Rwork0.14421 ---
obs0.14648 30324 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.021 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å2-0 Å20 Å2
2---0.62 Å2-0 Å2
3---0.34 Å2
Refinement stepCycle: 1 / Resolution: 1.77→58.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 96 253 2549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0123010
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162790
X-RAY DIFFRACTIONr_angle_refined_deg2.2641.8494196
X-RAY DIFFRACTIONr_angle_other_deg0.8151.796472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8545415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.4391330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31410491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1290.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023807
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02691
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_it3.5183.1141408
X-RAY DIFFRACTIONr_mcbond_other3.4843.1131408
X-RAY DIFFRACTIONr_mcangle_it4.6895.5581814
X-RAY DIFFRACTIONr_mcangle_other4.6885.5591815
X-RAY DIFFRACTIONr_scbond_it4.8713.5911602
X-RAY DIFFRACTIONr_scbond_other4.8513.5881598
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.966.3432337
X-RAY DIFFRACTIONr_long_range_B_refined9.61132.793520
X-RAY DIFFRACTIONr_long_range_B_other9.58932.543506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 91 -
Rwork0.352 2218 -
obs--100 %

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