[English] 日本語
Yorodumi
- PDB-9hs9: Cytochrome P460 from Methyloccocus capsulatus (unclear crosslink ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hs9
TitleCytochrome P460 from Methyloccocus capsulatus (unclear crosslink from Lys), damage-free
ComponentsCytochrome P460
KeywordsOXIDOREDUCTASE / Hydroxylamine / Nitrous Oxide / ferric
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsPfalzgraf, H.E. / Adams, H.R. / Sugimoto, H. / Tosha, T. / Horrell, S. / Jaho, S. / Beilsten-Edmands, J. / Tews, I. / Worrall, J.A.R. / Owen, R.L. / Hough, M.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V01577X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R021015/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X01844X/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 19, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-109 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.778, 81.002, 85.139
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.47 % / Description: Hexagon x rectangle x rhombus
Crystal growTemperature: 293 K / Method: batch mode / pH: 8
Details: 1:1 20-30 mg/mL protein:3.8-4.0 M ammonium sulfate, 0.1 M Tris pH 8

-
Data collection

DiffractionMean temperature: 301 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.13 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: May 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
ReflectionResolution: 1.28→29.35 Å / Num. obs: 84105 / % possible obs: 100 % / Redundancy: 173.4 % / CC1/2: 0.999 / R split: 0.041 / Rpim(I) all: 0.072 / Net I/σ(I): 28.2
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 179.8 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4186 / CC1/2: 0.283 / R split: 1.346 / Rpim(I) all: 1.568 / % possible all: 100
Serial crystallography measurementFocal spot size: 2.13 µm2 / Pulse duration: 10 fsec. / Pulse energy: 360 µJ / Pulse photon energy: 11 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: Oxford chip / Method: fixed target
Serial crystallography data reductionFrame hits: 18960 / Frames total: 51600 / Lattices indexed: 29559 / XFEL run numbers: 116701, 116725

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
DIALS3.dev.923data scaling
DIALS3.dev.923data reduction
REFMAC5.8.0352phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→29.35 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.15 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Used MEH restraints for heme
RfactorNum. reflection% reflectionSelection details
Rfree0.16139 4248 5.1 %RANDOM
Rwork0.13334 ---
obs0.13478 79785 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.211 Å2
Baniso -1Baniso -2Baniso -3
1--2.24 Å2-0 Å2-0 Å2
2--2.51 Å20 Å2
3----0.27 Å2
Refinement stepCycle: 1 / Resolution: 1.28→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 96 281 2559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0123097
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162908
X-RAY DIFFRACTIONr_angle_refined_deg2.1861.8974326
X-RAY DIFFRACTIONr_angle_other_deg0.6861.8046755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5175431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.07514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24210530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023943
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02705
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_it6.2222.271442
X-RAY DIFFRACTIONr_mcbond_other6.1982.271442
X-RAY DIFFRACTIONr_mcangle_it8.6784.1021867
X-RAY DIFFRACTIONr_mcangle_other8.6814.1031868
X-RAY DIFFRACTIONr_scbond_it8.0732.5951655
X-RAY DIFFRACTIONr_scbond_other8.0582.5941650
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.44.5932408
X-RAY DIFFRACTIONr_long_range_B_refined19.15124.623554
X-RAY DIFFRACTIONr_long_range_B_other18.69224.223538
X-RAY DIFFRACTIONr_rigid_bond_restr4.29136005
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.28→1.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 319 -
Rwork0.369 5810 -
obs--100 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more