[English] 日本語
Yorodumi
- PDB-6cvc: Mycobacterium marinum cytochrome P450 CYP124A1 in the substrate-f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cvc
TitleMycobacterium marinum cytochrome P450 CYP124A1 in the substrate-free form
ComponentsCytochrome P450 124A1, Cyp124A1
KeywordsOXIDOREDUCTASE / cytochrome P450 / monooxygenase / heme protein
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 124A1, Cyp124A1
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsChild, S.A. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT140100355 Australia
CitationJournal: To Be Published
Title: A comparison of the steroid binding cytochrome P450s from Mycobacterium marinum and Mycobacterium tuberculosis
Authors: Child, S.A. / Bruning, J.B. / Bell, S.G.
History
DepositionMar 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450 124A1, Cyp124A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3655
Polymers48,4611
Non-polymers9054
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-61 kcal/mol
Surface area17240 Å2
2
A: Cytochrome P450 124A1, Cyp124A1
hetero molecules

A: Cytochrome P450 124A1, Cyp124A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,73110
Polymers96,9212
Non-polymers1,8098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5520 Å2
ΔGint-136 kcal/mol
Surface area32560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.776, 72.359, 65.602
Angle α, β, γ (deg.)90.000, 109.720, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-866-

HOH

-
Components

#1: Protein Cytochrome P450 124A1, Cyp124A1


Mass: 48460.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / M / Gene: cyp124A1, MMAR_3361 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B2HHT9
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.26 M ammonium sulphate, 20% w/v polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→46.49 Å / Num. obs: 21973 / % possible obs: 99.1 % / Redundancy: 7.4 % / Biso Wilson estimate: 19.04 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.298 / Rpim(I) all: 0.118 / Rrim(I) all: 0.321 / Net I/σ(I): 7.7 / Num. measured all: 163114 / Scaling rejects: 342
Reflection shell

Diffraction-ID: 1 / % possible all: 98.5

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.2-2.277.11.1351354419060.8550.461.2263.1
9.07-46.496.50.06821593330.9940.0290.07418.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimless0.6.2data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wm5

2wm5


Resolution: 2.2→25.193 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 1070 4.88 %Random selection
Rwork0.2043 20848 --
obs0.2067 21918 98.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.59 Å2 / Biso mean: 29.4643 Å2 / Biso min: 4.4 Å2
Refinement stepCycle: final / Resolution: 2.2→25.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 58 297 3685
Biso mean--24.1 32.25 -
Num. residues----422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023518
X-RAY DIFFRACTIONf_angle_d0.4594809
X-RAY DIFFRACTIONf_chiral_restr0.036511
X-RAY DIFFRACTIONf_plane_restr0.003632
X-RAY DIFFRACTIONf_dihedral_angle_d16.862066
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.30010.43631320.40142543267597
2.3001-2.42130.30331440.25812573271799
2.4213-2.57280.27571400.22492588272899
2.5728-2.77130.27621310.20672596272799
2.7713-3.04970.25961450.20722622276799
3.0497-3.490.231110.19282620273199
3.49-4.39330.20941320.15942628276099
4.3933-25.19420.19981350.15952678281399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9952-0.02960.350.5699-0.09770.98430.0374-0.327-0.19430.06570.11920.13290.0054-0.2978-0.13950.1833-0.0193-0.02160.260.08230.219516.77620.799821.0531
20.80310.07580.49131.31730.46871.55890.08830.0342-0.2126-0.04220.1249-0.23620.32410.1309-0.15710.22340.0248-0.03330.1155-0.01670.185435.7858-8.84865.7472
31.03-0.08180.42331.03260.23651.32120.0027-0.0975-0.0423-0.05620.04090.0772-0.0023-0.0588-0.03430.1593-0.0153-0.00250.07810.02790.139525.10950.57239.957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 130 )A7 - 130
2X-RAY DIFFRACTION2chain 'A' and (resid 131 through 208 )A131 - 208
3X-RAY DIFFRACTION3chain 'A' and (resid 209 through 428 )A209 - 428

+
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://pdbjlvh1.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