[English] 日本語
Yorodumi
- PDB-5xnt: Structure of CYP106A2 from Bacillus sp. PAMC 23377 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xnt
TitleStructure of CYP106A2 from Bacillus sp. PAMC 23377
ComponentsCytochrome P450 CYP106
KeywordsHYDROLASE / Bacillus sp. cytochrome P450 steroid hydroxylase
Function / homology
Function and homology information


steroid 15beta-monooxygenase / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450(MEG)
Similarity search - Component
Biological speciesBacillus butanolivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsLee, C.W. / Kim, K.-H. / Bikash, D. / Park, S.-H. / Park, H. / Oh, T.-J. / Lee, J.H.
CitationJournal: J. Microbiol. Biotechnol. / Year: 2017
Title: Crystal Structure and Functional Characterization of a Cytochrome P450 (BaCYP106A2) fromBacillussp. PAMC 23377.
Authors: Kim, K.H. / Lee, C.W. / Dangi, B. / Park, S.H. / Park, H. / Oh, T.J. / Lee, J.H.
History
DepositionMay 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450 CYP106
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0502
Polymers47,4341
Non-polymers6161
Water43224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-24 kcal/mol
Surface area17880 Å2
Unit cell
Length a, b, c (Å)77.658, 77.658, 282.216
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Cytochrome P450 CYP106


Mass: 47433.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus butanolivorans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q06069*PLUS
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
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: 52.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate:HCl pH 6.5, 1.26 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 14704 / % possible obs: 99.4 % / Redundancy: 11.6 % / Net I/σ(I): 40.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
HKL-2000data processing
RefinementResolution: 2.7→48.68 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.91 / SU B: 12.218 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R: 1.021 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25674 714 4.9 %RANDOM
Rwork0.19066 ---
obs0.19406 13914 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.205 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.7→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 43 24 3263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193313
X-RAY DIFFRACTIONr_bond_other_d0.0020.023092
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.9924499
X-RAY DIFFRACTIONr_angle_other_deg1.03537188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3535390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27824.812160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.69915601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.391519
X-RAY DIFFRACTIONr_chiral_restr0.0930.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213621
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02658
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_it4.0335.4661566
X-RAY DIFFRACTIONr_mcbond_other4.0275.4631565
X-RAY DIFFRACTIONr_mcangle_it6.1568.1881954
X-RAY DIFFRACTIONr_mcangle_other6.1578.1921955
X-RAY DIFFRACTIONr_scbond_it4.7796.0361745
X-RAY DIFFRACTIONr_scbond_other4.7776.0381743
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.6838.7832544
X-RAY DIFFRACTIONr_long_range_B_refined9.89163.0143696
X-RAY DIFFRACTIONr_long_range_B_other9.8963.0133697
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.702→2.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 43 -
Rwork0.188 1026 -
obs--99.81 %

+
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