[English] 日本語
Yorodumi
- PDB-8b2p: CYP153A71 from Acinetobacter dieselolei bound to octanoic acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b2p
TitleCYP153A71 from Acinetobacter dieselolei bound to octanoic acid
ComponentsCytochrome P450 alkane hydroxylase
KeywordsOXIDOREDUCTASE / Alkane hydroxylase Cytochrome P450 monooxygenase CYP153 Octanoic acid
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OCTANOIC ACID (CAPRYLIC ACID) / Cytochrome P450 alkane hydroxylase
Similarity search - Component
Biological speciesAlcanivorax dieselolei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsOpperman, D.J. / Tolmie, C.
Funding support United Kingdom, South Africa, 3items
OrganizationGrant numberCountry
Global Challenges Research FundST/R002754/1 United Kingdom
National Research Foundation in South Africa112094 South Africa
Department of Science and Innovation, South Africac*change, PAR-02 South Africa
CitationJournal: Catalysts / Year: 2022
Title: CYP153A71 from Alcanivorax dieselolei: Oxidation beyond Monoterminal Hydroxylation of n-Alkanes
Authors: Jacobs, C.L. / do Aido-Machado, R. / Tolmie, C. / Smit, M.S. / Opperman, D.J.
History
DepositionSep 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450 alkane hydroxylase
B: Cytochrome P450 alkane hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,2856
Polymers107,7632
Non-polymers1,5214
Water5,062281
1
A: Cytochrome P450 alkane hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6423
Polymers53,8821
Non-polymers7612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 alkane hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6423
Polymers53,8821
Non-polymers7612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.661, 76.817, 107.344
Angle α, β, γ (deg.)90.000, 90.530, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 49 - 468 / Label seq-ID: 49 - 468

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Cytochrome P450 alkane hydroxylase


Mass: 53881.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcanivorax dieselolei (bacteria) / Gene: p450 / Production host: Escherichia coli (E. coli) / References: UniProt: D0Q1H3
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16O2
#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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M HEPES pH 7.5 12% (w/v) polyethylene glycol 3350 10 mM octanoic acid

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.95→46.11 Å / Num. obs: 66934 / % possible obs: 97.8 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.083 / Rrim(I) all: 0.154 / Net I/σ(I): 7.2 / Num. measured all: 227101 / Scaling rejects: 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.95-23.51.3651556644660.5190.8571.6151.297
9.15-46.113.20.03622256910.9970.0240.04324.797.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.08 Å46.11 Å
Translation5.08 Å46.11 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
autoPROC1.0.5data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FYF

5fyf


Resolution: 1.95→46.11 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2547 / WRfactor Rwork: 0.2119 / FOM work R set: 0.5859 / SU B: 11.558 / SU ML: 0.277 / SU R Cruickshank DPI: 0.2104 / SU Rfree: 0.1831 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2707 3379 5 %RANDOM
Rwork0.229 ---
obs0.2311 63554 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.25 Å2 / Biso mean: 40.926 Å2 / Biso min: 14.72 Å2
Baniso -1Baniso -2Baniso -3
1-5.17 Å20 Å23.75 Å2
2---2.65 Å20 Å2
3----2.59 Å2
Refinement stepCycle: final / Resolution: 1.95→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6843 0 106 285 7234
Biso mean--27.5 41.17 -
Num. residues----844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0137167
X-RAY DIFFRACTIONr_bond_other_d0.0050.0156815
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.6689709
X-RAY DIFFRACTIONr_angle_other_deg1.121.59615659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.01921.494435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.847151266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.641570
X-RAY DIFFRACTIONr_chiral_restr0.0510.2871
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028154
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021762
Refine LS restraints NCS

Ens-ID: 1 / Number: 14481 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 264 -
Rwork0.386 4632 -
all-4896 -
obs--97.05 %

+
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