[English] 日本語
Yorodumi
- PDB-8hkj: Crystal structure of the CYP102A5 haem Domain isolated from Bacil... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hkj
TitleCrystal structure of the CYP102A5 haem Domain isolated from Bacillus cereus
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Monooxygenase
Function / homology
Function and homology information


aromatase activity / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / unspecific monooxygenase / FMN binding / iron ion binding / heme binding
Similarity search - Function
Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding ...Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PALMITIC ACID / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsStanfield, J.K. / Onoda, H. / Sugimoto, H. / Shoji, O.
Funding support Japan, 4items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)21H04704 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)22H05129 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)22H05119 Japan
Japan Science and TechnologyJPMJAX22B5 Japan
CitationJournal: J.Inorg.Biochem. / Year: 2023
Title: Investigating the applicability of the CYP102A1-decoy-molecule system to other members of the CYP102A subfamily.
Authors: Stanfield, J.K. / Onoda, H. / Ariyasu, S. / Kasai, C. / Burfoot, E.M. / Sugimoto, H. / Shoji, O.
History
DepositionNov 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bifunctional cytochrome P450/NADPH--P450 reductase
B: Bifunctional cytochrome P450/NADPH--P450 reductase
C: Bifunctional cytochrome P450/NADPH--P450 reductase
D: Bifunctional cytochrome P450/NADPH--P450 reductase
E: Bifunctional cytochrome P450/NADPH--P450 reductase
F: Bifunctional cytochrome P450/NADPH--P450 reductase
G: Bifunctional cytochrome P450/NADPH--P450 reductase
H: Bifunctional cytochrome P450/NADPH--P450 reductase
I: Bifunctional cytochrome P450/NADPH--P450 reductase
J: Bifunctional cytochrome P450/NADPH--P450 reductase
K: Bifunctional cytochrome P450/NADPH--P450 reductase
L: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)645,58236
Polymers635,10712
Non-polymers10,47524
Water00
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7983
Polymers52,9261
Non-polymers8732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7983
Polymers52,9261
Non-polymers8732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7983
Polymers52,9261
Non-polymers8732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0554
Polymers52,9261
Non-polymers1,1293
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7983
Polymers52,9261
Non-polymers8732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5422
Polymers52,9261
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7983
Polymers52,9261
Non-polymers8732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7983
Polymers52,9261
Non-polymers8732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7983
Polymers52,9261
Non-polymers8732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7983
Polymers52,9261
Non-polymers8732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7983
Polymers52,9261
Non-polymers8732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7983
Polymers52,9261
Non-polymers8732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.620, 126.060, 141.440
Angle α, β, γ (deg.)86.66, 79.47, 84.97
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Bifunctional cytochrome P450/NADPH--P450 reductase


Mass: 52925.570 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: BKK64_01385 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A853ZNE6
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H32O2
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.95 / Details: 70 mM MgCl2, 4.75% PEG8000, 50 mM Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→91.18 Å / Num. obs: 157761 / % possible obs: 98.1 % / Redundancy: 2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.058 / Rrim(I) all: 0.082 / Net I/σ(I): 5 / Num. measured all: 312136
Reflection shellResolution: 2.8→2.85 Å / % possible obs: 97.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.582 / Num. measured all: 15467 / Num. unique obs: 7830 / CC1/2: 0.52 / Rpim(I) all: 0.582 / Rrim(I) all: 0.823 / Net I/σ(I) obs: 1.1

-
Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
iMOSFLM7.2.0data reduction
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
MOLREP11.6.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IJ2

2ij2


Resolution: 2.8→19.96 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0.24 / Phase error: 30.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2696 7974 5.05 %
Rwork0.2388 --
obs0.2404 157340 91.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40330 0 732 0 41062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642074
X-RAY DIFFRACTIONf_angle_d0.93257073
X-RAY DIFFRACTIONf_dihedral_angle_d14.02415874
X-RAY DIFFRACTIONf_chiral_restr0.0576184
X-RAY DIFFRACTIONf_plane_restr0.0077311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.830.37895240.35529049X-RAY DIFFRACTION89
2.83-2.860.34024880.34239121X-RAY DIFFRACTION89
2.86-2.90.36455060.34468986X-RAY DIFFRACTION89
2.9-2.940.36844410.33329249X-RAY DIFFRACTION90
2.94-2.970.3625080.34168891X-RAY DIFFRACTION89
2.97-3.020.34494850.32769169X-RAY DIFFRACTION89
3.02-3.060.33134890.31619117X-RAY DIFFRACTION90
3.06-3.10.35124480.30979131X-RAY DIFFRACTION90
3.1-3.150.33914770.30899237X-RAY DIFFRACTION90
3.15-3.20.34324720.31949149X-RAY DIFFRACTION90
3.2-3.260.34835140.30289071X-RAY DIFFRACTION90
3.26-3.320.32454570.29059365X-RAY DIFFRACTION91
3.32-3.380.3035110.27789113X-RAY DIFFRACTION91
3.38-3.450.30055040.26879307X-RAY DIFFRACTION91
3.45-3.520.28995270.26379180X-RAY DIFFRACTION91
3.52-3.610.27574900.25799283X-RAY DIFFRACTION91
3.61-3.70.30444710.2579306X-RAY DIFFRACTION91
3.7-3.790.28534710.24519311X-RAY DIFFRACTION92
3.79-3.910.27025090.23989281X-RAY DIFFRACTION92
3.91-4.030.26734960.23429448X-RAY DIFFRACTION92
4.03-4.170.25735280.22249252X-RAY DIFFRACTION92
4.17-4.340.26255160.22059399X-RAY DIFFRACTION92
4.34-4.530.21424520.20499399X-RAY DIFFRACTION93
4.53-4.770.24734580.20599512X-RAY DIFFRACTION93
4.77-5.060.23755190.21289492X-RAY DIFFRACTION93
5.06-5.450.26364950.22689542X-RAY DIFFRACTION94
5.45-5.980.2785260.23329505X-RAY DIFFRACTION94
5.98-6.820.26375650.2229505X-RAY DIFFRACTION94
6.82-8.480.21674650.18929691X-RAY DIFFRACTION95
8.48-19.960.18845050.17249769X-RAY DIFFRACTION96

+
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