[English] 日本語
Yorodumi
- PDB-8yrb: Structure of cyclohexanone monooxygenase mutant from Acinetobacte... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8yrb
TitleStructure of cyclohexanone monooxygenase mutant from Acinetobacter calcoaceticus
ComponentsPutative flavin-binding monooxygenase
KeywordsOXIDOREDUCTASE / Complex
Function / homology
Function and homology information


N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
: / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-NDP / Putative flavin-binding monooxygenase
Similarity search - Component
Biological speciesAcinetobacter calcoaceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsQiang, G. / Zheng, Y.C. / Feng, L. / Yu, H.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21922804 China
CitationJournal: To Be Published
Title: Loop Engineering Facilitates the Nicotinamide Cofactors Utilization of BVMOs
Authors: Qiang, G. / Zheng, Y.C. / Feng, L. / Yu, H.L.
History
DepositionMar 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative flavin-binding monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5633
Polymers62,0321
Non-polymers1,5312
Water7,026390
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.020, 53.220, 100.810
Angle α, β, γ (deg.)90.000, 96.485, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Putative flavin-binding monooxygenase


Mass: 62032.055 Da / Num. of mol.: 1
Mutation: L143P,A145S,A146S,N148H,K151V,F246Y,K326C,N386S,I388K,M390I,L426F,F432L,T433A,L435S,S438I,E488K,S489C,W490R,F505L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter calcoaceticus (bacteria) / Gene: P23_1101 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A8XFY0
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.75
Details: 0.1 M Tris (base)-Bicine pH 8.75; 20% (v/v) PEG 500*MME; 10% (w/v) PEG 20000; 0.2 M Monosaccharides (D-Glucose; D-Mannose; D-Galactose; L-Fucose; D-Xylose; N-Acetyl-D- Glucosamine)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.78→34.18 Å / Num. obs: 53646 / % possible obs: 99.72 % / Redundancy: 6.7 % / Biso Wilson estimate: 28.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08682 / Net I/σ(I): 13.8
Reflection shellResolution: 1.78→1.844 Å / Rmerge(I) obs: 1.359 / Num. unique obs: 5319 / CC1/2: 0.608

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.78→34.18 Å / SU ML: 0.2533 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2732
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2269 2656 4.95 %
Rwork0.1866 50981 -
obs0.1886 53637 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.04 Å2
Refinement stepCycle: LAST / Resolution: 1.78→34.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4098 0 101 390 4589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00994301
X-RAY DIFFRACTIONf_angle_d1.01575843
X-RAY DIFFRACTIONf_chiral_restr0.0632630
X-RAY DIFFRACTIONf_plane_restr0.0098740
X-RAY DIFFRACTIONf_dihedral_angle_d11.2762567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.810.33691580.29892638X-RAY DIFFRACTION100
1.81-1.850.32661550.28052611X-RAY DIFFRACTION100
1.85-1.880.34151320.27012728X-RAY DIFFRACTION99.97
1.88-1.930.36441150.28932659X-RAY DIFFRACTION99.32
1.93-1.970.33471480.24962708X-RAY DIFFRACTION99.72
1.97-2.020.25541310.22272628X-RAY DIFFRACTION100
2.02-2.070.26981220.23042693X-RAY DIFFRACTION99.68
2.07-2.140.25561190.22172698X-RAY DIFFRACTION99.89
2.14-2.20.23131660.19352676X-RAY DIFFRACTION100
2.2-2.280.24911290.21272648X-RAY DIFFRACTION99.28
2.28-2.370.2571290.19862688X-RAY DIFFRACTION99.96
2.37-2.480.25011280.18982698X-RAY DIFFRACTION100
2.48-2.610.23021540.19852654X-RAY DIFFRACTION100
2.61-2.780.25671630.19862692X-RAY DIFFRACTION99.93
2.78-2.990.24931520.18782684X-RAY DIFFRACTION100
2.99-3.290.24821180.19012722X-RAY DIFFRACTION99.89
3.29-3.770.2111380.16772694X-RAY DIFFRACTION99.4
3.77-4.750.19221550.14172703X-RAY DIFFRACTION99.51
4.75-34.180.15791440.16082759X-RAY DIFFRACTION98.84

+
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