[English] 日本語
Yorodumi
- PDB-8yq3: Structure of cyclohexanone monooxygenase mutant from Acinetobacte... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8yq3
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 / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Putative flavin-binding monooxygenase
Similarity search - Component
Biological speciesAcinetobacter calcoaceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 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 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 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)63,4833
Polymers62,0321
Non-polymers1,4512
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-12 kcal/mol
Surface area21080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.184, 53.052, 101.643
Angle α, β, γ (deg.)90.000, 96.975, 90.000
Int Tables number4
Space group name H-MP1211

-
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-Gold(DE3)pLysS AG' (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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: 0.1 M Tris (base)-Bicine pH 8.25; 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: Nov 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.52→100.891 Å / Num. obs: 18944 / % possible obs: 99.6 % / Redundancy: 6.2 % / CC1/2: 0.968 / CC star: 0.992 / Rmerge(I) obs: 0.1771 / Net I/σ(I): 6.29
Reflection shellResolution: 2.52→2.61 Å / Rmerge(I) obs: 1.202 / Num. unique obs: 1882 / CC1/2: 0.29 / CC star: 0.671 / % possible all: 99.79

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 2.52→100.891 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.864 / SU B: 19.209 / SU ML: 0.408 / Cross valid method: THROUGHOUT / ESU R: 3.096 / ESU R Free: 0.41
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.3216 912 4.822 %RANDOM
Rwork0.2177 18001 --
all0.223 ---
obs-18913 99.889 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 49.958 Å2
Baniso -1Baniso -2Baniso -3
1-1.155 Å20 Å2-2.009 Å2
2---0.693 Å2-0 Å2
3---0.028 Å2
Refinement stepCycle: LAST / Resolution: 2.52→100.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4049 0 97 318 4464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0124247
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163903
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.8445769
X-RAY DIFFRACTIONr_angle_other_deg0.5041.7899007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3895507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.576519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22910712
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.08310200
X-RAY DIFFRACTIONr_chiral_restr0.0650.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024955
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02984
X-RAY DIFFRACTIONr_nbd_refined0.2310.21180
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.24283
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22064
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22188
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2304
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0440.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1610.212
X-RAY DIFFRACTIONr_nbd_other0.1750.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1820.212
X-RAY DIFFRACTIONr_mcbond_it3.9525.1742034
X-RAY DIFFRACTIONr_mcbond_other3.9515.1742034
X-RAY DIFFRACTIONr_mcangle_it6.189.2852539
X-RAY DIFFRACTIONr_mcangle_other6.1799.2872540
X-RAY DIFFRACTIONr_scbond_it4.0595.6642213
X-RAY DIFFRACTIONr_scbond_other4.0585.6662214
X-RAY DIFFRACTIONr_scangle_it6.50710.2653230
X-RAY DIFFRACTIONr_scangle_other6.50610.2663231
X-RAY DIFFRACTIONr_lrange_it12.68852.4925332
X-RAY DIFFRACTIONr_lrange_other12.63252.6385271
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.52-2.5850.452590.31513220.3213810.8870.9481000.315
2.585-2.6560.442610.37613090.3813710.7660.86599.92710.364
2.656-2.7330.433680.31712390.32313090.8780.90399.84720.301
2.733-2.8170.358660.27311880.27812550.9080.95199.92030.257
2.817-2.910.38590.24512100.25112710.8960.95699.84260.227
2.91-3.0120.323550.21111160.21611710.9270.9711000.196
3.012-3.1250.379540.2211230.22711770.90.9671000.204
3.125-3.2530.366490.19110610.19911120.9010.97599.82010.18
3.253-3.3970.25580.21710080.21910670.9530.96499.90630.209
3.397-3.5630.358570.2649720.2710320.8560.95499.70930.261
3.563-3.7550.391460.2469360.2529870.8910.95599.49340.241
3.755-3.9830.294370.2338750.2369130.9470.95999.89050.228
3.983-4.2570.303410.1838170.1888580.9360.9821000.192
4.257-4.5980.298400.1767800.1828220.9470.98199.75670.189
4.598-5.0350.246370.1377130.1427500.9680.9881000.151
5.035-5.6280.251450.1626360.1686810.9620.9861000.18
5.628-6.4950.405220.1975860.2046080.9270.9811000.213
6.495-7.9470.349210.1894960.1955170.950.9771000.211
7.947-11.2040.249240.1733840.1784080.9670.9791000.21
11.204-100.8910.248130.2962290.2922430.9760.94199.58850.43

+
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