[English] 日本語
Yorodumi
- PDB-3ucl: Cyclohexanone-bound crystal structure of cyclohexanone monooxygen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ucl
TitleCyclohexanone-bound crystal structure of cyclohexanone monooxygenase in the Rotated conformation
ComponentsCyclohexanone monooxygenase
KeywordsOXIDOREDUCTASE / Baeyer-Villiger monooxygenase / Baeyer-Villiger oxidation / biocatalysis / flavoprotein / green chemistry / protein engineering / Rossmann fold / FAD / NADPH / cyclohexanone / oxygen / Cytosolic (bacterial)
Function / homology
Function and homology information


N,N-dimethylaniline monooxygenase activity / flavin adenine dinucleotide binding / NADP binding
Similarity search - Function
: / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
CYCLOHEXANONE / FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Cyclohexanone monooxygenase
Similarity search - Component
Biological speciesRhodococcus sp. HI-31 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.36 Å
AuthorsYachnin, B.J. / Berghuis, A.M.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: The Substrate-Bound Crystal Structure of a Baeyer-Villiger Monooxygenase Exhibits a Criegee-like Conformation.
Authors: Yachnin, B.J. / Sprules, T. / McEvoy, M.B. / Lau, P.C. / Berghuis, A.M.
History
DepositionOct 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclohexanone monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5044
Polymers63,8771
Non-polymers1,6273
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.538, 67.105, 131.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cyclohexanone monooxygenase


Mass: 63876.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. HI-31 (bacteria) / Gene: chnB, chnB1 / Plasmid: pJW234 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: C0STX7, cyclohexanone monooxygenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-CYH / CYCLOHEXANONE


Mass: 98.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M imidazole, 0.2% TMOS, 20% PEG 3350, 0.1 M cyclohexanone, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 4, 2009 / Details: VariMax HF
RadiationMonochromator: Rotating copper anode / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.36→50 Å / Num. all: 20262 / Num. obs: 20262 / % possible obs: 97.9 % / Redundancy: 11.2 % / Biso Wilson estimate: 39.4 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Χ2: 1.008 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allRsym valueΧ2% possible all
2.36-2.478.30.47218700.4720.73592.7
2.47-2.5610.50.42219290.4220.76394
2.56-2.6810.40.33519270.3350.78195.3
2.68-2.8210.10.26619860.2660.81597.2
2.82-310.20.220230.20.85199.7
3-3.2310.80.13820710.1380.916100
3.23-3.5511.90.08920490.0891.082100
3.55-4.0712.90.06520740.0651.111100
4.07-5.1313.30.0521150.051.246100
5.13-50130.04522180.0451.39199.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.47 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å26.64 Å
Translation2.5 Å26.64 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3GWF

3gwf


Resolution: 2.36→30.61 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.2212 / WRfactor Rwork: 0.1643 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8073 / SU B: 8.967 / SU ML: 0.213 / SU R Cruickshank DPI: 0.8521 / SU Rfree: 0.3151 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2644 2061 10.2 %RANDOM
Rwork0.1909 ---
all0.1983 20214 --
obs0.1983 20214 97.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.19 Å2 / Biso mean: 28.4441 Å2 / Biso min: 5.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2---0.57 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.36→30.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3986 0 108 121 4215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224206
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.9695755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1345508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68423.793203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.29615600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1591528
X-RAY DIFFRACTIONr_chiral_restr0.1140.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213286
X-RAY DIFFRACTIONr_mcbond_it0.7711.52531
X-RAY DIFFRACTIONr_mcangle_it1.45724073
X-RAY DIFFRACTIONr_scbond_it2.30331675
X-RAY DIFFRACTIONr_scangle_it3.7794.51682
LS refinement shellResolution: 2.36→2.425 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 134 -
Rwork0.236 1144 -
all-1278 -
obs-1278 83.97 %

+
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