[English] 日本語
Yorodumi
- PDB-5m0z: Cyclohexanone Monooxygenase from T. municipale: reduced enzyme bo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m0z
TitleCyclohexanone Monooxygenase from T. municipale: reduced enzyme bound to NADP+
ComponentsCyclohexanone Monooxygenase from Thermocrispum municipale.
KeywordsOXIDOREDUCTASE / Baeyer-Villiger Monooxygenases Flavoenzymes
Function / homology
Function and homology information


cyclohexanone monooxygenase / cyclohexanone monooxygenase activity / nucleotide binding
Similarity search - Function
: / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / 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
FLAVIN-ADENINE DINUCLEOTIDE / Chem-NA7 / Cyclohexanone Monooxygenase from Thermocrispum municipale
Similarity search - Component
Biological speciesThermocrispum municipale DSM 44069 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGomez-Castellanos, J.R. / Mattevi, A.
Funding support1items
OrganizationGrant numberCountry
EU Horizon 2020 Programme Research and Innovation actions H2020-LEIT BIO-2014-1635734
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2016
Title: Characterization and Crystal Structure of a Robust Cyclohexanone Monooxygenase.
Authors: Romero, E. / Castellanos, J.R. / Mattevi, A. / Fraaije, M.W.
History
DepositionOct 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 2.0Apr 22, 2020Group: Atomic model / Database references / Category: atom_site / pdbx_related_exp_data_set / Item: _atom_site.occupancy
Revision 2.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclohexanone Monooxygenase from Thermocrispum municipale.
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7885
Polymers60,1951
Non-polymers1,5934
Water14,538807
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-13 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.206, 114.677, 155.435
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1506-

HOH

-
Components

#1: Protein Cyclohexanone Monooxygenase from Thermocrispum municipale.


Mass: 60195.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermocrispum municipale DSM 44069 (bacteria)
Production host: Escherichia coli (E. coli) / Strain (production host): str. K-12 substr. DH10B
References: UniProt: A0A1L1QK39*PLUS, 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-NA7 / [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4S)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE


Mass: 623.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N5O16P3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 807 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris-HCl, 25 % PEG 6000

-
Data collection

DiffractionMean temperature: 273.15 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.96863 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.6→33.78 Å / Num. obs: 76543 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 10.11 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.064 / Net I/av σ(I): 12.23 / Net I/σ(I): 12.23
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 1.81 / CC1/2: 0.664 / % possible all: 97

-
Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
Aimless0.5.21data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M10

5m10


Resolution: 1.6→33.78 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.699 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.077 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17736 2340 3.1 %RANDOM
Rwork0.14785 ---
obs0.14877 76541 93.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.569 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å2-0 Å2
2--0.1 Å20 Å2
3----0.75 Å2
Refinement stepCycle: 1 / Resolution: 1.6→33.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4154 0 104 807 5065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0194398
X-RAY DIFFRACTIONr_bond_other_d0.0030.024007
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.9735997
X-RAY DIFFRACTIONr_angle_other_deg1.11339206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5245536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11323.585212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32315678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8321536
X-RAY DIFFRACTIONr_chiral_restr0.1270.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215017
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021049
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0350.9932135
X-RAY DIFFRACTIONr_mcbond_other1.0110.9912134
X-RAY DIFFRACTIONr_mcangle_it1.5391.4852674
X-RAY DIFFRACTIONr_mcangle_other1.541.4862675
X-RAY DIFFRACTIONr_scbond_it2.3211.2092263
X-RAY DIFFRACTIONr_scbond_other2.3211.2092263
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5431.7243324
X-RAY DIFFRACTIONr_long_range_B_refined6.6315.7926135
X-RAY DIFFRACTIONr_long_range_B_other5.9213.4455579
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 181 -
Rwork0.255 5611 -
obs-7786 96.71 %

+
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