[English] 日本語
Yorodumi
- PDB-6lqc: Crystal structure of Cyclohexylamine Oxidase from Erythrobacterac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lqc
TitleCrystal structure of Cyclohexylamine Oxidase from Erythrobacteraceae bacterium
ComponentsCyclohexylamine Oxidase
KeywordsOXIDOREDUCTASE / Cyclohexylamine Oxidase
Function / homology
Function and homology information


Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE
Similarity search - Component
Biological speciesErythrobacteraceae bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsHuang, Z.D.
CitationJournal: J.Org.Chem. / Year: 2020
Title: Asymmetric Synthesis of a Key Dextromethorphan Intermediate and Its Analogues Enabled by a New Cyclohexylamine Oxidase: Enzyme Discovery, Reaction Development, and Mechanistic Insight.
Authors: Wu, X. / Huang, Z. / Wang, Z. / Li, Z. / Wang, J. / Lin, J. / Chen, F.
History
DepositionJan 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Cyclohexylamine Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7762
Polymers48,9911
Non-polymers7861
Water9,692538
1
A: Cyclohexylamine Oxidase
hetero molecules

A: Cyclohexylamine Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5534
Polymers97,9822
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5410 Å2
ΔGint-27 kcal/mol
Surface area30270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.591, 82.591, 175.279
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-671-

HOH

21A-795-

HOH

-
Components

#1: Protein Cyclohexylamine Oxidase /


Mass: 48990.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erythrobacteraceae bacterium (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10 % PEG 8000,100 mM Potassium phosphate monobasic/ Sodium phosphate dibasic pH 6.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 50354 / % possible obs: 100 % / Redundancy: 25.6 % / Biso Wilson estimate: 31.06 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.042 / Net I/σ(I): 41
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 24.1 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2452 / Rpim(I) all: 0.254 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I59

4i59


Resolution: 1.88→24.3 Å / SU ML: 0.1769 / Cross valid method: FREE R-VALUE / σ(F): 0.61 / Phase error: 19.8862
RfactorNum. reflection% reflection
Rfree0.1895 1851 3.96 %
Rwork0.172 --
obs0.1727 46754 92.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.7 Å2
Refinement stepCycle: LAST / Resolution: 1.88→24.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 53 538 4025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01553598
X-RAY DIFFRACTIONf_angle_d1.66014910
X-RAY DIFFRACTIONf_chiral_restr0.0962527
X-RAY DIFFRACTIONf_plane_restr0.0113638
X-RAY DIFFRACTIONf_dihedral_angle_d16.97291263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.930.28811230.23823086X-RAY DIFFRACTION84.71
1.93-1.990.22031300.22173063X-RAY DIFFRACTION83.94
1.99-2.050.22771290.21193130X-RAY DIFFRACTION85.99
2.05-2.120.26091340.20983288X-RAY DIFFRACTION89.39
2.12-2.210.20251320.2013245X-RAY DIFFRACTION89.01
2.21-2.310.21061410.18913517X-RAY DIFFRACTION95.33
2.31-2.430.21751470.19263441X-RAY DIFFRACTION93.15
2.43-2.580.24741420.19353515X-RAY DIFFRACTION95.46
2.58-2.780.23021470.19543574X-RAY DIFFRACTION96.57
2.78-3.060.20871530.19193666X-RAY DIFFRACTION98.2
3.06-3.50.18781500.16443681X-RAY DIFFRACTION98.51
3.5-4.410.12911580.13673780X-RAY DIFFRACTION99.19
4.41-24.30.17721650.15393917X-RAY DIFFRACTION97.87

+
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