[English] 日本語
Yorodumi
- PDB-4i59: Cyclohexylamine Oxidase from Brevibacterium oxydans IH-35A comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i59
TitleCyclohexylamine Oxidase from Brevibacterium oxydans IH-35A complexed with cyclohexanone
ComponentsCyclohexylamine Oxidase
KeywordsOXIDOREDUCTASE / flavoprotein / monoamine oxidase / cyclohexylamine oxidase / biocatalysis
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / : / Polyamine Oxidase; Chain A, domain 2 - #10 / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain ...Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / : / Polyamine Oxidase; Chain A, domain 2 - #10 / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CYCLOHEXANONE / FLAVIN-ADENINE DINUCLEOTIDE / Cyclohexylamine Oxidase
Similarity search - Component
Biological speciesBrevibacterium oxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.93 Å
AuthorsMirza, I.A. / Berghuis, A.M.
CitationJournal: Plos One / Year: 2013
Title: Structural Analysis of a Novel Cyclohexylamine Oxidase from Brevibacterium oxydans IH-35A.
Authors: Mirza, I.A. / Burk, D.L. / Xiong, B. / Iwaki, H. / Hasegawa, Y. / Grosse, S. / Lau, P.C. / Berghuis, A.M.
History
DepositionNov 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Cyclohexylamine Oxidase
B: Cyclohexylamine Oxidase
C: Cyclohexylamine Oxidase
D: Cyclohexylamine Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,09412
Polymers204,5604
Non-polymers3,5358
Water00
1
A: Cyclohexylamine Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0243
Polymers51,1401
Non-polymers8842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cyclohexylamine Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0243
Polymers51,1401
Non-polymers8842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cyclohexylamine Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0243
Polymers51,1401
Non-polymers8842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cyclohexylamine Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0243
Polymers51,1401
Non-polymers8842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.518, 139.457, 177.206
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain AAAA,CCCC, using strict)
NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.2492, -0.9448, 0.2128), (-0.9481, -0.2828, -0.1455), (0.1977, -0.1655, -0.9662)187.17, 331.812, 390.993
3given(-0.8581, 0.2796, 0.4306), (0.2831, -0.4421, 0.8511), (0.4284, 0.8523, 0.3003)-52.1363, 122.448, -62.6086
4given(-0.4034, 0.6543, -0.6396), (0.6686, -0.2665, -0.6943), (-0.6247, -0.7077, -0.3299)49.7779, 356.824, 420.353

-
Components

#1: Protein
Cyclohexylamine Oxidase


Mass: 51139.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacterium oxydans (bacteria) / Strain: IH-35A / Gene: chaA / Plasmid: pSD80 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: R4GRV2*PLUS
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-CYH / CYCLOHEXANONE


Mass: 98.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 1.6 M ammonium sulfate, 10% v/v dioxane and 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Details: Mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.93→50 Å / Num. all: 46823 / Num. obs: 44529 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 104.3 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.93-3.032.90.288195.3
3.03-3.163.80.261196.8
3.16-3.34.20.219196.5
3.3-3.474.30.184196.2
3.47-3.694.30.136195.8
3.69-3.984.30.112195.5
3.98-4.384.30.089195.1
4.38-5.014.30.078194.6
5.01-6.314.30.082193.7
6.31-504.20.058191.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNS1.3refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Structure of holoenzyme (PDB code 4I58)

4i58


Resolution: 2.93→48.78 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 152482.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.255 4250 10.1 %RANDOM
Rwork0.228 ---
obs0.228 42275 90.2 %-
all-48300 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.1524 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1-23.25 Å20 Å20 Å2
2---10.24 Å20 Å2
3----13.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.93→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13728 0 240 0 13968
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 570 10.5 %
Rwork0.313 4872 -
obs--68.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6chao.5.parchao.5.top

+
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