[English] 日本語
Yorodumi
- PDB-2gew: Atomic resolution structure of cholesterol oxidase @ pH 9.0 (Stre... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gew
TitleAtomic resolution structure of cholesterol oxidase @ pH 9.0 (Streptomyces sp. SA-COO)
ComponentsCholesterol oxidase
KeywordsOXIDOREDUCTASE / FLAVOENZYME / STEROID METABOLISM / ATOMIC RESOLUTION / HYDROGEN BOND
Function / homology
Function and homology information


cholesterol oxidase / cholesterol oxidase activity / steroid Delta-isomerase / steroid delta-isomerase activity / cholesterol catabolic process / flavin adenine dinucleotide binding / extracellular region
Similarity search - Function
Cholesterol Oxidase; domain 2 / Cholesterol Oxidase; domain 2 / GMC oxidoreductases signature 1. / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / FAD/NAD(P)-binding domain ...Cholesterol Oxidase; domain 2 / Cholesterol Oxidase; domain 2 / GMC oxidoreductases signature 1. / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / OXYGEN MOLECULE / Cholesterol oxidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.97 Å
AuthorsLyubimov, A.Y. / Vrielink, A.
CitationJournal: Nat.Chem.Biol. / Year: 2006
Title: Atomic resolution crystallography reveals how changes in pH shape the protein microenvironment.
Authors: Lyubimov, A.Y. / Lario, P.I. / Moustafa, I. / Vrielink, A.
History
DepositionMar 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Dec 18, 2019Group: Advisory / Derived calculations / Category: pdbx_distant_solvent_atoms / struct_conn
Revision 1.5Aug 30, 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
Remark 999SEQUENCE THE SEQUENCE OF MATURE CHOLESTEROL OXIDASE ENZYME RUNS FROM RESIDUES 43 - 546 IN THE ...SEQUENCE THE SEQUENCE OF MATURE CHOLESTEROL OXIDASE ENZYME RUNS FROM RESIDUES 43 - 546 IN THE SEQUENCE DATABASE. THE NUMBERING OF THE RESIDUES DIFFERS FROM THAT IN THE DATABASE DUE TO THIS DESCREPANCY IN THE SEQUENCE. IN ADDITION, THE NUMBERING HAS BEEN ADJUSTED TO CONFORM TO THAT FOUND IN THE STRUCTURE OF CHOLESTEROL OXIDASE FROM BREVIBACTERIUM STEROLICUM (ACCESSION CODE 3COX). THIS CHANGE IN THE NUMBERING SCHEME FACILITATES EASY COMPARISON OF THE TWO STRUCTURES.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cholesterol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8834
Polymers54,9701
Non-polymers9143
Water15,133840
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.110, 73.256, 62.432
Angle α, β, γ (deg.)90.00, 104.05, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cholesterol oxidase / / CHOD


Mass: 54969.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FAD COFACTOR NON-COVALENTLY BOUND TO THE ENZYME / Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: SA-COO / Gene: choA / Plasmid: PCO202 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P12676, cholesterol oxidase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 840 / 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: 2.06 Å3/Da / Density % sol: 40.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 8000, AMMONIUM SULFATE, PIPES PH 7.5,VAPOR DIFFUSION, HANGING DROP, temperature 298K, SOAK CONDITION STEP 1: PEG 8000, AMMONIUM SULFATE, HEPES PH 8.0 SOAK CONDITION STEP 2: PEG 8000, ...Details: PEG 8000, AMMONIUM SULFATE, PIPES PH 7.5,VAPOR DIFFUSION, HANGING DROP, temperature 298K, SOAK CONDITION STEP 1: PEG 8000, AMMONIUM SULFATE, HEPES PH 8.0 SOAK CONDITION STEP 2: PEG 8000, AMMONIUM SULFATE, TRICINE PH 8.5 SOAK CONDITION STEP 3: PEG 8000, AMMONIUM SULFATE, CHES PH 9.0,

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 22, 2003
RadiationMonochromator: CRYSTALS SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 0.97→31.3 Å / Num. obs: 243484 / % possible obs: 93 % / Redundancy: 4.5 % / Biso Wilson estimate: 7.8 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.8
Reflection shellResolution: 0.97→1 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.9 / Num. unique all: 20631 / % possible all: 79

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXLrefinement
SHELXL-97refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1MXT

1mxt


Resolution: 0.97→31.3 Å / Num. parameters: 46825 / Num. restraintsaints: 130462 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.14 12194 5 %RANDOM
Rwork0.113 ---
all0.113 243484 --
obs0.113 243484 92.7 %-
Refine analyzeNum. disordered residues: 112 / Occupancy sum hydrogen: 3423.06 / Occupancy sum non hydrogen: 4574.04
Refinement stepCycle: LAST / Resolution: 0.97→31.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3842 0 60 840 4742
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.034
X-RAY DIFFRACTIONs_zero_chiral_vol0.098
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.102
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.04
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.048
X-RAY DIFFRACTIONs_approx_iso_adps0.074

+
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