[English] 日本語
Yorodumi
- PDB-4u2l: Dithionite reduced cholesterol in complex with sulfite -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4u2l
TitleDithionite reduced cholesterol in complex with sulfite
ComponentsCholesterol oxidase
KeywordsOXIDOREDUCTASE / ISOMERASE / cholesterol oxidase / flavoenzymes / redox chemistry
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
: / GMC oxidoreductase, C-terminal / 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. ...: / GMC oxidoreductase, C-terminal / 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
Chem-SFD / Cholesterol oxidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.337 Å
AuthorsGolden, E.A. / Vrielink, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: High-resolution structures of cholesterol oxidase in the reduced state provide insights into redox stabilization.
Authors: Golden, E. / Karton, A. / Vrielink, A.
History
DepositionJul 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Jun 1, 2016Group: Data collection
Revision 1.4Nov 22, 2017Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Sep 27, 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: Cholesterol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9545
Polymers55,7991
Non-polymers1,1564
Water11,944663
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.375, 73.565, 63.431
Angle α, β, γ (deg.)90.000, 105.030, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cholesterol oxidase / CHOD / Cholesterol isomerase


Mass: 55798.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: SA-COO / Gene: choA / Production host: Escherichia coli (E. coli) / Variant (production host): BL21(DE3)
References: UniProt: P12676, cholesterol oxidase, steroid Delta-isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SFD / (S)-10-((2S,3S,4R)-5-((S)-((S)-(((2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHOXY)(HYDROXY)PHOSPHORYLOXY)(HYDROXY)PHOSPHORYLOXY)-2,3,4-TRIHYDROXYPENTYL)-7,8-DIMETHYL-2,4-DIOXO-2,3,4,4A-TETRAHYDROBENZO[G]PTERIDINE-5(10H)-SULFONIC ACID / N5-SULFONO FLAVIN-ADENINE DINUCLEOTIDE


Mass: 867.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O18P2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 663 / 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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: PEG 8000, manganese chloride, cacodylate / PH range: 5.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.32→61.262 Å / Num. all: 100763 / Num. obs: 100763 / % possible obs: 94.2 % / Redundancy: 12 % / Biso Wilson estimate: 6.6 Å2 / Rpim(I) all: 0.115 / Rrim(I) all: 0.398 / Rsym value: 0.381 / Net I/av σ(I): 1.22 / Net I/σ(I): 12.3 / Num. measured all: 1209726
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.32-1.398.91.1660.68399594330.3721.166360.7
1.39-1.4812.60.9890.7185994147490.2880.9895.1100
1.48-1.5812.90.8090.8178380138310.2340.8096.6100
1.58-1.713.10.6980.9169086128990.20.6988.4100
1.7-1.8713.10.5831155435118940.1680.58310.9100
1.87-2.0912.60.4531.3134896107250.1330.45314.7100
2.09-2.4111.90.3641.511264094870.110.36418.6100
2.41-2.9511.20.3231.69013780500.10.32322.1100
2.95-4.1710.30.1892.36447462500.0610.18931100
4.17-19.97510.10.1283.23468934450.0420.12829.199

-
Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
RefinementStarting model: 1MXT

1mxt


Resolution: 1.337→19.975 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 10.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1328 9945 10.08 %
Rwork0.097 88724 -
obs0.1006 98669 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.21 Å2 / Biso mean: 9.6697 Å2 / Biso min: 1.57 Å2
Refinement stepCycle: final / Resolution: 1.337→19.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 103 682 4619
Biso mean--5.35 20.41 -
Num. residues----499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114501
X-RAY DIFFRACTIONf_angle_d1.386102
X-RAY DIFFRACTIONf_chiral_restr0.09642
X-RAY DIFFRACTIONf_plane_restr0.008830
X-RAY DIFFRACTIONf_dihedral_angle_d12.7051653
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3373-1.35251.816231.752569
1.3525-1.36840.33152930.24382463275683
1.3684-1.38510.18083750.117830793454100
1.3851-1.40260.16033740.103929903364100
1.4026-1.42110.15073520.101230763428100
1.4211-1.44050.15393350.099730923427100
1.4405-1.46110.14833330.098330383371100
1.4611-1.48290.13933380.093531043442100
1.4829-1.50610.14413400.091830593399100
1.5061-1.53080.14123640.087230303394100
1.5308-1.55720.12383340.083431223456100
1.5572-1.58550.12583510.078330283379100
1.5855-1.61590.11563220.079630973419100
1.6159-1.64890.12383400.077530823422100
1.6489-1.68480.12413360.082530663402100
1.6848-1.72390.12633470.081431123459100
1.7239-1.7670.12693420.084830853427100
1.767-1.81480.12983320.081630423374100
1.8148-1.86810.11243460.081131113457100
1.8681-1.92840.11223380.085330643402100
1.9284-1.99720.133320.086530913423100
1.9972-2.07710.11373800.090430473427100
2.0771-2.17150.1323530.088230743427100
2.1715-2.28590.12023500.085430593409100
2.2859-2.42890.11653280.092831393467100
2.4289-2.6160.12123420.095630803422100
2.616-2.87860.1383330.10431033436100
2.8786-3.29350.13483500.109130843434100
3.2935-4.14340.12673130.103831563469100
4.1434-19.97720.14183690.127331453514100

+
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