[English] 日本語
Yorodumi
- PDB-1n4u: CHOLESTEROL OXIDASE FROM STREPTOMYCES @ pH 4.5 (STREPTOMYCES SP. ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n4u
TitleCHOLESTEROL OXIDASE FROM STREPTOMYCES @ pH 4.5 (STREPTOMYCES SP. SA-COO)
ComponentsCholesterol oxidase
KeywordsOXIDOREDUCTASE / FLAVOENZYME / STEROID METABOLISM / ATOMIC RESOLUTION
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 / FAD/NAD(P)-binding domain ...: / 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 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-N7 PROTONATED-ADENINE DINUCLEOTIDE / OXYGEN MOLECULE / PHOSPHATE ION / Cholesterol oxidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.95 Å
AuthorsVrielink, A. / Lario, P.I.
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
DepositionNov 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: 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: Cholesterol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3559
Polymers54,9701
Non-polymers1,3868
Water12,592699
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.248, 73.276, 63.098
Angle α, β, γ (deg.)90.00, 105.07, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 1 molecules A

#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

-
Non-polymers , 5 types, 707 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-FAE / FLAVIN-N7 PROTONATED-ADENINE DINUCLEOTIDE


Mass: 786.558 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H34N9O15P2
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / 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: 1.71 Å3/Da / Density % sol: 28.1 %
Crystal growpH: 4.5 / Details: pH 4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 1999
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: 0.95→46.8 Å / Num. obs: 266037 / % possible obs: 94.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 11.1
Reflection shellResolution: 0.95→0.97 Å / Redundancy: 3.09 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.49 / % possible all: 89.3

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementMethod to determine structure: AB INITIO PHASING
Starting model: 1MXT

1mxt


Resolution: 0.95→46.9 Å / Num. parameters: 45412 / Num. restraintsaints: 60231 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: THE FOLLOWING ARE RESIDUES THAT WERE NOT LOCATED IN THE EXPERIMENT: ASP A 6, ASN A 7, GLY A 8, THR A 507 (ONLY N WAS LOCATED), ALA A 508, SER A 509. SOME VERY MOBILE SIDE CHAINS WERE MODELED ...Details: THE FOLLOWING ARE RESIDUES THAT WERE NOT LOCATED IN THE EXPERIMENT: ASP A 6, ASN A 7, GLY A 8, THR A 507 (ONLY N WAS LOCATED), ALA A 508, SER A 509. SOME VERY MOBILE SIDE CHAINS WERE MODELED AT EITHER 50% OR WERE NOT MODELLED. THE FOLLOWING ATOMS WERE NOT MODELLED: RES 278 CG -> END IS MISSING.; RES 396 CZ->END IS MISSING.; RES 436 CG->END IS MISSING; PARTIALLY OCCUPIED SIDE CHAIN ATOMS MODELED AT 50% FOR THE FOLLOWING: RES 73 ATOMS CG 1HG1 2HG CD OE1 OE2; RESI 127 ATOMS CG 1HD 2HD NE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES RES 163 ATOMS CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 172 CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 183 CG 1HG 2HG CD 1HD 2HD CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 241 CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 396 CG 1HG 2HG CD 1HD 2HD NE 1HE 2HE ; RES 398 CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 435 ATOMS CB HB OG1 CG2 1HG2 2HG2 3HG2; RES 436 ATOMS CB 1HB 2HB; RES 468 ATOMS CG 1HG 2HG CD 1HD 2HD CE 1HE 2HE NZ 1HZ 2HZ 3HZ;
RfactorNum. reflection% reflectionSelection details
Rfree0.1358 60231 5 %RANDOM
Rwork0.1134 ---
all0.1141 265994 --
obs-265994 94.3 %-
Refine analyzeNum. disordered residues: 98 / Occupancy sum hydrogen: 3708.35 / Occupancy sum non hydrogen: 4437.13
Refinement stepCycle: LAST / Resolution: 0.95→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3823 0 86 699 4608
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.034
X-RAY DIFFRACTIONs_zero_chiral_vol0.094
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.102
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.042
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.039
X-RAY DIFFRACTIONs_approx_iso_adps0.083

+
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