[English] 日本語
Yorodumi
- PDB-5ai1: Crystal structure of ketosteroid isomerase containing Y32F, D40N,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ai1
TitleCrystal structure of ketosteroid isomerase containing Y32F, D40N, Y57F and Y119F mutations in the equilenin-bound form
ComponentsKETOSTEROID ISOMERASE
KeywordsISOMERASE / KETOSTEROID ISOMERASE / PSEUDOMONAS PUTIDA / EQUILENIN
Function / homology
Function and homology information


steroid Delta-isomerase / steroid Delta-isomerase activity / steroid metabolic process
Similarity search - Function
Ketosteroid isomerase / SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
EQUILENIN / Steroid Delta-isomerase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.103 Å
AuthorsCha, H.J. / Jeong, J.H. / Kim, Y.G.
CitationJournal: Mol.Cells / Year: 2015
Title: Contribution of a Low-Barrier Hydrogen Bond to Catalysis is not Significant in Ketosteroid Isomerase.
Authors: Jang, D.S. / Choi, G. / Cha, H.J. / Shin, S. / Hong, B.H. / Lee, H.J. / Lee, H.C. / Choi, K.Y.
History
DepositionFeb 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Jun 17, 2015Group: Data collection
Revision 1.3Sep 23, 2015Group: Data collection
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: KETOSTEROID ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7662
Polymers14,5001
Non-polymers2661
Water1,04558
1
A: KETOSTEROID ISOMERASE
hetero molecules

A: KETOSTEROID ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5324
Polymers28,9992
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3320 Å2
ΔGint-5.7 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.195, 95.769, 73.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein KETOSTEROID ISOMERASE


Mass: 14499.515 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Variant: BIOTYPE B / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07445
#2: Chemical ChemComp-EQU / EQUILENIN


Mass: 266.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.17 % / Description: NONE
Crystal growpH: 4.6
Details: 0.1M SODIUM ACETATE (PH 4.5), 0.6M AMMONIUM ACETATE, 30% PEG 4,000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2014 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.1→30.13 Å / Num. obs: 7126 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 26.51 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 23
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.9 / % possible all: 89.6

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OPY

1opy


Resolution: 2.103→30.134 Å / SU ML: 0.26 / σ(F): 1.5 / Phase error: 26.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2594 712 10 %
Rwork0.1901 --
obs0.1971 7121 94.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.103→30.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms921 0 20 58 999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008962
X-RAY DIFFRACTIONf_angle_d1.1341304
X-RAY DIFFRACTIONf_dihedral_angle_d16.938346
X-RAY DIFFRACTIONf_chiral_restr0.046142
X-RAY DIFFRACTIONf_plane_restr0.004172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.103-2.26530.29521270.24841150X-RAY DIFFRACTION87
2.2653-2.49320.32821380.23051240X-RAY DIFFRACTION93
2.4932-2.85370.31041440.23071288X-RAY DIFFRACTION96
2.8537-3.59440.2651470.19041317X-RAY DIFFRACTION97
3.5944-30.13680.21411560.15381414X-RAY DIFFRACTION99

+
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