[English] 日本語
Yorodumi
- PDB-1w00: Crystal structure of mutant enzyme D103L of Ketosteroid Isomerase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1w00
TitleCrystal structure of mutant enzyme D103L of Ketosteroid Isomerase from Pseudomonas putida biotype B
ComponentsSTEROID DELTA-ISOMERASE
KeywordsISOMERASE / CONESHELL / CLOSED BARREL / CURVED B-SHEET
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
Steroid Delta-isomerase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKim, D.H. / Jang, D.S. / Nam, G.H. / Oh, B.H. / Choi, K.Y.
Citation
Journal: Biochem.J. / Year: 2004
Title: Structural Double-Mutant Cycle Analysis of a Hydrogen Bond Network in Ketosteroid Isomerase from Pseudomonas Putida Biotype B
Authors: Jang, D.S. / Cha, H.J. / Cha, S.-S. / Hong, B.H. / Ha, N.-C. / Lee, J.Y. / Oh, B.-H. / Lee, H.-S. / Choi, K.Y.
#1: Journal: Biochemistry / Year: 2000
Title: Contribution of the Hydrogen-Bond Network Involving a Tyrosine Triad in the Active Site to the Structure and Function of a Highly Proficient Ketosteroid Isomerase from Pseudomonas Putida Biotype B
Authors: Kim, D.H. / Jang, D.S. / Nam, G.H. / Choi, G. / Kim, J.S. / Ha, N.C. / Kim, M.S. / Oh, B.H. / Choi, K.Y.
#2: Journal: Biochemistry / Year: 1999
Title: Crystal Structure of Delta(5)-3-Ketosteroid Isomerase from Pseudomonas Testosteroni in Complex with Equilenin Settles the Correct Hydrogen Bonding Scheme for Transition State Stabilization
Authors: Cho, H.S. / Ha, N.C. / Choi, G. / Kim, H.J. / Lee, D. / Oh, K.S. / Kim, K.S. / Lee, W. / Choi, K.Y. / Oh, B.H.
#3: Journal: Biochemistry / Year: 1998
Title: Crystal Structure and Enzyme Mechanism of Delta(5)-3-Ketosteroid Isomerase from Pseudomonas Testosteroni
Authors: Cho, H.S. / Choi, G. / Choi, K.Y. / Oh, B.H.
#4: Journal: Biochemistry / Year: 1997
Title: High-Resolution Crystal Structures of Delta(5)-3-Ketosteroid Isomerase with and without a Reaction Intermediate Analogue
Authors: Kim, S.W. / Cha, S.S. / Cho, H.S. / Kim, J.S. / Ha, N.C. / Cho, M.J. / Joo, S. / Kim, K.K. / Choi, K.Y. / Oh, B.H.
History
DepositionMay 30, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2005Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: STEROID DELTA-ISOMERASE
B: STEROID DELTA-ISOMERASE


Theoretical massNumber of molelcules
Total (without water)29,0932
Polymers29,0932
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-13.9 kcal/mol
Surface area14210 Å2
MethodPQS
Unit cell
Length a, b, c (Å)35.651, 73.166, 95.615
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein STEROID DELTA-ISOMERASE / DELTA-5-3-KETOSTEROID ISOMERASE


Mass: 14546.571 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07445, steroid Delta-isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUES CHAINS A, B : ASP (103) LEU

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growpH: 4.6 / Details: SODIUM ACETATE, AMMONIUM ACETATE, pH 4.60

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 5, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 6746 / % possible obs: 91.7 % / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 6.3
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.226 / % possible all: 82.3

-
Processing

Software
NameVersionClassification
X-PLOR1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.37 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 895941.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1276 9.8 %RANDOM
Rwork0.231 ---
obs0.231 12999 98 %-
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.26 Å20 Å20 Å2
2---0.75 Å20 Å2
3----2.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å-
Refinement stepCycle: LAST / Resolution: 2.2→19.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 0 136 2059
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.8
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.274 214 10 %
Rwork0.195 1917 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

+
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