[English] 日本語
Yorodumi
- PDB-5dre: Crystal Structure of Ketosteroid Isomerase D38GP39GD99N mutant fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dre
TitleCrystal Structure of Ketosteroid Isomerase D38GP39GD99N mutant from Pseudomonas Testosteroni (tKSI)
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE / ENZYME
Function / homology
Function and homology information


steroid Delta-isomerase / steroid delta-isomerase activity / steroid metabolic process
Similarity search - Function
Steroid delta5-4-isomerase / Ketosteroid isomerase / Nuclear transport factor 2 (NTF2) domain / 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 speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 Å
AuthorsLamba, V. / Yabukarski, F. / Herschlag, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1121778 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Evaluation of the Catalytic Contribution from a Positioned General Base in Ketosteroid Isomerase.
Authors: Lamba, V. / Yabukarski, F. / Pinney, M. / Herschlag, D.
History
DepositionSep 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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: Steroid Delta-isomerase


Theoretical massNumber of molelcules
Total (without water)13,3131
Polymers13,3131
Non-polymers00
Water55831
1
A: Steroid Delta-isomerase

A: Steroid Delta-isomerase


Theoretical massNumber of molelcules
Total (without water)26,6262
Polymers26,6262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1890 Å2
ΔGint-6 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.362, 60.362, 142.103
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Steroid Delta-isomerase / Delta(5)-3-ketosteroid isomerase


Mass: 13313.019 Da / Num. of mol.: 1 / Mutation: D38G, P39G, D99N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Gene: ksi / Production host: Escherichia coli (E. coli) / References: UniProt: P00947, steroid Delta-isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: Potassium Phosphate 40 mM, Ammonium Sulfate 0.6 M

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2015
RadiationMonochromator: Si(111) Side scattering bent cube-root I-beam single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→42.11 Å / Num. obs: 8865 / % possible obs: 99.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 12.89
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.01 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NXJ

3nxj


Resolution: 2.151→42.107 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / Phase error: 31.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2676 459 5.19 %Random selection
Rwork0.2212 ---
obs0.2236 8850 99.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.151→42.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms921 0 0 31 952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007937
X-RAY DIFFRACTIONf_angle_d0.961269
X-RAY DIFFRACTIONf_dihedral_angle_d14.341330
X-RAY DIFFRACTIONf_chiral_restr0.037144
X-RAY DIFFRACTIONf_plane_restr0.004169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.151-2.46220.33711590.2642681X-RAY DIFFRACTION99
2.4622-3.1020.3511520.25132755X-RAY DIFFRACTION99
3.102-42.11460.22391480.20262955X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6180.52170.32461.463-0.83030.7350.1150.2067-0.0408-0.273-0.2325-0.6577-0.07550.53530.00070.37920.03660.01530.44220.06270.4533-21.196310.3656-11.9088
20.7058-0.34070.25691.0436-0.99381.5806-0.06020.10950.0563-0.2006-0.27120.01770.12170.0974-0.00140.40740.0078-0.03420.36590.02210.3339-28.16382.0641-9.4046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 58 )
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 125 )

+
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