[English] 日本語
Yorodumi
- PDB-2pzv: Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pzv
TitleCrystal Structure of Ketosteroid Isomerase D40N from Pseudomonas Putida (pksi) with bound Phenol
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE / transition state analog bound
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
PHENOL / Steroid Delta-isomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsPybus, B. / Caaveiro, J.M.M. / Petsko, G.A. / Ringe, D.
CitationJournal: PLoS Biol. / Year: 2006
Title: Testing Electrostatic complementarity in Enzyme Catalysis: Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole
Authors: Kraut, D.A. / Sigala, P.A. / Pybus, B. / Liu, C.W. / Ringe, D. / Petsko, G.A. / Herschlag, D.
History
DepositionMay 18, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionJun 12, 2007ID: 2B32
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
C: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5678
Polymers58,1904
Non-polymers3764
Water5,711317
1
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2834
Polymers29,0952
Non-polymers1882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-1 kcal/mol
Surface area11990 Å2
MethodPISA
2
C: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2834
Polymers29,0952
Non-polymers1882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-1 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.905, 50.540, 72.290
Angle α, β, γ (deg.)90.02, 89.98, 110.21
Int Tables number1
Space group name H-MP1

-
Components

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


Mass: 14547.515 Da / Num. of mol.: 4 / Mutation: D40N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Plasmid: pKK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P07445, steroid Delta-isomerase
#2: Chemical
ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.06 Å3/Da / Density % sol: 40.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.4 M ammonium sulphate, 7% (v/v) 2-propanol, 40 mM potasium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. all: 119468 / Num. obs: 111105 / % possible obs: 93 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.037
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.415

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→22.54 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.344 / SU ML: 0.044 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: hydrogens have been added in the riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.227 11094 10 %RANDOM
Rwork0.183 ---
obs0.188 110554 86.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å2-0.03 Å20.11 Å2
2---0.19 Å20.09 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.25→22.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 28 322 4366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224158
X-RAY DIFFRACTIONr_angle_refined_deg2.0241.9445675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1575541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16424.049205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45315682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6721533
X-RAY DIFFRACTIONr_chiral_restr0.1390.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023273
X-RAY DIFFRACTIONr_nbd_refined0.2280.22071
X-RAY DIFFRACTIONr_nbtor_refined0.320.22928
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2334
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.232
X-RAY DIFFRACTIONr_mcbond_it2.8591.52636
X-RAY DIFFRACTIONr_mcangle_it3.94824162
X-RAY DIFFRACTIONr_scbond_it4.90131736
X-RAY DIFFRACTIONr_scangle_it6.7124.51494
X-RAY DIFFRACTIONr_rigid_bond_restr3.2134372
X-RAY DIFFRACTIONr_sphericity_free12.4463322
X-RAY DIFFRACTIONr_sphericity_bonded8.54234044
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 634 -
Rwork0.318 5696 -
obs-6330 66.63 %

+
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