[English] 日本語
Yorodumi
- PDB-3ipt: Crystal Structure of Ketosteroid Isomerase Y16S/D40N from Pseudom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ipt
TitleCrystal Structure of Ketosteroid Isomerase Y16S/D40N from Pseudomonas putida with Bound Equilenin
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE / enzyme-ligand complex / protein cavity / Lipid metabolism / Steroid metabolism
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: 1.632 Å
AuthorsFenn, T.D. / Sigala, P.A. / Herschlag, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole.
Authors: Kraut, D.A. / Sigala, P.A. / Fenn, T.D. / Herschlag, D.
History
DepositionAug 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 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 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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)58,9518
Polymers57,8864
Non-polymers1,0654
Water3,981221
1
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4764
Polymers28,9432
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-11 kcal/mol
Surface area12620 Å2
MethodPISA
2
C: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4764
Polymers28,9432
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-11 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.694, 72.401, 81.328
Angle α, β, γ (deg.)90.000, 91.160, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 2:61 or resseq 65:127 )
211chain B and (resseq 2:61 or resseq 65:127 )
311chain C and (resseq 2:61 or resseq 65:127 )
411chain D and (resseq 2:61 or resseq 65:127 )
DetailsThe biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D).

-
Components

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


Mass: 14471.419 Da / Num. of mol.: 4 / Mutation: Y16S,D40N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Plasmid: pET21c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07445, steroid Delta-isomerase
#2: Chemical
ChemComp-EQU / EQUILENIN


Mass: 266.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H18O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.9 M ammonium sulfate, 40 mM potassium phosphate, pH 7.2, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2008
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→43.41 Å / Num. obs: 60155 / % possible obs: 82.3 % / Biso Wilson estimate: 22.09 Å2 / Rmerge(I) obs: 0.166 / Net I/σ(I): 9.7
Reflection shellHighest resolution: 1.63 Å / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 9.7

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2PZV

2pzv


Resolution: 1.632→43.408 Å / Occupancy max: 1 / Occupancy min: 0.31 / SU ML: 1.29 / Isotropic thermal model: Isotropic / σ(F): 0.09 / Phase error: 30.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2451 3023 5.03 %
Rwork0.207 --
obs0.2089 60155 82.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.762 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 50.786 Å2
Baniso -1Baniso -2Baniso -3
1--13.861 Å2-0 Å23.965 Å2
2---10.001 Å2-0 Å2
3---7.375 Å2
Refinement stepCycle: LAST / Resolution: 1.632→43.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3827 0 80 221 4128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0314175
X-RAY DIFFRACTIONf_angle_d2.6965702
X-RAY DIFFRACTIONf_dihedral_angle_d18.5721548
X-RAY DIFFRACTIONf_chiral_restr0.211604
X-RAY DIFFRACTIONf_plane_restr0.015761
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A894X-RAY DIFFRACTIONPOSITIONAL
12B894X-RAY DIFFRACTIONPOSITIONAL0.225
13C971X-RAY DIFFRACTIONPOSITIONAL0.182
14D923X-RAY DIFFRACTIONPOSITIONAL0.191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6322-1.65770.3473390.2875784X-RAY DIFFRACTION25
1.6577-1.68480.3267520.27571162X-RAY DIFFRACTION37
1.6848-1.71390.304770.28511323X-RAY DIFFRACTION43
1.7139-1.74510.29851030.26661658X-RAY DIFFRACTION53
1.7451-1.77860.32381090.25881896X-RAY DIFFRACTION61
1.7786-1.81490.33461280.26162182X-RAY DIFFRACTION70
1.8149-1.85440.28751230.26882444X-RAY DIFFRACTION78
1.8544-1.89750.32361380.25742636X-RAY DIFFRACTION84
1.8975-1.9450.32071410.24382911X-RAY DIFFRACTION92
1.945-1.99760.28331680.24542914X-RAY DIFFRACTION94
1.9976-2.05630.29121450.23263016X-RAY DIFFRACTION95
2.0563-2.12270.25621410.23373024X-RAY DIFFRACTION96
2.1227-2.19860.27121710.20983042X-RAY DIFFRACTION96
2.1986-2.28660.26221560.2063035X-RAY DIFFRACTION97
2.2866-2.39070.23541680.20513092X-RAY DIFFRACTION98
2.3907-2.51670.26181630.21463096X-RAY DIFFRACTION98
2.5167-2.67440.22821600.21483111X-RAY DIFFRACTION98
2.6744-2.88080.29141590.23373119X-RAY DIFFRACTION99
2.8808-3.17060.25711750.21493175X-RAY DIFFRACTION100
3.1706-3.62920.21241660.1873153X-RAY DIFFRACTION99
3.6292-4.57170.18791710.1663143X-RAY DIFFRACTION99
4.5717-43.42360.22241700.18213217X-RAY DIFFRACTION99
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined1.47910.07790.11050.7277-0.41570.42730.0105-0.0310.10630.0313-0.1082-0.19670.04020.17430.06530.14960.0042-0.0070.1935-0.01780.206112.9794-5.67050.869
21.12850.02370.19380.8596-0.18781.2088-0.0586-0.15540.03950.03310.06230.29760.0036-0.1997-0.01720.12720.00160.00580.17430.00730.2205
36.46520.5025-1.76250.34250.46022.5891-0.25050.26840.2940.0221-0.06410.29990.1882-0.28230.24980.2443-0.01690.02390.25980.02030.3553
47.2589-0.7182-1.29480.1957-0.22981.3795-0.1420.64510.3691-0.0350.0357-0.25290.01660.22370.06070.2378-0.03330.02880.40530.00660.4322
Refinement TLS groupSelection details: chain D

+
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