[English] 日本語
Yorodumi
- PDB-3rgr: Crystal structure of ketosteroid isomerase M116A from Pseudomonas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rgr
TitleCrystal structure of ketosteroid isomerase M116A from Pseudomonas putida
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE
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 / molecular replacement / Resolution: 1.594 Å
AuthorsGonzalez, A. / Tsai, Y. / Schwans, J. / Sunden, F. / Herschlag, D.
CitationJournal: To be Published
Title: Crystal structure of ketosteroid isomerase M116A from Pseudomonas putida
Authors: Gonzalez, A. / Tsai, Y. / Schwans, J. / Sunden, F. / Herschlag, D.
History
DepositionApr 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Steroid Delta-isomerase


Theoretical massNumber of molelcules
Total (without water)14,4881
Polymers14,4881
Non-polymers00
Water1,71195
1
A: Steroid Delta-isomerase

A: Steroid Delta-isomerase


Theoretical massNumber of molelcules
Total (without water)28,9772
Polymers28,9772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2020 Å2
ΔGint-10 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.820, 94.723, 72.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

-
Components

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


Mass: 14488.382 Da / Num. of mol.: 1 / Mutation: M116A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Plasmid: pKK / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: P07445, steroid Delta-isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.12 Å3/Da / Density % sol: 42.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 1 M ammonium sulfate, 40 mM potassium phosphate pH 7.2, 1 mM EDTA, 2 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.097 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2011
RadiationMonochromator: Si single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.097 Å / Relative weight: 1
ReflectionResolution: 1.594→36.195 Å / Num. all: 16562 / Num. obs: 16562 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.066 / Net I/σ(I): 14.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.594-1.683.30.5661.30.566187.3
1.68-1.7840.4121.70.412199.9
1.78-1.940.2772.50.2771100
1.9-2.064.10.154.60.151100
2.06-2.254.20.16.70.1199.9
2.25-2.524.30.0818.30.081199.9
2.52-2.914.30.05811.50.058199.8
2.91-3.564.20.0414.80.04199.7
3.56-5.044.10.0319.80.03199.7
5.04-36.19540.02719.80.027199.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CPO

3cpo


Resolution: 1.594→33.5 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 4.256 / SU ML: 0.068 / SU R Cruickshank DPI: 0.1067 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22535 837 5.1 %RANDOM
Rwork0.17861 ---
obs0.18098 15695 98.05 %-
all-16532 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.736 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å20 Å20 Å2
2---0.99 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.594→33.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 0 0 95 1083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211316
X-RAY DIFFRACTIONr_bond_other_d0.0020.02892
X-RAY DIFFRACTIONr_angle_refined_deg1.9891.9341820
X-RAY DIFFRACTIONr_angle_other_deg1.06332171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2955185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64823.7572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77715219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3011515
X-RAY DIFFRACTIONr_chiral_restr0.1260.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211657
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02292
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2991.5823
X-RAY DIFFRACTIONr_mcbond_other0.4041.5327
X-RAY DIFFRACTIONr_mcangle_it2.15721355
X-RAY DIFFRACTIONr_scbond_it3.0443493
X-RAY DIFFRACTIONr_scangle_it4.7794.5465
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.594→1.635 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 53 -
Rwork0.285 938 -
obs--79.6 %
Refinement TLS params.Method: refined / Origin x: 5.52 Å / Origin y: 11.736 Å / Origin z: -1.067 Å
111213212223313233
T0.0365 Å20.0007 Å2-0.0022 Å2-0.0154 Å20.004 Å2--0.0081 Å2
L0.4132 °20.1174 °20.0106 °2-0.7991 °20.1798 °2--0.0646 °2
S0.0042 Å °0.0148 Å °0.0449 Å °-0.0344 Å °-0.0113 Å °0.0063 Å °-0.0285 Å °-0.0048 Å °0.007 Å °

+
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