[English] 日本語
Yorodumi
- PDB-4kvh: Crystal structure of ketosteroid isomerase fold protein Hmuk_0747 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kvh
TitleCrystal structure of ketosteroid isomerase fold protein Hmuk_0747
ComponentsKetosteroid isomerase fold protein Hmuk_0747
KeywordsUNKNOWN FUNCTION / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homology
Function and homology information


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
BROMIDE ION / CACODYLATE ION / FORMIC ACID / SnoaL-like domain-containing protein
Similarity search - Component
Biological speciesHalomicrobium mukohataei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.61 Å
AuthorsChang, C. / Holowicki, J. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of ketosteroid isomerase fold protein Hmuk_0747
Authors: Chang, C. / Holowicki, J. / Bearden, J. / Joachimiak, A.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ketosteroid isomerase fold protein Hmuk_0747
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,31719
Polymers12,8431
Non-polymers1,47418
Water2,234124
1
A: Ketosteroid isomerase fold protein Hmuk_0747
hetero molecules

A: Ketosteroid isomerase fold protein Hmuk_0747
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,63438
Polymers25,6862
Non-polymers2,94736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6190 Å2
ΔGint-10 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.785, 91.785, 77.963
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-205-

BR

21A-218-

FMT

31A-404-

HOH

41A-413-

HOH

51A-424-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Ketosteroid isomerase fold protein Hmuk_0747


Mass: 12843.147 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halomicrobium mukohataei (archaea) / Strain: DSM 12286 / Gene: Hmuk_0747 / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: C7NZX0

-
Non-polymers , 5 types, 142 molecules

#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.69 Å3/Da / Density % sol: 66.67 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Magnesium chloride, 0.1M Sodium cacodylate, 50% PEG 200, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.91951 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 18, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91951 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. all: 25742 / Num. obs: 25722 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 20.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 48.3
Reflection shellResolution: 1.61→1.64 Å / Redundancy: 16.2 % / Num. unique all: 1254 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SBC-CollectCOLLECTdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
ARP/wARPmodel building
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.61→28.05 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 2.31 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.065
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1807 1272 5.1 %RANDOM
Rwork0.1564 ---
all0.1576 25014 --
obs0.1576 25014 97.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.94 Å2 / Biso mean: 19.5008 Å2 / Biso min: 6.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.06 Å2-0 Å2
2---0.06 Å2-0 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.61→28.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms888 0 29 124 1041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191024
X-RAY DIFFRACTIONr_bond_other_d0.0030.02926
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9481402
X-RAY DIFFRACTIONr_angle_other_deg0.80132121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4745131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.7822.45961
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99615160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.051516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211240
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02264
X-RAY DIFFRACTIONr_rigid_bond_restr4.72131948
X-RAY DIFFRACTIONr_sphericity_free38.455542
X-RAY DIFFRACTIONr_sphericity_bonded9.03552022
LS refinement shellResolution: 1.609→1.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 57 -
Rwork0.177 1233 -
all-1290 -
obs-1290 69.39 %

+
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