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- PDB-4kvh: Crystal structure of ketosteroid isomerase fold protein Hmuk_0747 -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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Components

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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

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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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

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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

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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 %

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