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

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Basic information

Entry
Database: PDB / ID: 4mjd
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 / unkonw fuction
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / metal ion binding / Alpha Beta / SnoaL-like domain-containing protein
Function and homology information
Biological speciesHalomicrobium mukohataei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 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
DepositionSep 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
B: Ketosteroid isomerase fold protein Hmuk_0747
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7585
Polymers25,6862
Non-polymers723
Water5,783321
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-31 kcal/mol
Surface area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.915, 76.858, 39.297
Angle α, β, γ (deg.)90.000, 109.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ketosteroid isomerase fold protein Hmuk_0747


Mass: 12843.147 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halomicrobium mukohataei (archaea) / Strain: DSM 12286 / Gene: Hmuk_0747 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: C7NZX0
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M MgCl2, 0.1M HEPES, 30% PEG400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.28→50 Å / Num. all: 54846 / Num. obs: 53619 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 39
Reflection shellResolution: 1.28→1.29 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1136 / % possible all: 85.9

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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
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4KVH

4kvh


Resolution: 1.28→22.39 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.312 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1654 2725 5.1 %RANDOM
Rwork0.1348 ---
obs0.1364 53604 98.81 %-
all-53604 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.52 Å2 / Biso mean: 18.2347 Å2 / Biso min: 7.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å2-0 Å21.05 Å2
2---1.1 Å2-0 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.28→22.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 3 321 2133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191914
X-RAY DIFFRACTIONr_bond_other_d0.0010.021741
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.9452610
X-RAY DIFFRACTIONr_angle_other_deg0.74533988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2895238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.85222.294109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24115299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1561528
X-RAY DIFFRACTIONr_chiral_restr0.0730.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212246
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02478
X-RAY DIFFRACTIONr_rigid_bond_restr1.37533655
X-RAY DIFFRACTIONr_sphericity_free30.971570
X-RAY DIFFRACTIONr_sphericity_bonded9.34753864
LS refinement shellResolution: 1.284→1.317 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 204 -
Rwork0.204 3584 -
all-3788 -
obs-3788 94.87 %

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