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- PDB-3hx8: Crystal structure of putative ketosteroid isomerase (NP_103587.1)... -

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Basic information

Entry
Database: PDB / ID: 3hx8
TitleCrystal structure of putative ketosteroid isomerase (NP_103587.1) from Mesorhizobium loti at 1.45 A resolution
Componentsputative ketosteroid isomerase
KeywordsISOMERASE / NP_103587.1 / putative ketosteroid isomerase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Domain of unknown function DUF4440 / Domain of unknown function (DUF4440) / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Unknown ligand / Mlr2180 protein
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative ketosteroid isomerase (NP_103587.1) from MESORHIZOBIUM LOTI at 1.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: 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 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative ketosteroid isomerase
B: putative ketosteroid isomerase
C: putative ketosteroid isomerase
D: putative ketosteroid isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,54314
Polymers56,7534
Non-polymers79010
Water11,313628
1
A: putative ketosteroid isomerase
B: putative ketosteroid isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5156
Polymers28,3762
Non-polymers1384
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-11 kcal/mol
Surface area11780 Å2
MethodPISA
2
C: putative ketosteroid isomerase
D: putative ketosteroid isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0288
Polymers28,3762
Non-polymers6526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-6 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.336, 55.111, 56.862
Angle α, β, γ (deg.)69.020, 76.890, 64.830
Int Tables number1
Space group name H-MP1
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
putative ketosteroid isomerase / Mlr2180 protein


Mass: 14188.201 Da / Num. of mol.: 4 / Fragment: sequence database residues 23-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Gene: mlr2180, NP_103587.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q98IZ3
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE THIS CONSTRUCT (RESIDUES 23-150) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. ...SEQUENCE THIS CONSTRUCT (RESIDUES 23-150) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 30.0000% PEG-6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97929,0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 19, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979291
30.979151
ReflectionResolution: 1.45→28.028 Å / Num. obs: 83844 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.22 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 9.05
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.45-1.50.4521.3215281494887.8
1.5-1.560.3251.8239311658193.5
1.56-1.630.2282.5235531633193.8
1.63-1.720.1773.3251761744094.5
1.72-1.830.1174.7244791698294.7
1.83-1.970.0756.9238301652795.2
1.97-2.170.04910.8243741692195.7
2.17-2.480.0414239821666796.3
2.48-3.120.03318.5243541694696.5
3.12-28.0280.02625.5245991712396.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.45→28.028 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.719 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.068
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. PEG (PG4) AND IMIDAZOLE (IMD) MOLECULES FROM THE CRYSTALLIZATION / PROTEIN BUFFER SOLUTIONS ARE MODELED. AN UNKNOWN LIGAND (UNL) IS MODELED IN EACH PROTOMER.
RfactorNum. reflection% reflectionSelection details
Rfree0.186 4214 5 %RANDOM
Rwork0.147 ---
obs0.149 83844 95.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 63.32 Å2 / Biso mean: 23.576 Å2 / Biso min: 11.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20.49 Å20.04 Å2
2--0.6 Å2-0.67 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.45→28.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4034 0 116 637 4787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224190
X-RAY DIFFRACTIONr_bond_other_d0.0010.022908
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9535685
X-RAY DIFFRACTIONr_angle_other_deg0.88837115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1245573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.56124.947190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32115718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3161522
X-RAY DIFFRACTIONr_chiral_restr0.0940.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024825
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02871
X-RAY DIFFRACTIONr_mcbond_it1.5811.52621
X-RAY DIFFRACTIONr_mcbond_other0.6921.51080
X-RAY DIFFRACTIONr_mcangle_it2.48724162
X-RAY DIFFRACTIONr_scbond_it3.50431569
X-RAY DIFFRACTIONr_scangle_it5.0764.51489
X-RAY DIFFRACTIONr_rigid_bond_restr1.59937096
X-RAY DIFFRACTIONr_sphericity_free8.1873710
X-RAY DIFFRACTIONr_sphericity_bonded3.68436983
LS refinement shellResolution: 1.448→1.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 306 -
Rwork0.243 5516 -
all-5822 -
obs--89.83 %

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