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- PDB-3ke7: Crystal structure of putative ketosteroid isomerase (YP_001303366... -

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Basic information

Entry
Database: PDB / ID: 3ke7
TitleCrystal structure of putative ketosteroid isomerase (YP_001303366.1) from Parabacteroides distasonis ATCC 8503 at 1.45 A resolution
ComponentsPutative ketosteroid isomerase
KeywordsISOMERASE / putative ketosteroid isomerase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
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 / Alpha Beta / DI(HYDROXYETHYL)ETHER / SnoaL-like domain-containing protein
Function and homology information
Biological speciesParabacteroides distasonis ATCC 8503 (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 (YP_001303366.1) from Parabacteroides distasonis ATCC 8503 at 1.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 17, 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 1.5Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3697
Polymers31,7482
Non-polymers6215
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-22 kcal/mol
Surface area12590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.660, 60.897, 52.280
Angle α, β, γ (deg.)90.00, 102.30, 90.00
Int Tables number5
Space group name H-MC121
DetailsCRYSTAL PACKING AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY ANALYSES SUPPORT THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative ketosteroid isomerase


Mass: 15874.207 Da / Num. of mol.: 2 / Fragment: sequence database residues 22-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis ATCC 8503 (bacteria)
Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_2009 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LDI0

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Non-polymers , 5 types, 252 molecules

#2: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHIS CONSTRUCT (22-154) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT (22-154) WAS EXPRESSED WITH THE 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: 1.83 Å3/Da / Density % sol: 32.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 2.4000M (NH4)2SO4, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97805,0.97862
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 16, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978051
30.978621
ReflectionResolution: 1.45→27.077 Å / Num. obs: 39881 / % possible obs: 98.5 % / Redundancy: 2.2 % / Biso Wilson estimate: 13.881 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.2 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.45-1.490.3542.1640628720.35497
1.49-1.530.3022.4628028150.30297.5
1.53-1.570.2492.9618227740.24997.7
1.57-1.620.2133.5604827010.21397.8
1.62-1.670.1853.9585326220.18598.4
1.67-1.730.1554.7565825380.15598.1
1.73-1.80.1355.2545824460.13598.6
1.8-1.870.1136.1526823610.11398.5
1.87-1.960.16.7510022760.199
1.96-2.050.0798.2481821550.07998.8
2.05-2.160.0778.6467920950.07799.3
2.16-2.290.078.8445119870.0799.2
2.29-2.450.0669.2409118280.06699.4
2.45-2.650.0610.7388217400.0699.4
2.65-2.90.05511.3355415910.05599.5
2.9-3.240.04912.6322914550.04999.7
3.24-3.740.04512.9282112630.04599.2
3.74-4.590.04413.9238410710.04499.3
4.59-6.480.04812.618748410.04898.8
6.48-27.080.0531210054500.05395.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.45→27.077 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 2.513 / SU ML: 0.043 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.07
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. BICINE (BCN) AND GLYCEROL (GOL) FROM THE CRYSTALLIZATION/ CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 5. THE ELECTRON DENSITY FOR RESIDUES B119-B122 IS POOR. 6. THE CONFORMATION OF THE N-TERMINAL RESIDUES PRECEDING ASN-34 DIFFER CONSIDERABLY BETWEEN THE TWO NCS-RELATED PROTOMERS.
RfactorNum. reflection% reflectionSelection details
Rfree0.182 2004 5 %RANDOM
Rwork0.152 ---
obs0.153 39881 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.55 Å2 / Biso mean: 13.291 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20.61 Å2
2---0.47 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.45→27.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2129 0 39 247 2415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222391
X-RAY DIFFRACTIONr_bond_other_d0.0020.021626
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9743285
X-RAY DIFFRACTIONr_angle_other_deg0.91734036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9935314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95225.225111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.21215437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2221511
X-RAY DIFFRACTIONr_chiral_restr0.0960.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212641
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02448
X-RAY DIFFRACTIONr_mcbond_it1.79931420
X-RAY DIFFRACTIONr_mcbond_other0.4743545
X-RAY DIFFRACTIONr_mcangle_it2.89752353
X-RAY DIFFRACTIONr_scbond_it4.1648971
X-RAY DIFFRACTIONr_scangle_it5.78411905
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 143 -
Rwork0.26 2717 -
all-2860 -
obs--96.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.53260.1742-0.0240.71090.16430.78580.0099-0.03950.0240.0518-0.05020.08140.0245-0.07420.04030.06520.00410.02670.0526-0.00440.01696.89148.99515.5
20.7860.0433-0.61230.3559-0.09121.68370.0476-0.10290.0929-0.0328-0.0266-0.0594-0.08050.2587-0.0210.0562-0.0130.02350.0692-0.00090.02924.80856.5018.857
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 154
2X-RAY DIFFRACTION2B22 - 154

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