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- PDB-3unl: Crystal structure of ketosteroid isomerase F54G from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 3unl
TitleCrystal structure of ketosteroid isomerase F54G from Pseudomonas testosteroni
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE
Function / homology
Function and homology information


steroid Delta-isomerase / steroid delta-isomerase activity / steroid metabolic process
Similarity search - Function
Steroid delta5-4-isomerase / Ketosteroid isomerase / Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) 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
Steroid Delta-isomerase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.52 Å
AuthorsGonzalez, A. / Tsai, Y. / Schwans, J. / Sunden, F. / Herschlag, D.
CitationJournal: To be Published
Title: Crystal structure of ketosteroid isomerase F54G from Pseudomonas testosteroni
Authors: Schwans, J. / Sunden, F. / Gonzalez, A. / Tsai, Y. / Herschlag, D.
History
DepositionNov 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
C: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,63318
Polymers53,2884
Non-polymers1,34514
Water1,820101
1
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3169
Polymers26,6442
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-67 kcal/mol
Surface area12470 Å2
MethodPISA
2
C: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3169
Polymers26,6442
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-64 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.571, 64.571, 502.154
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein
Steroid Delta-isomerase / Delta(5)-3-ketosteroid isomerase


Mass: 13321.979 Da / Num. of mol.: 4 / Mutation: F54G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Gene: ksi / Plasmid: pKK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00947, steroid Delta-isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 1.4 M ammonium sulfate, 20 mM potassium phosphate, 1 mM EDTA, 2mM DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2011
RadiationMonochromator: Si single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.52→39.5 Å / Num. obs: 22617 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 43.6 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 18.1
Reflection shellResolution: 2.52→2.66 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 4.2 / Num. unique all: 3118 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.89 Å38.14 Å
Translation2.89 Å38.14 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
Web-Icedata collection
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3M8C

3m8c


Resolution: 2.52→37.36 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.86 / WRfactor Rfree: 0.2466 / WRfactor Rwork: 0.2072 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8623 / SU B: 20.076 / SU ML: 0.205 / SU R Cruickshank DPI: 0.4886 / SU Rfree: 0.2962 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 1147 5.1 %RANDOM
Rwork0.224 ---
all0.2262 22472 --
obs0.2262 22472 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 115.89 Å2 / Biso mean: 25.9096 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20.54 Å20 Å2
2--1.09 Å20 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.52→37.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3728 0 70 101 3899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223920
X-RAY DIFFRACTIONr_bond_other_d0.0020.022552
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9615334
X-RAY DIFFRACTIONr_angle_other_deg0.83536193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2585504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90623.591181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5815598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4281532
X-RAY DIFFRACTIONr_chiral_restr0.0740.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214461
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02823
X-RAY DIFFRACTIONr_mcbond_it0.4131.52492
X-RAY DIFFRACTIONr_mcbond_other0.0721.51020
X-RAY DIFFRACTIONr_mcangle_it0.77923983
X-RAY DIFFRACTIONr_scbond_it1.21931428
X-RAY DIFFRACTIONr_scangle_it2.0184.51351
LS refinement shellResolution: 2.52→2.584 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 79 -
Rwork0.287 1492 -
all-1571 -
obs--96.44 %
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)
11.0577-0.04060.52120.634-0.00361.28930.01690.07230.0101-0.0244-0.00160.0126-0.05580.1113-0.01530.0627-0.01090.0170.0146-0.01040.023225.2121-10.603349.338
21.49750.00740.20730.48050.45641.25350.0313-0.0874-0.0757-0.0239-0.03770.0114-0.0561-0.20260.00640.04720.0259-0.01220.05280.01030.02823.1155-18.187544.6307
30.27270.2232-0.26480.8171-0.20450.4308-0.05230.0124-0.0585-0.03780.0345-0.01050.04780.01960.01770.02750.0113-0.01440.052-0.01530.06988.3999-38.0685-2.456
41.1101-0.05330.10660.63250.50911.2072-0.035-0.0671-0.06380.0047-0.0086-0.03790.033-0.07970.04360.01080.0062-0.01290.0465-0.0010.0654-6.5673-33.085415.2345
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 124
2X-RAY DIFFRACTION2B1 - 124
3X-RAY DIFFRACTION3C1 - 124
4X-RAY DIFFRACTION4D1 - 124

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