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- PDB-3mki: Crystal Structure of Ketosteroid Isomerase D38ED99N from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 3mki
TitleCrystal Structure of Ketosteroid Isomerase D38ED99N from Pseudomonas Testosteroni (tKSI)
ComponentsSteroid Delta-Isomerase
KeywordsISOMERASE / Steroid Metabolism
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 / 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
Steroid Delta-isomerase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsGonzalez, A. / Tsai, Y. / Schwans, J. / Sunden, F. / Herschlag, D.
CitationJournal: To be Published
Title: Crystal Structure of Ketosteroid Isomerase D38E,D99N from Pseudomonas Testosteroni (tKSI)
Authors: Schwans, J. / Sunden, F. / Gonzalez, A. / Tsai, Y. / Herschlag, D.
History
DepositionApr 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: 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 1.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)56,17830
Polymers53,7014
Non-polymers2,47826
Water7,170398
1
A: Steroid Delta-Isomerase
B: Steroid Delta-Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,09115
Polymers26,8502
Non-polymers1,24113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-116 kcal/mol
Surface area12150 Å2
MethodPISA
2
C: Steroid Delta-Isomerase
D: Steroid Delta-Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,08715
Polymers26,8502
Non-polymers1,23713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-119 kcal/mol
Surface area11980 Å2
MethodPISA
3
A: Steroid Delta-Isomerase
B: Steroid Delta-Isomerase
C: Steroid Delta-Isomerase
D: Steroid Delta-Isomerase
hetero molecules

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)112,35760
Polymers107,4018
Non-polymers4,95652
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area23940 Å2
ΔGint-550 kcal/mol
Surface area42030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.041, 64.041, 502.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-144-

HOH

21B-225-

HOH

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Components

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


Mass: 13425.144 Da / Num. of mol.: 4 / Mutation: D38E, D99N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Strain: ATCC 11996 / 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.: 21 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 1.2 M ammonium sulfate, 20 mM potassium phosphate, 1 mM EDTA, 2 mM DTT, pH 7.2, vapor diffusion, sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-110.98
SYNCHROTRONSSRL BL9-220.98
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELFeb 6, 2010
MARMOSAIC 325 mm CCD2CCDJan 6, 2010
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1Si single crystalSINGLE WAVELENGTHx-ray1
2Si double crystalSINGLE WAVELENGTHx-ray1
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→29.909 Å / Num. all: 43283 / Num. obs: 43283 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 26.4 % / Biso Wilson estimate: 21.4 Å2 / Rsym value: 0.162 / Net I/σ(I): 21.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 21.4 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 5933 / Rsym value: 0.812 / % possible all: 97.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 8CHO

8cho


Resolution: 2→29.9 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.193 / WRfactor Rwork: 0.151 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.886 / SU B: 7.055 / SU ML: 0.09 / SU R Cruickshank DPI: 0.153 / SU Rfree: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2159 5 %RANDOM
Rwork0.167 ---
all0.169 42975 --
obs0.169 42975 99.58 %-
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: 104.28 Å2 / Biso mean: 21.123 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20.59 Å20 Å2
2--1.17 Å20 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 2→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 0 135 398 4293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0224249
X-RAY DIFFRACTIONr_angle_refined_deg1.961.9675808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2475556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28823.776196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81915643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6051533
X-RAY DIFFRACTIONr_chiral_restr0.1540.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213301
X-RAY DIFFRACTIONr_mcbond_it1.1591.52672
X-RAY DIFFRACTIONr_mcangle_it1.94424305
X-RAY DIFFRACTIONr_scbond_it3.54131577
X-RAY DIFFRACTIONr_scangle_it5.4774.51503
LS refinement shellResolution: 2→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 134 -
Rwork0.235 2792 -
all-2926 -
obs--95.22 %
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)
10.718-0.14120.48070.5347-0.1450.9675-0.0079-0.01280.04180.02240.03550.0123-0.0784-0.0737-0.02750.03150.01120.00870.0140.01120.0129-26.1401-10.0212-49.3597
21.0941-0.19490.15290.4952-0.4151.1850.03950.0110.01540.0024-0.008-0.0699-0.05890.1185-0.03150.0223-0.0188-0.00530.0229-0.00380.0264-3.8754-17.8469-44.2327
30.69960.160.02440.66040.15381.41650.0159-0.0456-0.05570.0223-0.02230.00460.11090.00210.00640.0114-0.008-0.00270.02460.01010.0071-9.565-37.90122.3581
40.73470.077-0.04690.3948-0.19671.3497-0.04390.0521-0.071-0.01960.0598-0.01240.05020.0825-0.01590.005-0.00040.00290.0496-0.00020.01185.9434-32.779-15.2364
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 125
2X-RAY DIFFRACTION2B1 - 125
3X-RAY DIFFRACTION3C1 - 125
4X-RAY DIFFRACTION4D1 - 125

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