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- PDB-3oxa: Crystal Structure of Ketosteroid Isomerase D40N/C69S/C81S/C97S/M1... -

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Basic information

Entry
Database: PDB / ID: 3oxa
TitleCrystal Structure of Ketosteroid Isomerase D40N/C69S/C81S/C97S/M116C-CN from P. putida
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE / steroid isomerase / steroid / cyanylation
Function / homology
Function and homology information


steroid Delta-isomerase / steroid Delta-isomerase activity / steroid metabolic process
Similarity search - Function
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 speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsSigala, P.A. / Fenn, T.D. / Herschlag, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase.
Authors: Fafarman, A.T. / Sigala, P.A. / Schwans, J.P. / Fenn, T.D. / Herschlag, D. / Boxer, S.G.
History
DepositionSep 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Database references
Revision 1.2Mar 7, 2012Group: Database references
Revision 1.3Sep 6, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)57,9854
Polymers57,9854
Non-polymers00
Water79344
1
A: Steroid Delta-isomerase
C: Steroid Delta-isomerase


Theoretical massNumber of molelcules
Total (without water)28,9932
Polymers28,9932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-11 kcal/mol
Surface area12500 Å2
MethodPISA
2
B: Steroid Delta-isomerase
D: Steroid Delta-isomerase


Theoretical massNumber of molelcules
Total (without water)28,9932
Polymers28,9932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-11 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.920, 93.576, 75.407
Angle α, β, γ (deg.)90.000, 103.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14496.276 Da / Num. of mol.: 4 / Mutation: D40N, C69S, C81S, C97S, M116(XCN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P07445, steroid Delta-isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.1 M ammonium sulfate, 5% isopropanol, 40 mM potassium phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2007
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→41.67 Å / Num. all: 46319 / Num. obs: 39383 / % possible obs: 85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 39.888 Å2
Reflection shellResolution: 1.89→1.9 Å / % possible all: 25

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PZV

2pzv


Resolution: 1.89→41.67 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6179 / Cross valid method: THROUGHOUT / Stereochemistry target values: ml
RfactorNum. reflection% reflectionSelection details
Rfree0.2902 1858 5.15 %random
Rwork0.2437 ---
all-46319 --
obs-36068 77.96 %-
Solvent computationBsol: 79.487 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 189.96 Å2 / Biso mean: 74.7407 Å2 / Biso min: 28.55 Å2
Baniso -1Baniso -2Baniso -3
1-2.851 Å2-0 Å2-0.577 Å2
2---3.932 Å20 Å2
3----8.746 Å2
Refinement stepCycle: LAST / Resolution: 1.89→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 0 0 44 4034
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.6521
X-RAY DIFFRACTIONf_bond_d0.0051
X-RAY DIFFRACTIONf_chiral_restr0.0531
X-RAY DIFFRACTIONf_dihedral_angle_d10.8911
X-RAY DIFFRACTIONf_plane_restr0.0031
X-RAY DIFFRACTIONf_nbd_refined4.081
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
1.89-1.90010.3783167X-RAY DIFFRACTION6825
1.9001-1.90960.3498194X-RAY DIFFRACTION6828
1.9096-1.91940.3648202X-RAY DIFFRACTION6831
1.9194-1.92930.3551228X-RAY DIFFRACTION6833
1.9293-1.93950.3587222X-RAY DIFFRACTION6833
1.9395-1.94990.3485240X-RAY DIFFRACTION6834
1.9499-1.96040.3637260X-RAY DIFFRACTION6840
1.9604-1.97130.3641277X-RAY DIFFRACTION6843
1.9713-1.98240.3549296X-RAY DIFFRACTION6841
1.9824-1.99370.3232275X-RAY DIFFRACTION6842
1.9937-2.00530.3407294X-RAY DIFFRACTION6845
2.0053-2.01710.339317X-RAY DIFFRACTION6845
2.0171-2.02930.3342330X-RAY DIFFRACTION6848
2.0293-2.04170.3296340X-RAY DIFFRACTION6850
2.0417-2.05450.3246347X-RAY DIFFRACTION6852
2.0545-2.06760.3119354X-RAY DIFFRACTION6855
2.0676-2.0810.3525388X-RAY DIFFRACTION6857
2.081-2.09480.3181388X-RAY DIFFRACTION6858
2.0948-2.10890.3232413X-RAY DIFFRACTION6861
2.1089-2.12350.3064431X-RAY DIFFRACTION6862
2.1235-2.13840.3018435X-RAY DIFFRACTION6864
2.1384-2.15380.3304459X-RAY DIFFRACTION6867
2.1538-2.16960.3466473X-RAY DIFFRACTION6873
2.1696-2.1860.3298489X-RAY DIFFRACTION6872
2.186-2.20280.3019492X-RAY DIFFRACTION6875
2.2028-2.22010.3154534X-RAY DIFFRACTION6875
2.2201-2.2380.3158494X-RAY DIFFRACTION6876
2.238-2.25650.292546X-RAY DIFFRACTION6877
2.2565-2.27560.3087526X-RAY DIFFRACTION6877
2.2756-2.29540.3094518X-RAY DIFFRACTION6880
2.2954-2.31590.3201536X-RAY DIFFRACTION6881
2.3159-2.33720.3215560X-RAY DIFFRACTION6881
2.3372-2.35920.3173559X-RAY DIFFRACTION6882
2.3592-2.38210.3278579X-RAY DIFFRACTION6883
2.3821-2.40590.3158533X-RAY DIFFRACTION6881
2.4059-2.43070.315576X-RAY DIFFRACTION6885
2.4307-2.45660.324564X-RAY DIFFRACTION6886
2.4566-2.48360.3245573X-RAY DIFFRACTION6883
2.4836-2.51180.306620X-RAY DIFFRACTION6887
2.5118-2.54130.3096561X-RAY DIFFRACTION6886
2.5413-2.57230.3018591X-RAY DIFFRACTION6887
2.5723-2.60490.2987604X-RAY DIFFRACTION6890
2.6049-2.63910.2904581X-RAY DIFFRACTION6885
2.6391-2.67530.3183623X-RAY DIFFRACTION6890
2.6753-2.71350.3047595X-RAY DIFFRACTION6887
2.7135-2.7540.3023587X-RAY DIFFRACTION6889
2.754-2.7970.2745621X-RAY DIFFRACTION6890
2.797-2.84290.3207625X-RAY DIFFRACTION6892
2.8429-2.89190.3151632X-RAY DIFFRACTION6892
2.8919-2.94450.3014626X-RAY DIFFRACTION6893
2.9445-3.00110.2794626X-RAY DIFFRACTION6892
3.0011-3.06230.3029648X-RAY DIFFRACTION6895
3.0623-3.12890.2911634X-RAY DIFFRACTION6893
3.1289-3.20160.2777614X-RAY DIFFRACTION6892
3.2016-3.28170.2575650X-RAY DIFFRACTION6893
3.2817-3.37040.2626615X-RAY DIFFRACTION6893
3.3704-3.46950.2408636X-RAY DIFFRACTION6893
3.4695-3.58140.2161651X-RAY DIFFRACTION6893
3.5814-3.70930.2193623X-RAY DIFFRACTION6892
3.7093-3.85780.2187645X-RAY DIFFRACTION6893
3.8578-4.03320.2123632X-RAY DIFFRACTION6894
4.0332-4.24560.1989644X-RAY DIFFRACTION6894
4.2456-4.51140.1665652X-RAY DIFFRACTION6895
4.5114-4.85920.1678647X-RAY DIFFRACTION6894
4.8592-5.34730.1771651X-RAY DIFFRACTION6894
5.3473-6.1190.2097655X-RAY DIFFRACTION6894
6.119-7.70130.2002637X-RAY DIFFRACTION6893
7.7013-41.670.1987675X-RAY DIFFRACTION6894
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)
10.52140.624-0.28790.64790.15991.3103-0.05450.07090.02070.12240.0873-0.0071-0.0172-0.1519-0.02710.34590.01-0.0230.29440.00770.378-1.2699-0.04667.4329
2-0.0036-0.4286-1.99820.8553-0.37915.56150.03310.132-0.0940.17880.13770.01760.0054-0.5635-0.12010.30810.033-0.02610.3650.00480.3583-10.3403-0.1686-21.5554
30.79351.45680.61562.2682-0.67510.95370.01410.22920.0741-0.79250.07930.12360.35010.2615-0.10610.60130.049-0.07170.1928-0.00140.21952.925927.4087-19.83
42.5765-0.4356-0.1412-1.2427-1.70986.97630.283-0.1858-0.6859-0.01130.00450.06583.29970.5451-0.27031.31590.1678-0.1630.24450.0530.4417-15.57327.2966-39.1595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 130
2X-RAY DIFFRACTION2chain BB2 - 130
3X-RAY DIFFRACTION3chain CC2 - 131
4X-RAY DIFFRACTION4chain DD2 - 131

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