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- PDB-3nxj: Crystal Structure of Ketosteroid Isomerase D99N from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 3nxj
TitleCrystal Structure of Ketosteroid Isomerase D99N from Pseudomonas Testosteroni (tKSI)
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: 1.966 Å
AuthorsGonzalez, A. / Tsai, Y. / Schwans, J. / Sunden, F. / Herschlag, D.
CitationJournal: To be Published
Title: Crystal Structure of Ketosteroid Isomerase D99N from Pseudomonas Testosteroni (tKSI)
Authors: Schwans, J. / Sunden, F. / Gonzalez, A. / Tsai, Y. / Herschlag, D.
History
DepositionJul 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Sep 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,3037
Polymers26,8222
Non-polymers4805
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-49 kcal/mol
Surface area12720 Å2
MethodPISA
2
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
hetero molecules

A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,60514
Polymers53,6444
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area7370 Å2
ΔGint-110 kcal/mol
Surface area23410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.357, 104.786, 141.435
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-339-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 1 - 125 / Label seq-ID: 1 - 125

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 13411.117 Da / Num. of mol.: 2 / Mutation: D99N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Strain: ATC 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.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 4.17 Å3/Da / Density % sol: 70.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.0 M ammonium sulfate, 100 mM Tris-HCl, 1 mM EDTA, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.97946
SYNCHROTRONSSRL BL9-120.97946
Detector
TypeIDDetectorDate
MARMOSAIC 325 mm CCD1CCDMar 24, 2010
ADSC QUANTUM 315r2CCDMay 10, 2010
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1Si double crystalSINGLE WAVELENGTHx-ray1
2Si single crystalSINGLE WAVELENGTHx-ray1
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
111.000H, 1.000K, L10.341
110.500H+0.500K, 1.500H-0.500K, -L20.318
11-0.500H+0.500K, 1.500H+0.500K, -L30.341
ReflectionResolution: 1.966→29.309 Å / Num. all: 32154 / Num. obs: 32154 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 34.805 Å2 / Rsym value: 0.092 / Net I/σ(I): 13.9
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.966-2.073.30.6131.21476545360.61397.1
2.07-2.24.20.4941.51861943990.49499.9
2.2-2.354.10.4561.61690941460.45699.8
2.35-2.544.20.24131642438790.24199.9
2.54-2.784.20.1594.61509535710.159100
2.78-3.114.20.098.31369232420.0999.9
3.11-3.594.20.05413.91208228930.05499.9
3.59-4.440.04217.3982124580.04299.7
4.4-6.2240.02922.2771719240.02999.8
6.22-29.3093.90.02524.3427411060.02598.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.14 Å29.31 Å
Translation2.14 Å29.31 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
Web-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 8CHO

8cho


Resolution: 1.966→29.309 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.831 / WRfactor Rfree: 0.2875 / WRfactor Rwork: 0.2427 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.6977 / SU B: 9.575 / SU ML: 0.125 / SU R Cruickshank DPI: 0.0356 / SU Rfree: 0.0371 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3143 1565 5.1 %RANDOM
Rwork0.2521 ---
all0.2551 30919 --
obs0.2551 30919 95.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 327.65 Å2 / Biso mean: 27.8626 Å2 / Biso min: 3.75 Å2
Baniso -1Baniso -2Baniso -3
1-10.25 Å20 Å20 Å2
2--8.82 Å20 Å2
3----19.07 Å2
Refinement stepCycle: LAST / Resolution: 1.966→29.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 25 286 2201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221960
X-RAY DIFFRACTIONr_bond_other_d0.0030.021264
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9562667
X-RAY DIFFRACTIONr_angle_other_deg1.83533070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6295250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04823.84691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.21515294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8771514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212230
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02412
X-RAY DIFFRACTIONr_mcbond_it0.271.51248
X-RAY DIFFRACTIONr_mcbond_other0.071.5508
X-RAY DIFFRACTIONr_mcangle_it0.46521993
X-RAY DIFFRACTIONr_scbond_it0.8043712
X-RAY DIFFRACTIONr_scangle_it1.1564.5674
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1559 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.490.5
MEDIUM THERMAL0.312
LS refinement shellResolution: 1.966→2.015 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 106 -
Rwork0.232 2095 -
all-2201 -
obs--91.94 %
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)
10.032-0.0050.00440.0461-0.00110.0475-0.0017-0.0003-0.00220.0075-0.00050.00640.0004-0.00650.00230.0081-0.0054-0.00680.038-0.00070.010416.67434.27334.294
20.0426-0.0182-0.00210.04280.0134-0.012-0.00320.0109-0.02040.0063-0.00190.0087-0.0026-0.00360.0050.0157-0.0010.00290.0391-0.00490.01537.71228.86212.856
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 125
2X-RAY DIFFRACTION2B1 - 125

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