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- PDB-3m8c: Crystal Structure of Ketosteroid Isomerase D99N from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 3m8c
TitleCrystal Structure of Ketosteroid Isomerase D99N from Pseudomonas Testosteroni (tKSI) with Equilenin Bound
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE / Lipid metabolism / 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 / 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
EQUILENIN / Steroid Delta-isomerase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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) with Equilenin Bound
Authors: Schwans, J. / Sunden, F. / Gonzalez, A. / Tsai, Y. / Herschlag, D.
History
DepositionMar 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations / Refinement description
Category: database_2 / software ...database_2 / software / 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 / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 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)55,87622
Polymers53,6444
Non-polymers2,23218
Water8,395466
1
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,94512
Polymers26,8222
Non-polymers1,12310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-70 kcal/mol
Surface area12080 Å2
MethodPISA
2
C: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,93110
Polymers26,8222
Non-polymers1,1098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-57 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.312, 64.312, 506.174
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-377-

HOH

21C-559-

HOH

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Components

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


Mass: 13411.117 Da / Num. of mol.: 4 / Mutation: D99N
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EQU / EQUILENIN


Mass: 266.334 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H18O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 298 K / Method: sitting drop / pH: 7.2
Details: 1.4 M ammonium sulfate, 40 mM potassium phosphate, 1 mM EDTA, 2 mM DTT, pH 7.2, sitting drop, temperature 298K

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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 6M1PIXELJan 16, 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: 2.1→33.63 Å / Num. all: 38027 / Num. obs: 38027 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 20.6
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 4.9 / Num. unique all: 5131 / % possible all: 94.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0106refinement
PDB_EXTRACT3.1data extraction
Web-Icedata collection
Blu-Icedata collection
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8CHO

8cho


Resolution: 2.1→84.36 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.127 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1895 5 %RANDOM
Rwork0.166 ---
all0.169 38027 --
obs0.169 37837 99.15 %-
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: 91.99 Å2 / Biso mean: 26.739 Å2 / Biso min: 5.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20.51 Å20 Å2
2--1.02 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.1→84.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3756 0 137 466 4359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224335
X-RAY DIFFRACTIONr_angle_refined_deg1.9891.9765945
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5515565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22823.529204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5615662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.811538
X-RAY DIFFRACTIONr_chiral_restr0.1460.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213429
X-RAY DIFFRACTIONr_mcbond_it1.171.52697
X-RAY DIFFRACTIONr_mcangle_it2.01824355
X-RAY DIFFRACTIONr_scbond_it3.22331638
X-RAY DIFFRACTIONr_scangle_it4.8454.51590
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 118 -
Rwork0.238 2348 -
all-2466 -
obs--89.48 %

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