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- PDB-3mhe: Crystal Structure of Ketosteroid Isomerase P39A from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 3mhe
TitleCrystal Structure of Ketosteroid Isomerase P39A 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
N-PROPANOL / Steroid Delta-isomerase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.722 Å
AuthorsGonzalez, A. / Tsai, Y. / Schwans, J. / Sunden, F. / Herschlag, D.
CitationJournal: To be Published
Title: Crystal Structure of Ketosteroid Isomerase P39A from Pseudomonas Testosteroni (tKSI)
Authors: Schwans, J. / Sunden, F. / Gonzalez, A. / Tsai, Y. / Herschlag, D.
History
DepositionApr 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 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 1.2Sep 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,50510
Polymers26,7722
Non-polymers7338
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-4 kcal/mol
Surface area12220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.763, 66.026, 86.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 13386.064 Da / Num. of mol.: 2 / Mutation: P39A
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.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 2.0 M ammonium sulfate, 5% propanol, 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
ADSC QUANTUM 315r1CCDMar 16, 2010
MARMOSAIC 325 mm CCD2CCDJan 5, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si single crystalSINGLE WAVELENGTHMx-ray1
2Si double crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.722→29.732 Å / Num. all: 25533 / Num. obs: 25533 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Biso Wilson estimate: 23.8 Å2 / Rsym value: 0.046 / Net I/σ(I): 37.3
Reflection shellResolution: 1.722→1.81 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 38331 / Rsym value: 0.539 / % possible all: 100

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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
Web-Icedata collection
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 8CHO

8cho


Resolution: 1.722→29.73 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.182 / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.873 / SU B: 5.12 / SU ML: 0.076 / SU R Cruickshank DPI: 0.123 / SU Rfree: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1291 5.1 %RANDOM
Rwork0.187 ---
obs0.189 25479 99.75 %-
all-25533 --
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: 116.42 Å2 / Biso mean: 26.212 Å2 / Biso min: 5.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.722→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 39 156 2053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222052
X-RAY DIFFRACTIONr_angle_refined_deg2.251.9572792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5415264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33923.06198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.48815322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3241520
X-RAY DIFFRACTIONr_chiral_restr0.1730.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211588
X-RAY DIFFRACTIONr_mcbond_it1.4771.51289
X-RAY DIFFRACTIONr_mcangle_it2.36822066
X-RAY DIFFRACTIONr_scbond_it3.8223763
X-RAY DIFFRACTIONr_scangle_it5.6424.5726
LS refinement shellResolution: 1.722→1.766 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 82 -
Rwork0.27 1712 -
all-1794 -
obs-1574 96.76 %
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)
10.50580.00690.27291.5001-0.20740.8872-0.01580.004-0.0453-0.0049-0.0259-0.0420.07090.06380.04170.01020.0010.00540.05330.01010.025537.095348.816915.5017
21.01960.0675-0.21841.1990.23750.9588-0.09950.06690.0632-0.26060.10080.1158-0.19630.0172-0.00130.0949-0.0297-0.02810.0313-0.00350.057834.91269.84394.0747
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 125
2X-RAY DIFFRACTION2B1 - 125

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