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- PDB-6tzd: Crystal Structure of Ketosteroid Isomerase from Pseudomonas Putid... -

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Basic information

Entry
Database: PDB / ID: 6tzd
TitleCrystal Structure of Ketosteroid Isomerase from Pseudomonas Putida (pKSI) bound to 4-Androstenedione at 280 K
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE
Function / homologyKetosteroid isomerase / steroid Delta-isomerase / SnoaL-like domain / steroid Delta-isomerase activity / SnoaL-like domain / steroid metabolic process / NTF2-like domain superfamily / 4-ANDROSTENE-3-17-DIONE / Steroid Delta-isomerase
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4507 Å
AuthorsYabukarski, F. / Herschlag, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1714723 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray-derived conformational ensembles.
Authors: Yabukarski, F. / Biel, J.T. / Pinney, M.M. / Doukov, T. / Powers, A.S. / Fraser, J.S. / Herschlag, D.
History
DepositionAug 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,7657
Polymers29,0972
Non-polymers6685
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-43 kcal/mol
Surface area12590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.229, 74.385, 95.345
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14548.501 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07445, steroid Delta-isomerase
#2: Chemical ChemComp-ASD / 4-ANDROSTENE-3-17-DIONE


Mass: 286.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H26O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 17-23 % PEG 3350, 0.2 M MAGNESIUM CHLORIDE / Temp details: room temperature

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Data collection

DiffractionMean temperature: 280 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.886 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 1.45→37.19 Å / Num. obs: 46456 / % possible obs: 99.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 19.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.023 / Rrim(I) all: 0.054 / Net I/σ(I): 18 / Num. measured all: 256187 / Scaling rejects: 35
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.45-1.485.61.6851243522240.5570.7831.8631.199.1
7.95-37.1950.02417543540.9990.0120.02766.299.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimless0.5.25data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VSY

3vsy


Resolution: 1.4507→34.6595 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.33
RfactorNum. reflection% reflection
Rfree0.1741 2273 4.9 %
Rwork0.1456 --
obs0.147 46342 99.686 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.99 Å2 / Biso mean: 33.3043 Å2 / Biso min: 10.75 Å2
Refinement stepCycle: final / Resolution: 1.4507→34.6595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 97 126 2167
Biso mean--44.62 40.13 -
Num. residues----252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082386
X-RAY DIFFRACTIONf_angle_d0.943290
X-RAY DIFFRACTIONf_chiral_restr0.075339
X-RAY DIFFRACTIONf_plane_restr0.007466
X-RAY DIFFRACTIONf_dihedral_angle_d15.464950
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4507-1.48220.34151350.2915265298
1.4822-1.51670.26551490.24852724100
1.5167-1.55460.23891420.2062692100
1.5546-1.59660.22731380.18132737100
1.5966-1.64360.17571400.15842740100
1.6436-1.69670.20611450.14142695100
1.6967-1.75730.14771310.1323272899
1.7573-1.82770.17831420.1216270999
1.8277-1.91080.15091520.10322745100
1.9108-2.01160.13641480.1022751100
2.0116-2.13760.15851360.10362749100
2.1376-2.30260.15141270.10392772100
2.3026-2.53430.15841330.1222781100
2.5343-2.90080.15641450.1392783100
2.9008-3.65410.16261560.1512838100
3.6541-34.65950.19111530.1732295499

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