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

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Basic information

Entry
Database: PDB / ID: 6ubq
TitleCrystal Structure of Ketosteroid Isomerase from Pseudomonas Putida (pKSI) bound to 4-Androstenedione at 100 K
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE
Function / homologyKetosteroid isomerase / steroid Delta-isomerase / SnoaL-like domain / SnoaL-like domain / steroid delta-isomerase activity / 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: 1.2991 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
DepositionSep 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 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
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7657
Polymers29,0972
Non-polymers6685
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-44 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.209, 74.316, 95.562
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 (E. coli) / References: UniProt: P07445, steroid Delta-isomerase
#2: Chemical ChemComp-ASD / 4-ANDROSTENE-3-17-DIONE / Androstenedione


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


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 / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 298 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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.78719 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: 0.78719 Å / Relative weight: 1
ReflectionResolution: 1.2991→37.16 Å / Num. obs: 64423 / % possible obs: 99.8 % / Redundancy: 13.2 % / Biso Wilson estimate: 15.55 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.018 / Rrim(I) all: 0.064 / Net I/σ(I): 19.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.2991-1.3212.41.97230450.5860.5772.05897.4
7.12-37.16120.0214780.9770.0070.02299.6

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Processing

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

3vsy


Resolution: 1.2991→34.6443 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.75
RfactorNum. reflection% reflection
Rfree0.1699 3176 4.94 %
Rwork0.152 --
obs0.1528 64304 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.53 Å2 / Biso mean: 28.8549 Å2 / Biso min: 7.7 Å2
Refinement stepCycle: final / Resolution: 1.2991→34.6443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 97 292 2355
Biso mean--34.91 35.58 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082346
X-RAY DIFFRACTIONf_angle_d0.9633231
X-RAY DIFFRACTIONf_chiral_restr0.075338
X-RAY DIFFRACTIONf_plane_restr0.008451
X-RAY DIFFRACTIONf_dihedral_angle_d15.822916
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2991-1.31850.30671350.2681253297
1.3185-1.33910.27391390.24782625100
1.3391-1.36110.27651350.21972616100
1.3611-1.38450.23531330.2082638100
1.3845-1.40970.2051380.19552612100
1.4097-1.43680.22661440.18042618100
1.4368-1.46620.21761390.16482624100
1.4662-1.4980.21370.14922651100
1.498-1.53290.15831400.13712606100
1.5329-1.57120.17051370.13152653100
1.5712-1.61370.16621330.12092625100
1.6137-1.66120.15431370.12282670100
1.6612-1.71480.16381490.11892621100
1.7148-1.77610.14761260.11772627100
1.7761-1.84720.1351320.12372684100
1.8472-1.93130.16551580.12912641100
1.9313-2.03310.16451360.13752673100
2.0331-2.16040.14711300.13742677100
2.1604-2.32720.15981270.13672698100
2.3272-2.56130.15121310.14252701100
2.5613-2.93180.14481400.1532711100
2.9318-3.69310.16261520.15512746100
3.6931-34.64430.18681480.17362879100

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