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- PDB-6ucw: Multi-conformer model of Apo Ketosteroid Isomerase from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 6ucw
TitleMulti-conformer model of Apo Ketosteroid Isomerase from Pseudomonas Putida (pKSI) at 250 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 / Steroid Delta-isomerase
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsYabukarski, F. / Herschlag, D. / Biel, J.T. / Fraser, J.S.
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 17, 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)29,2176
Polymers29,0972
Non-polymers1204
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-46 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.849, 73.437, 95.989
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 44.99 %
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: 250 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 1.25→36.72 Å / Num. obs: 70573 / % possible obs: 99.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 13.23 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.038 / Rrim(I) all: 0.085 / Net I/σ(I): 9.9 / Num. measured all: 336888 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.7 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.25-1.271.4591625334380.410.7461.6441.198.6
6.85-36.720.04323104950.9920.0220.04833.995.8

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Processing

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

3vsy


Resolution: 1.25→36.719 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.69
RfactorNum. reflection% reflection
Rfree0.1731 3491 4.96 %
Rwork0.1488 --
obs0.15 70423 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.67 Å2 / Biso mean: 20.0003 Å2 / Biso min: 5.94 Å2
Refinement stepCycle: final / Resolution: 1.25→36.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 4 295 2273
Biso mean--19.55 30.56 -
Num. residues----253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074782
X-RAY DIFFRACTIONf_angle_d0.9586416
X-RAY DIFFRACTIONf_chiral_restr0.073689
X-RAY DIFFRACTIONf_plane_restr0.006845
X-RAY DIFFRACTIONf_dihedral_angle_d14.6811750
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2502-1.26730.27711450.2943256997
1.2673-1.28540.34271370.27642677100
1.2854-1.30460.28391500.2714259199
1.3046-1.3250.25611230.2556269399
1.325-1.34670.28941510.24942638100
1.3467-1.36990.28871300.24282681100
1.3699-1.39480.24471400.22732631100
1.3948-1.42170.24671380.2128267199
1.4217-1.45070.2031540.19752644100
1.4507-1.48220.22151380.17542694100
1.4822-1.51670.18691440.1642641100
1.5167-1.55460.14941340.15242705100
1.5546-1.59670.18991380.1461264799
1.5967-1.64360.17241370.14642679100
1.6436-1.69670.18091440.142669100
1.6967-1.75730.1631380.1335267499
1.7573-1.82770.17761290.12762695100
1.8277-1.91090.16331560.12242666100
1.9109-2.01160.14891430.12032703100
2.0116-2.13760.15071330.11822704100
2.1376-2.30270.13081230.1157271499
2.3027-2.53430.14281290.1173269798
2.5343-2.90090.14161390.1324271199
2.9009-3.65430.15521510.1357273898
3.6543-36.7190.17821470.1592280096

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