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- PDB-6c1j: Crystal Structure of Ketosteroid Isomerase Y32F/Y57F/D40N mutant ... -

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Basic information

Entry
Database: PDB / ID: 6c1j
TitleCrystal Structure of Ketosteroid Isomerase Y32F/Y57F/D40N mutant from Pseudomonas Putida (pKSI) bound to 3,4-dinitrophenol
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE / ENZYME
Function / homology
Function and homology information


steroid Delta-isomerase / steroid delta-isomerase activity / steroid metabolic process
Similarity search - Function
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
3,4-dinitrophenol / Steroid Delta-isomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.063 Å
AuthorsYabukarski, F. / Pinney, M.M. / Herschlag, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1121778 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein.
Authors: Pinney, M.M. / Natarajan, A. / Yabukarski, F. / Sanchez, D.M. / Liu, F. / Liang, R. / Doukov, T. / Schwans, J.P. / Martinez, T.J. / Herschlag, D.
History
DepositionJan 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7845
Polymers14,5161
Non-polymers2684
Water3,045169
1
A: Steroid Delta-isomerase
hetero molecules

A: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,56710
Polymers29,0312
Non-polymers5368
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2720 Å2
ΔGint-58 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.902, 94.998, 72.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-428-

HOH

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Components

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


Mass: 14515.515 Da / Num. of mol.: 1 / Mutation: Y32F, Y57F, D40N
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-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.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-DNX / 3,4-dinitrophenol


Mass: 184.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4N2O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.2
Details: 18-22 % PEG 3350, 0.2 M magnesium chloride, 0.04 M potassium phosphate
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.88558 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88558 Å / Relative weight: 1
ReflectionResolution: 1.06→36.46 Å / Num. obs: 55563 / % possible obs: 98.5 % / Redundancy: 11.2 % / Biso Wilson estimate: 10.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.02 / Rrim(I) all: 0.068 / Net I/σ(I): 17.6 / Num. measured all: 623131 / Scaling rejects: 321
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
1.06-1.085.91.0431241421190.6760.4251.1341.776.7
5.82-36.4611.40.04546314080.9990.0130.04747.899.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimless0.5.25data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FZW

3fzw


Resolution: 1.063→36.455 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 12.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1538 2778 5 %
Rwork0.1289 52732 -
obs0.1301 55510 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.87 Å2 / Biso mean: 17.5422 Å2 / Biso min: 6.6 Å2
Refinement stepCycle: final / Resolution: 1.063→36.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms978 0 34 190 1202
Biso mean--18.7 29.91 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071593
X-RAY DIFFRACTIONf_angle_d0.9682202
X-RAY DIFFRACTIONf_chiral_restr0.076216
X-RAY DIFFRACTIONf_plane_restr0.006321
X-RAY DIFFRACTIONf_dihedral_angle_d15.299629
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0635-1.08180.26491180.25512028214676
1.0818-1.10150.20851270.1872583271098
1.1015-1.12270.16731250.15872647277299
1.1227-1.14560.15911260.133626222748100
1.1456-1.17050.1441400.127126212761100
1.1705-1.19770.13921550.121926712826100
1.1977-1.22770.141320.123726272759100
1.2277-1.26090.12961440.117426382782100
1.2609-1.2980.14581450.112526442789100
1.298-1.33990.14811310.106426642795100
1.3399-1.38780.12651440.109826652809100
1.3878-1.44330.13351530.107526462799100
1.4433-1.5090.11541480.103326482796100
1.509-1.58860.12611460.102826712817100
1.5886-1.68810.13481560.1126592815100
1.6881-1.81850.13631310.11326952826100
1.8185-2.00140.13471270.11727072834100
2.0014-2.2910.13571400.122826942834100
2.291-2.88630.16711310.134827512882100
2.8863-36.47640.18371590.14928513010100

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