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- PDB-7epn: Ketosteroid Isomerase KSI native -

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Basic information

Entry
Database: PDB / ID: 7epn
TitleKetosteroid Isomerase KSI native
ComponentsSnoaL-like domain-containing protein
KeywordsISOMERASE / Kemp elimination / MsKSI / Mycobacterium smegmatis / Crystal structure.
Function / homologySnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / SnoaL-like domain-containing protein
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLiang, Y. / Zhang, Q. / Bartlam, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800627 China
National Natural Science Foundation of China (NSFC)31870053 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural characterization and Kemp eliminase activity of the Mycobacterium smegmatis Ketosteroid Isomerase.
Authors: Liang, Y. / Li, W. / Liang, H. / Lou, X. / Liu, R. / Zhang, Q. / Bartlam, M.
History
DepositionApr 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: SnoaL-like domain-containing protein
B: SnoaL-like domain-containing protein


Theoretical massNumber of molelcules
Total (without water)32,7892
Polymers32,7892
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-14 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.011, 60.064, 121.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein SnoaL-like domain-containing protein


Mass: 16394.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEI_6677 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7FVV8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.2 M Sodium acetate trihydrate, 0.1M Tris, pH 8.5, 30% PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 25005 / % possible obs: 99.4 % / Redundancy: 13 % / Biso Wilson estimate: 17.14 Å2 / Rpim(I) all: 0.019 / Net I/σ(I): 35.78
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 20.59 / Num. unique obs: 1237 / Rpim(I) all: 0.042 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GRD

3grd


Resolution: 1.9→42.8 Å / SU ML: 0.1833 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.4408
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2386 2000 8.02 %
Rwork0.2009 22949 -
obs0.204 24949 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.59 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2102 0 0 89 2191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592150
X-RAY DIFFRACTIONf_angle_d0.71572925
X-RAY DIFFRACTIONf_chiral_restr0.0551328
X-RAY DIFFRACTIONf_plane_restr0.0057381
X-RAY DIFFRACTIONf_dihedral_angle_d15.6283295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.30331410.22011619X-RAY DIFFRACTION98.82
1.95-20.24081410.19321620X-RAY DIFFRACTION99.77
2-2.060.24071370.19761577X-RAY DIFFRACTION98.79
2.06-2.130.23081420.19721624X-RAY DIFFRACTION99.94
2.13-2.20.24331420.19371629X-RAY DIFFRACTION99.89
2.2-2.290.24541420.19641628X-RAY DIFFRACTION99.77
2.29-2.390.23571410.19621616X-RAY DIFFRACTION99.83
2.39-2.520.24561410.2161619X-RAY DIFFRACTION98.32
2.52-2.680.2671420.21231628X-RAY DIFFRACTION99.83
2.68-2.880.25271430.2271643X-RAY DIFFRACTION99.72
2.88-3.170.25551440.23881655X-RAY DIFFRACTION99.28
3.17-3.630.25841430.20541644X-RAY DIFFRACTION99.06
3.63-4.580.20841480.17451694X-RAY DIFFRACTION99.57
4.58-42.80.20451530.18221753X-RAY DIFFRACTION98.05
Refinement TLS params.Method: refined / Origin x: 30.8392479715 Å / Origin y: 14.1760496534 Å / Origin z: -16.2592277046 Å
111213212223313233
T0.0449280665699 Å2-0.00771467545771 Å2-0.000373900463501 Å2-0.0883816980169 Å2-0.0053492992072 Å2--0.0864027986069 Å2
L1.01721008245 °20.0057792345738 °2-0.211358524609 °2-1.07027548548 °2-0.0705322569532 °2--1.777178765 °2
S0.039680097149 Å °0.0383492068959 Å °-0.0289066032968 Å °-0.0688736055554 Å °-0.0030498650636 Å °-0.0545487639851 Å °0.0301129834166 Å °0.0484185707659 Å °-0.0376823933987 Å °
Refinement TLS groupSelection details: all

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