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- PDB-7epo: Ketosteroid Isomerase KSI with 5-nitrobenzoxazole (5NBI) -

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Basic information

Entry
Database: PDB / ID: 7epo
TitleKetosteroid Isomerase KSI with 5-nitrobenzoxazole (5NBI)
ComponentsSnoaL-like domain-containing protein
KeywordsISOMERASE / Kemp elimination / MsKSI / Mycobacterium smegmatis / Crystal structure.
Function / homologySnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / 5-nitro-1,2-benzoxazole / SnoaL-like domain-containing protein
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5582
Polymers16,3941
Non-polymers1641
Water54030
1
A: SnoaL-like domain-containing protein
hetero molecules

A: SnoaL-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1174
Polymers32,7892
Non-polymers3282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2000 Å2
ΔGint-14 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.636, 59.636, 69.499
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein SnoaL-like domain-containing protein / Ketosteroid Isomerase


Mass: 16394.328 Da / Num. of mol.: 1
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: Chemical ChemComp-H5J / 5-nitro-1,2-benzoxazole


Mass: 164.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H4N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.2 M Sodium acetate trihydrate, 0.1 M Tris, pH 8.5, 30% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 6258 / % possible obs: 99.9 % / Redundancy: 18.4 % / Biso Wilson estimate: 70.38 Å2 / Rpim(I) all: 0.019 / Net I/σ(I): 39.77
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 15 % / Mean I/σ(I) obs: 1.29 / Num. unique obs: 312 / Rpim(I) all: 0.424 / % possible all: 100

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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: 7EPN

7epn


Resolution: 2.35→24.21 Å / SU ML: 0.4253 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.7489
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2574 619 9.94 %
Rwork0.1925 5609 -
obs0.1987 6228 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.95 Å2
Refinement stepCycle: LAST / Resolution: 2.35→24.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1015 0 12 30 1057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711051
X-RAY DIFFRACTIONf_angle_d0.82941430
X-RAY DIFFRACTIONf_chiral_restr0.0551158
X-RAY DIFFRACTIONf_plane_restr0.0065186
X-RAY DIFFRACTIONf_dihedral_angle_d5.9974142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.590.39161510.27921367X-RAY DIFFRACTION99.41
2.59-2.960.37831510.24251383X-RAY DIFFRACTION99.93
2.96-3.730.30711540.21181391X-RAY DIFFRACTION100
3.73-24.210.21071630.17071468X-RAY DIFFRACTION99.63
Refinement TLS params.Method: refined / Origin x: -27.6370394468 Å / Origin y: 4.5944811018 Å / Origin z: 0.85362577942 Å
111213212223313233
T0.561820928635 Å2-0.0803434038021 Å2-0.0202398879943 Å2-0.527279241103 Å20.00243734486251 Å2--0.502138579007 Å2
L4.73398790872 °20.160204299543 °20.33661853449 °2-6.64770752234 °2-2.00817717742 °2--4.58159185385 °2
S-0.185259215873 Å °0.529984477998 Å °-0.018050684598 Å °-0.693018453634 Å °0.139363697121 Å °-0.09521529878 Å °0.0656504923106 Å °-0.071709144945 Å °0.0740981663822 Å °
Refinement TLS groupSelection details: all

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