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- PDB-5z3r: Crystal Structure of Delta 5-3-Ketosteroid Isomerase from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 5z3r
TitleCrystal Structure of Delta 5-3-Ketosteroid Isomerase from Mycobacterium sp.
ComponentsSteroid delta-isomerase
KeywordsBIOSYNTHETIC PROTEIN / Ketosteroid Isomerase
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / isomerase activity / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Steroid delta-isomerase
Function and homology information
Biological speciesMycobacterium neoaurum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsCheng, X.Y. / Peng, F. / Yang, F. / Huang, Y.Q. / Su, Z.D.
Funding support China, 1items
OrganizationGrant numberCountry
Department of Science and Technology, Hubei Province2016ACA128 China
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2019
Title: Structure-based reconstruction of a Mycobacterium hypothetical protein into an active Delta5-3-ketosteroid isomerase.
Authors: Peng, F. / Cheng, X.Y. / Wang, H. / Song, S. / Chen, T. / Li, X. / He, Y. / Huang, Y.Q. / Liu, S. / Yang, F. / Su, Z.D.
History
DepositionJan 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Category: refln
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 1.3Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Steroid delta-isomerase
D: Steroid delta-isomerase
F: Steroid delta-isomerase
C: Steroid delta-isomerase
G: Steroid delta-isomerase
H: Steroid delta-isomerase
E: Steroid delta-isomerase
B: Steroid delta-isomerase


Theoretical massNumber of molelcules
Total (without water)125,6998
Polymers125,6998
Non-polymers00
Water23413
1
A: Steroid delta-isomerase
G: Steroid delta-isomerase


Theoretical massNumber of molelcules
Total (without water)31,4252
Polymers31,4252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-10 kcal/mol
Surface area11970 Å2
MethodPISA
2
D: Steroid delta-isomerase
H: Steroid delta-isomerase


Theoretical massNumber of molelcules
Total (without water)31,4252
Polymers31,4252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-10 kcal/mol
Surface area11810 Å2
MethodPISA
3
F: Steroid delta-isomerase
B: Steroid delta-isomerase


Theoretical massNumber of molelcules
Total (without water)31,4252
Polymers31,4252
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-10 kcal/mol
Surface area12120 Å2
MethodPISA
4
C: Steroid delta-isomerase
E: Steroid delta-isomerase


Theoretical massNumber of molelcules
Total (without water)31,4252
Polymers31,4252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-10 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.630, 107.840, 301.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Steroid delta-isomerase / / Delta 5-3-Ketosteroid isomerase


Mass: 15712.435 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium neoaurum (bacteria) / Gene: ksi / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: V5XH97
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tri-Sodium acetate pH 4.5, 0.1M Bis-Tris pH 5.5, 21%-29% Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.42→47.815 Å / Num. obs: 59832 / % possible obs: 100 % / Redundancy: 14 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.029 / Net I/σ(I): 1.9
Reflection scaleGroup code: 1
Reflection shellResolution: 2.42→2.49 Å / Rmerge(I) obs: 1.698 / Num. unique obs: 57477 / CC1/2: 0.7 / Rpim(I) all: 0.408

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Processing

Software
NameVersionClassification
HKL-2000data collection
xia2data reduction
Aimlessdata scaling
BUCCANEERmodel building
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A15, 1OH0

2a15

1oh0


Resolution: 2.42→47.81 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.249
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2703 2867 4.8 %RANDOM
Rwork0.2203 ---
obs0.2227 56965 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 142.92 Å2 / Biso mean: 61.934 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--2.18 Å2-0 Å2-0 Å2
2--3.63 Å2-0 Å2
3----1.46 Å2
Refinement stepCycle: final / Resolution: 2.42→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7955 0 0 13 7968
Biso mean---53.73 -
Num. residues----1047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.028131
X-RAY DIFFRACTIONr_bond_other_d00.027344
X-RAY DIFFRACTIONr_angle_refined_deg1.7881.93711119
X-RAY DIFFRACTIONr_angle_other_deg3.934316919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.15551039
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57723.591362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.787151168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3351564
X-RAY DIFFRACTIONr_chiral_restr0.0950.21283
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219225
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021751
X-RAY DIFFRACTIONr_mcbond_it4.9236.1314180
X-RAY DIFFRACTIONr_mcbond_other4.9196.134179
X-RAY DIFFRACTIONr_mcangle_it6.8559.1895211
LS refinement shellResolution: 2.42→2.483 Å
RfactorNum. reflection% reflection
Rfree0.45 214 -
Rwork0.35 4197 -
obs--100 %

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