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- PDB-4if2: Structure of the phosphotriesterase from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 4if2
TitleStructure of the phosphotriesterase from Mycobacterium tuberculosis
ComponentsPhosphotriesterase homology protein
KeywordsHYDROLASE / double metal ions binding protein / enzymatic antidotes for organophosphates
Function / homology
Function and homology information


catabolic process / hydrolase activity, acting on ester bonds / zinc ion binding
Similarity search - Function
Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Phosphotriesterase homology protein / Phosphotriesterase homology protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsZhang, L. / Li, X. / Rao, Z.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: The crystal structure of the phosphotriesterase from M. tuberculosis, another member of phosphotriesterase-like lactonase family.
Authors: Zhang, L. / Wang, H. / Liu, X. / Zhou, W. / Rao, Z.
History
DepositionDec 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_conn / struct_site
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphotriesterase homology protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1043
Polymers35,9731
Non-polymers1312
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Phosphotriesterase homology protein
hetero molecules

A: Phosphotriesterase homology protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2076
Polymers71,9462
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area3980 Å2
ΔGint-175 kcal/mol
Surface area22870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.032, 149.596, 74.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Phosphotriesterase homology protein


Mass: 35972.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: php, Rv0230c, MT0240, MTCY08D5.26c / Production host: Escherichia coli (E. coli) / References: UniProt: P96413, UniProt: P9WHN9*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.63 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7
Details: 0.1M HEPES pH 7.0, 55% MPD, 150mM NaSCN, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.005 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. all: 128223 / Num. obs: 128164 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→35.362 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.44 / σ(F): 1.9 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 906 5.1 %RANDOM
Rwork0.1786 ---
all0.1867 17750 --
obs0.1811 17750 99.13 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.542 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 87.13 Å2 / Biso mean: 36.8741 Å2 / Biso min: 15.19 Å2
Baniso -1Baniso -2Baniso -3
1--11.2145 Å20 Å20 Å2
2--0.3753 Å2-0 Å2
3---10.8391 Å2
Refinement stepCycle: LAST / Resolution: 2.27→35.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2507 0 2 75 2584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082604
X-RAY DIFFRACTIONf_angle_d1.1033545
X-RAY DIFFRACTIONf_dihedral_angle_d14.679954
X-RAY DIFFRACTIONf_chiral_restr0.076395
X-RAY DIFFRACTIONf_plane_restr0.005472
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2701-2.41230.2711570.2133273498
2.4123-2.59850.26381470.1935273599
2.5985-2.85990.25451600.1808278499
2.8599-3.27350.2471390.17172812100
3.2735-4.12320.20441550.15592830100
4.1232-35.36610.2031480.1851294999

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