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- PDB-5wrt: Crystal structure of type I inorganic pyrophosphatase from Toxopl... -

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Basic information

Entry
Database: PDB / ID: 5wrt
TitleCrystal structure of type I inorganic pyrophosphatase from Toxoplasma gondii.
ComponentsSoluble inorganic pyrophosphatase
KeywordsHYDROLASE / PPi / PPase / novel interface
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Inorganic Pyrophosphatase / Inorganic pyrophosphatase / Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Inorganic diphosphatase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.348 Å
AuthorsJamwal, A. / Yogavel, M. / Sharma, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology, Govt. of India India
CitationJournal: Sci Rep / Year: 2017
Title: Structural and Biochemical Characterization of Apicomplexan Inorganic Pyrophosphatases
Authors: Jamwal, A. / Yogavel, M. / Abdin, M.Z. / Jain, S.K. / Sharma, A.
History
DepositionDec 3, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble inorganic pyrophosphatase
B: Soluble inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6706
Polymers53,5732
Non-polymers974
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-43 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.957, 88.957, 158.665
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-625-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 74 through 75 or (resid 76...
21(chain B and (resid 74 through 98 or (resid 99...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALTYRTYR(chain A and (resid 74 through 75 or (resid 76...AA74 - 751 - 2
12ARGARGARGARG(chain A and (resid 74 through 75 or (resid 76...AA763
13VALVALGLUGLU(chain A and (resid 74 through 75 or (resid 76...AA74 - 3081 - 235
14VALVALGLUGLU(chain A and (resid 74 through 75 or (resid 76...AA74 - 3081 - 235
15VALVALGLUGLU(chain A and (resid 74 through 75 or (resid 76...AA74 - 3081 - 235
16VALVALGLUGLU(chain A and (resid 74 through 75 or (resid 76...AA74 - 3081 - 235
17VALVALGLUGLU(chain A and (resid 74 through 75 or (resid 76...AA74 - 3081 - 235
21VALVALGLUGLU(chain B and (resid 74 through 98 or (resid 99...BB74 - 981 - 25
22ARGARGARGARG(chain B and (resid 74 through 98 or (resid 99...BB9926
23VALVALLEULEU(chain B and (resid 74 through 98 or (resid 99...BB74 - 3051 - 232
24VALVALLEULEU(chain B and (resid 74 through 98 or (resid 99...BB74 - 3051 - 232
25VALVALLEULEU(chain B and (resid 74 through 98 or (resid 99...BB74 - 3051 - 232
26VALVALLEULEU(chain B and (resid 74 through 98 or (resid 99...BB74 - 3051 - 232
27VALVALLEULEU(chain B and (resid 74 through 98 or (resid 99...BB74 - 3051 - 232

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Components

#1: Protein Soluble inorganic pyrophosphatase


Mass: 26786.551 Da / Num. of mol.: 2 / Fragment: UNP residues 74-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: sPP1 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4VUZ3
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 3.39 Å3/Da / Density % sol: 63.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 10% PEG20000, 20 % glycerol, 0.03M glycols, 0.1 M HEPES/MOPS pH7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.348→50 Å / Num. obs: 30191 / % possible obs: 95.6 % / Redundancy: 38 % / CC1/2: 0.93 / Net I/σ(I): 104.2

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575_1496refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.348→43.602 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 1890 6.66 %RANDOM
Rwork0.2041 26507 --
obs0.206 28397 91.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.34 Å2 / Biso mean: 38.1487 Å2 / Biso min: 20.21 Å2
Refinement stepCycle: final / Resolution: 2.348→43.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3729 0 4 226 3959
Biso mean--28.67 37.18 -
Num. residues----467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053827
X-RAY DIFFRACTIONf_angle_d0.9145198
X-RAY DIFFRACTIONf_chiral_restr0.051551
X-RAY DIFFRACTIONf_plane_restr0.005684
X-RAY DIFFRACTIONf_dihedral_angle_d5.8942290
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2184X-RAY DIFFRACTION10.198TORSIONAL
12B2184X-RAY DIFFRACTION10.198TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3479-2.40660.28081000.2751333143364
2.4066-2.47160.29481090.26541544165377
2.4716-2.54440.32151150.26361663177881
2.5444-2.62650.25841220.25711778190088
2.6265-2.72030.28031220.25291853197590
2.7203-2.82920.26891340.23391883201793
2.8292-2.9580.28551400.23151943208394
2.958-3.11390.25161420.22451966210896
3.1139-3.30890.22621470.21472028217598
3.3089-3.56430.2671520.20672042219498
3.5643-3.92280.23441470.18220502197100
3.9228-4.48990.1721480.160120792227100
4.4899-5.65490.1911500.171221222272100
5.6549-43.60980.20581620.190422232385100
Refinement TLS params.Method: refined / Origin x: -23.8851 Å / Origin y: -18.3103 Å / Origin z: -19.0658 Å
111213212223313233
T0.1919 Å2-0.0391 Å2-0.1009 Å2-0.2597 Å20.0557 Å2--0.2432 Å2
L2.8341 °2-0.1711 °2-1.0554 °2-0.5335 °20.084 °2--1.1738 °2
S-0.0969 Å °-0.1074 Å °0.0262 Å °-0.0168 Å °0.12 Å °0.0429 Å °0.0353 Å °-0.1685 Å °-0.0172 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA74 - 308
2X-RAY DIFFRACTION1allB74 - 305
3X-RAY DIFFRACTION1allS2 - 248
4X-RAY DIFFRACTION1allC1
5X-RAY DIFFRACTION1allD1
6X-RAY DIFFRACTION1allE1
7X-RAY DIFFRACTION1allF1

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