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- PDB-4z72: Crystal structure of inorganic pyrophosphatase from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 4z72
TitleCrystal structure of inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with two phosphate ions
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / PYROPHOSPHATASE / PHOSPHATASE / INORGANIC PYROPHOSPHATE
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / host cell surface / magnesium ion binding / extracellular region / plasma membrane / cytosol
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
PHOSPHATE ION / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.352 Å
AuthorsPratt, A.C. / Biswas, T. / Barnard-Britson, S. / Tsodikov, O.V.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structural and computational dissection of the catalytic mechanism of the inorganic pyrophosphatase from Mycobacterium tuberculosis.
Authors: Pratt, A.C. / Dewage, S.W. / Pang, A.H. / Biswas, T. / Barnard-Britson, S. / Cisneros, G.A. / Tsodikov, O.V.
History
DepositionApr 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7656
Polymers19,4551
Non-polymers3105
Water54030
1
A: Inorganic pyrophosphatase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)118,59036
Polymers116,7296
Non-polymers1,86130
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_535-y,x-y-2,z1
crystal symmetry operation3_755-x+y+2,-x,z1
crystal symmetry operation10_557-y,-x,-z+5/21
crystal symmetry operation11_757-x+y+2,y,-z+5/21
crystal symmetry operation12_537x,x-y-2,-z+5/21
Buried area17160 Å2
ΔGint-323 kcal/mol
Surface area35840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.319, 99.319, 96.732
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

21A-325-

HOH

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Components

#1: Protein Inorganic pyrophosphatase / Pyrophosphate phospho-hydrolase / PPase


Mass: 19454.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: ppa, Rv3628, MTCY15C10.24 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WI55, inorganic diphosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.54 Å3/Da / Density % sol: 65.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: reservoir: 1.6 M KH2PO4, 100 mM HEPES pH 7.75 and 2 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 11538 / % possible obs: 99.3 % / Redundancy: 7.1 % / Net I/σ(I): 18.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z71

4z71


Resolution: 2.352→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.556 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24094 606 5 %RANDOM
Rwork0.20806 ---
obs0.20965 11538 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.437 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20.26 Å20 Å2
2--0.53 Å20 Å2
3----1.71 Å2
Refinement stepCycle: 1 / Resolution: 2.352→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1278 0 13 30 1321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191330
X-RAY DIFFRACTIONr_bond_other_d0.0050.021219
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9661797
X-RAY DIFFRACTIONr_angle_other_deg0.72832810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8985159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.68323.91369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01415206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2231510
X-RAY DIFFRACTIONr_chiral_restr0.0710.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211496
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02300
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0383.866647
X-RAY DIFFRACTIONr_mcbond_other1.6543.842640
X-RAY DIFFRACTIONr_mcangle_it2.6075.758797
X-RAY DIFFRACTIONr_mcangle_other2.6065.764798
X-RAY DIFFRACTIONr_scbond_it2.0974.068682
X-RAY DIFFRACTIONr_scbond_other2.0884.055675
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3595.978989
X-RAY DIFFRACTIONr_long_range_B_refined5.38330.9051457
X-RAY DIFFRACTIONr_long_range_B_other5.19630.7661442
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.352→2.413 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 50 -
Rwork0.298 809 -
obs--99.08 %

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