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- PDB-4z70: Crystal structure of inorganic pyrophosphatase from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 4z70
TitleCrystal structure of inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with Ca 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
Inorganic pyrophosphatase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPratt, A.C. / Biswas, T. / 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 1.3Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
C: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4856
Polymers58,3653
Non-polymers1203
Water8,827490
1
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
C: Inorganic pyrophosphatase
hetero molecules

A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
C: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,97012
Polymers116,7296
Non-polymers2406
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area12950 Å2
ΔGint-121 kcal/mol
Surface area38820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.118, 102.118, 80.426
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-395-

HOH

21B-444-

HOH

DetailsHexamer confirmed by size-exclusion chromatography and homology to characterized hexamers

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Components

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


Mass: 19454.867 Da / Num. of mol.: 3
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-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: GROWN IN 9% PEG 4,000, 100 MM HEPES PH 7.0 AND 100 MM CACL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.95→32 Å / Num. obs: 33886 / % possible obs: 100 % / Redundancy: 12.4 % / Net I/σ(I): 44.2

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JQQ

4jqq
PDB Unreleased entry


Resolution: 1.95→31.59 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.083 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1788 5 %RANDOM
Rwork0.206 ---
obs0.209 33886 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.85 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→31.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3854 0 3 490 4347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193964
X-RAY DIFFRACTIONr_bond_other_d0.0010.023673
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9575391
X-RAY DIFFRACTIONr_angle_other_deg1.92738468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9475480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.48123.876209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42815620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6971530
X-RAY DIFFRACTIONr_chiral_restr0.0880.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214521
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02911
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 134 -
Rwork0.252 2518 -
obs--100 %

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