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- PDB-4z73: Crystal structure of inorganic pyrophosphatase from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 4z73
TitleCrystal structure of inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with a phosphate ion and an inorganic pyrophosphate
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / INORGANIC PYROPHOSPHATASE / TUBERCULOSIS / DRUG TARGET
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 / PYROPHOSPHATE 2- / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 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 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / 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_oper_list.symmetry_operation / _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
D: Inorganic pyrophosphatase
F: Inorganic pyrophosphatase
G: Inorganic pyrophosphatase
E: Inorganic pyrophosphatase
H: Inorganic pyrophosphatase
I: Inorganic pyrophosphatase
J: Inorganic pyrophosphatase
K: Inorganic pyrophosphatase
L: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,32451
Polymers233,45812
Non-polymers2,86639
Water1,946108
1
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
C: Inorganic pyrophosphatase
D: Inorganic pyrophosphatase
F: Inorganic pyrophosphatase
E: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,09425
Polymers116,7296
Non-polymers1,36519
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15910 Å2
ΔGint-155 kcal/mol
Surface area38260 Å2
MethodPISA
2
G: Inorganic pyrophosphatase
H: Inorganic pyrophosphatase
I: Inorganic pyrophosphatase
J: Inorganic pyrophosphatase
K: Inorganic pyrophosphatase
L: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,23026
Polymers116,7296
Non-polymers1,50120
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16130 Å2
ΔGint-154 kcal/mol
Surface area38000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.620, 105.112, 254.729
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 19454.867 Da / Num. of mol.: 12
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) / Strain (production host): BL21(DE3) / References: UniProt: P9WI55, inorganic diphosphatase
#2: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2O7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.45 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: reservoir solution: 1.57 M NaKHPO4, 100 mM HEPES pH 7.75 and 2 mM MnCl2

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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: 3.3→50 Å / Num. obs: 35382 / % possible obs: 100 % / Redundancy: 6.9 % / Net I/σ(I): 14.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.3→35 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.859 / Cross valid method: THROUGHOUT / ESU R Free: 0.595 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26048 1772 5 %RANDOM
Rwork0.21849 ---
obs0.22057 33600 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.963 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2--0.18 Å20 Å2
3---0.07 Å2
Refinement stepCycle: 1 / Resolution: 3.3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15346 0 99 108 15553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01915827
X-RAY DIFFRACTIONr_bond_other_d00.0214636
X-RAY DIFFRACTIONr_angle_refined_deg0.8321.96421528
X-RAY DIFFRACTIONr_angle_other_deg3.569333738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.73251909
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.47423.908829
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.526152473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.93215120
X-RAY DIFFRACTIONr_chiral_restr0.0510.22245
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02117965
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023605
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_it0.6686.4447672
X-RAY DIFFRACTIONr_mcbond_other0.6686.4447671
X-RAY DIFFRACTIONr_mcangle_it1.2579.6629569
X-RAY DIFFRACTIONr_mcangle_other1.2579.6639570
X-RAY DIFFRACTIONr_scbond_it0.3256.4488155
X-RAY DIFFRACTIONr_scbond_other0.3236.4428128
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.689.63411917
X-RAY DIFFRACTIONr_long_range_B_refined2.69250.416766
X-RAY DIFFRACTIONr_long_range_B_other2.61150.38716757
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 129 -
Rwork0.287 2407 -
obs--99.65 %

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