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- PDB-2prd: CRYSTAL STRUCTURE OF INORGANIC PYROPHOSPHATASE FROM THERMUS THERM... -

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Basic information

Entry
Database: PDB / ID: 2prd
TitleCRYSTAL STRUCTURE OF INORGANIC PYROPHOSPHATASE FROM THERMUS THERMOPHILUS
ComponentsPYROPHOSPHATE PHOSPHOHYDROLASE
KeywordsHYDROLASE
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 pyrophosphatase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsTeplyakov, A.
Citation
Journal: Protein Sci. / Year: 1994
Title: Crystal structure of inorganic pyrophosphatase from Thermus thermophilus.
Authors: Teplyakov, A. / Obmolova, G. / Wilson, K.S. / Ishii, K. / Kaji, H. / Samejima, T. / Kuranova, I.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Purification, Crystallization and Preliminary X-Ray Analysis of Inorganic Pyrophosphatase from Thermus Thermophilus
Authors: Obmolova, G. / Kuranova, I. / Teplyakov, A.
History
DepositionDec 21, 1993Processing site: BNL
Revision 1.0Oct 28, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: PYROPHOSPHATE PHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2062
Polymers19,1101
Non-polymers961
Water1,62190
1
A: PYROPHOSPHATE PHOSPHOHYDROLASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)115,23512
Polymers114,6596
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area16150 Å2
ΔGint-166 kcal/mol
Surface area36820 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)110.300, 110.300, 82.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Atom site foot note1: CIS PROLINE - PRO 13
Components on special symmetry positions
IDModelComponents
11A-177-

HOH

21A-226-

HOH

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Components

#1: Protein PYROPHOSPHATE PHOSPHOHYDROLASE


Mass: 19109.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P38576, inorganic diphosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
220 mMTris-HCl1drop
347 %ammonium sulfate1drop
43 %MPD1drop
52 mM1dropMgSO4

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Data collection

ReflectionNum. obs: 11673 / % possible obs: 89.1 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 2 Å / % possible obs: 90 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→10 Å / σ(F): 0 /
RfactorNum. reflection% reflection
obs0.153 11553 89.1 %
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1347 0 5 90 1442
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0360.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it43
X-RAY DIFFRACTIONp_mcangle_it5.55
X-RAY DIFFRACTIONp_scbond_it6.34
X-RAY DIFFRACTIONp_scangle_it8.66
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.1620.15
X-RAY DIFFRACTIONp_singtor_nbd0.1330.3
X-RAY DIFFRACTIONp_multtor_nbd0.1890.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.33
X-RAY DIFFRACTIONp_staggered_tor18.115
X-RAY DIFFRACTIONp_orthonormal_tor21.520
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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