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- PDB-1jfd: STRUCTURE OF INORGANIC PYROPHOSPHATASE -

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Basic information

Entry
Database: PDB / ID: 1jfd
TitleSTRUCTURE OF INORGANIC PYROPHOSPHATASE
ComponentsINORGANIC PYROPHOSPHATASE
KeywordsHYDROLASE / ACID ANHYDRIDE HYDROLASE
Function / homology
Function and homology information


inorganic triphosphate phosphatase activity / inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / zinc ion binding / 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsOganesyan, V. / Avaeva, S.M. / Huber, R. / Harutyunyan, E.H.
Citation
Journal: FEBS Lett. / Year: 1997
Title: Crystal structure of Escherichia coli inorganic pyrophosphatase complexed with SO4(2-). Ligand-induced molecular asymmetry.
Authors: Avaeva, S. / Kurilova, S. / Nazarova, T. / Rodina, E. / Vorobyeva, N. / Sklyankina, V. / Grigorjeva, O. / Harutyunyan, E. / Oganessyan, V. / Wilson, K. / Dauter, Z. / Huber, R. / Mather, T.
#1: Journal: FEBS Lett. / Year: 1994
Title: X-Ray Crystallographic Studies of Recombinant Inorganic Pyrophosphatase from Escherichia Coli
Authors: Oganessyan, V.Yu. / Kurilova, S.A. / Vorobyeva, N.N. / Nazarova, T.I. / Popov, A.N. / Lebedev, A.A. / Avaeva, S.M. / Harutyunyan, E.H.
History
DepositionMay 31, 1997Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

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Assembly

Deposited unit
A: INORGANIC PYROPHOSPHATASE
B: INORGANIC PYROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3874
Polymers39,1952
Non-polymers1922
Water3,729207
1
A: INORGANIC PYROPHOSPHATASE
B: INORGANIC PYROPHOSPHATASE
hetero molecules

A: INORGANIC PYROPHOSPHATASE
B: INORGANIC PYROPHOSPHATASE
hetero molecules

A: INORGANIC PYROPHOSPHATASE
B: INORGANIC PYROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,16012
Polymers117,5846
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
Buried area14100 Å2
ΔGint-184 kcal/mol
Surface area40030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)110.400, 110.400, 154.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.999803, 0.019396, -0.004307), (0.019341, -0.999737, -0.012348), (-0.004546, 0.012263, -0.999914)
Vector: -1.10135, 128.03801, 121.33388)

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Components

#1: Protein INORGANIC PYROPHOSPHATASE / PYROPHOSPHATE HYDROLASE


Mass: 19597.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Plasmid: PUC19
Gene (production host): PYROPHOSPHATASE FROM ESCHERICHIA COLI
Production host: Escherichia coli (E. coli) / References: UniProt: P0A7A9, inorganic diphosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.31 Å3/Da / Density % sol: 40 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTris-HCl1drop
235 %ammonium sulfate1drop
34 mg/mlprotein1drop
40.1 MTris-HCl1reservoir
545 %ammonium sulfate1reservoir

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Data collection

Diffraction sourceWavelength: 1.09
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Apr 1, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.09 Å / Relative weight: 1
ReflectionNum. obs: 18662 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.077
Reflection
*PLUS
Highest resolution: 2.196 Å / Num. measured all: 153537

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
RefinementResolution: 2.2→15 Å / σ(F): 3
Details: ESTIMATED COORD. ERROR 0.35 ANGSTROMS FINAL RMS COORD. SHIFT 0.002 ANGSTROMS
RfactorNum. reflection
Rfree0.266 -
Rwork0.192 -
obs-153538
Displacement parametersBiso mean: 21.34 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2762 0 10 207 2979
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0370.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.95
X-RAY DIFFRACTIONp_mcangle_it2.316
X-RAY DIFFRACTIONp_scbond_it2.86
X-RAY DIFFRACTIONp_scangle_it3.996
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1430.15
X-RAY DIFFRACTIONp_singtor_nbd0.1810.3
X-RAY DIFFRACTIONp_multtor_nbd0.2480.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.170.3
X-RAY DIFFRACTIONp_planar_tor8.17
X-RAY DIFFRACTIONp_staggered_tor20.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.120
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS

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