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- PDB-2eip: INORGANIC PYROPHOSPHATASE -

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Basic information

Entry
Database: PDB / ID: 2eip
TitleINORGANIC PYROPHOSPHATASE
ComponentsSOLUBLE INORGANIC PYROPHOSPHATASE
KeywordsINORGANIC PYROPHOSPHATASE / HYDROLASE / MAGNESIUM / INORGANIC PYROPHOSHATASE
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
AuthorsKankare, J.A. / Salminen, T. / Goldman, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure of Escherichia coli inorganic pyrophosphatase at 2.2 A resolution.
Authors: Kankare, J. / Salminen, T. / Lahti, R. / Cooperman, B.S. / Baykov, A.A. / Goldman, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: New Crystal Forms of Escherichia Coli and Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase
Authors: Heikinheimo, P. / Salminen, T. / Cooperman, B. / Lahti, R. / Goldman, A.
#2: Journal: Protein Eng. / Year: 1994
Title: The Structure of E.Coli Soluble Inorganic Pyrophosphatase at 2.7 A Resolution
Authors: Kankare, J. / Neal, G.S. / Salminen, T. / Glumhoff, T. / Cooperman, B.S. / Lahti, R. / Goldman, A.
History
DepositionJan 10, 1996Processing site: BNL
SupersessionNov 8, 1996ID: 1EIP
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SOLUBLE INORGANIC PYROPHOSPHATASE
B: SOLUBLE INORGANIC PYROPHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)39,1952
Polymers39,1952
Non-polymers00
Water2,540141
1
A: SOLUBLE INORGANIC PYROPHOSPHATASE
B: SOLUBLE INORGANIC PYROPHOSPHATASE

A: SOLUBLE INORGANIC PYROPHOSPHATASE
B: SOLUBLE INORGANIC PYROPHOSPHATASE

A: SOLUBLE INORGANIC PYROPHOSPHATASE
B: SOLUBLE INORGANIC PYROPHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)117,5846
Polymers117,5846
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area12780 Å2
ΔGint-108 kcal/mol
Surface area39210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)110.200, 110.200, 156.000
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: (-0.51, 0.86, 0.005), (0.86, 0.51, 0.003), (0.006, -1)
Vector: -0.267, -0.16, 70.72)
DetailsTHE ACTIVE ENZYME IS A HEXAMER. THE ASYMMETRIC UNIT OF THIS CRYSTAL FORM CONTAINS TWO MONOMERS OF THE ACTIVE HEXAMER. THE WHOLE HEXAMER CAN BE GENERATED BY APPLYING TWICE THE CRYSTALLOGRAPHIC THREE-FOLD ROTATIONS AROUND C-AXIS. THE TWO MONOMERS IN THE ASYMMETRIC UNIT ARE RELATED BY A LOCAL TWO-FOLD OPERATOR PARALLEL TO THE CRYSTALLOGRAPHIC TWO-FOLD.

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Components

#1: Protein SOLUBLE INORGANIC PYROPHOSPHATASE


Mass: 19597.334 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7A9, inorganic diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.32 Å3/Da / Density % sol: 47.07 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
20.1 MTris-HCl1drop
32 mM1dropMnCl2
40.1 MHEPES1reservoir
50.75 Msodium citrate1reservoir
64 mM1reservoirKH2PO4

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 16178 / % possible obs: 86.5 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.082
Reflection
*PLUS
Num. measured all: 140425
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 72 % / Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.2→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.234 -5 %
Rwork0.183 --
obs0.183 15787 86.5 %
Displacement parametersBiso mean: 30.5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2690 0 0 141 2831
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.4
X-RAY DIFFRACTIONx_improper_angle_deg

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