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- PDB-1ipw: INORGANIC PYROPHOSPHATASE FROM ESCHERICHIA COLI WITH THREE MAGNES... -

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Basic information

Entry
Database: PDB / ID: 1ipw
TitleINORGANIC PYROPHOSPHATASE FROM ESCHERICHIA COLI WITH THREE MAGNESIUM IONS
ComponentsSOLUBLE INORGANIC PYROPHOSPHATASE
KeywordsHYDROLASE / SOLUBLE INORGANIC PYROPHOSPHATASE / MAGNESIUM
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: 2.3 Å
AuthorsKankare, J.A. / Goldman, A.
Citation
Journal: Biochemistry / Year: 1996
Title: Crystallographic identification of metal-binding sites in Escherichia coli inorganic pyrophosphatase.
Authors: Kankare, J. / Salminen, T. / Lahti, R. / Cooperman, B.S. / Baykov, A.A. / Goldman, A.
#1: Journal: To be Published
Title: Structure of Escherichia Coli Inorganic Pyrophosphatase at 2.2 Angstroms Resolution
Authors: Kankare, J. / Salminen, T. / Lahti, R. / Cooperman, B.S. / Baykov, A.A. / Goldman, A.
#2: 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.
#3: 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. / Glumoff, T. / Cooperman, B.S. / Lahti, R. / Goldman, A.
#4: Journal: Protein Eng. / Year: 1994
Title: Erratum. The Structure of E.Coli Soluble Inorganic Pyrophosphatase at 2.7 A Resolution
Authors: Kankare, J. / Neal, G.S. / Salminen, T. / Glumoff, T. / Cooperman, B.S. / Lahti, R. / Goldman, A.
History
DepositionMar 4, 1996Processing site: BNL
Revision 1.0Aug 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 / _struct_conn.ptnr2_label_seq_id / _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: SOLUBLE INORGANIC PYROPHOSPHATASE
B: SOLUBLE INORGANIC PYROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2685
Polymers39,1952
Non-polymers733
Water2,000111
1
A: SOLUBLE INORGANIC PYROPHOSPHATASE
B: SOLUBLE INORGANIC PYROPHOSPHATASE
hetero molecules

A: SOLUBLE INORGANIC PYROPHOSPHATASE
B: SOLUBLE INORGANIC PYROPHOSPHATASE
hetero molecules

A: SOLUBLE INORGANIC PYROPHOSPHATASE
B: SOLUBLE INORGANIC PYROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,80315
Polymers117,5846
Non-polymers2199
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 area13640 Å2
ΔGint-161 kcal/mol
Surface area37650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)109.400, 109.400, 154.300
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: (-0.504066, 0.863638, 0.006824), (0.863651, 0.503996, 0.009751), (0.004982, 0.010809, -0.999929)
Vector: -0.22358, -0.05337, 69.57375)

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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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal grow
*PLUS
pH: 8 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.8 Msodium citrate11
2100 mMHEPES11

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Data collection

Diffraction sourceSource: SEALED TUBE / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 13745 / % possible obs: 79.7 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.048
Reflection
*PLUS
Highest resolution: 2.3 Å
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / % possible obs: 67.9 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.3→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.239 -
Rwork0.171 -
obs0.171 13745
Displacement parametersBiso mean: 24.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 3 111 2809
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
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 / Version: 3.1 / 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_deg24.4

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