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- PDB-1obw: STRUCTURE OF INORGANIC PYROPHOSPHATASE -

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Basic information

Entry
Database: PDB / ID: 1obw
TitleSTRUCTURE OF INORGANIC PYROPHOSPHATASE
ComponentsINORGANIC PYROPHOSPHATASE
KeywordsHYDROLASE / MAGNESIUM / METAL BINDING
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 / MOLECULAR REPL. / Resolution: 1.9 Å
AuthorsOganessyan, V.Yu. / Harutyunyan, E.H. / Avaeva, S.M. / Oganessyan, N.N. / Mather, T. / Huber, R.
Citation
Journal: Biochemistry / Year: 1997
Title: Crystal structure of holo inorganic pyrophosphatase from Escherichia coli at 1.9 A resolution. Mechanism of hydrolysis.
Authors: Harutyunyan, E.H. / Oganessyan, V.Y. / Oganessyan, N.N. / Avaeva, S.M. / Nazarova, T.I. / Vorobyeva, N.N. / Kurilova, S.A. / 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
DepositionOct 9, 1996Processing site: BNL
Revision 1.0Sep 4, 1997Provider: 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_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.ptnr3_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,92610
Polymers58,7563
Non-polymers1707
Water4,504250
1
A: INORGANIC PYROPHOSPHATASE
B: INORGANIC PYROPHOSPHATASE
C: INORGANIC PYROPHOSPHATASE
hetero molecules

A: INORGANIC PYROPHOSPHATASE
B: INORGANIC PYROPHOSPHATASE
C: INORGANIC PYROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,85220
Polymers117,5126
Non-polymers34014
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area15060 Å2
ΔGint-186 kcal/mol
Surface area39070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)110.300, 110.300, 78.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-176-

MG

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.47705, -0.8749, -0.08355), (0.87743, -0.47956, 0.01185), (-0.05043, -0.06765, 0.99643)3.28619, 63.82998, 1.17431
2given(-0.51375, 0.85661, -0.04777), (-0.85198, -0.51594, -0.08908), (-0.10096, -0.00507, 0.99488)-54.36329, 35.1912, -1.55517

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Components

#1: Protein INORGANIC PYROPHOSPHATASE / / PYROPHOSPHATE HYDROLASE


Mass: 19585.279 Da / Num. of mol.: 3
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.34 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMTris-HCl1drop
225 %1dropNH4Cl
30.2 Mprotein1drop
4250 mM1dropMgCl2
5100 mMTris-HCl1reservoir
658 %1reservoirNH4Cl
7250 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 41190 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 4 / % possible all: 99.2
Reflection
*PLUS
% possible obs: 99.6 % / Num. measured all: 360600 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.241

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPL.
Starting model: REFINED STRUCTURE OF APO-FORM OF THIS ENZYME AT 2.2A. (HARUTYUNYAN ET AL., 1996, CRYSTALLOGRAPHIA(RUS), V.14 ,PP84-96.

Resolution: 1.9→15 Å / σ(F): 1
Details: ESTIMATED COORD. ERROR 0.26 ANGSTROMS FINAL RMS COORD. SHIFT 0.002 ANGSTROMS
RfactorNum. reflection
Rfree0.22 -
Rwork0.176 -
obs-360600
Displacement parametersBiso mean: 34 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4137 0 7 250 4394
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.9274
X-RAY DIFFRACTIONp_mcangle_it4.6646
X-RAY DIFFRACTIONp_scbond_it5.1666
X-RAY DIFFRACTIONp_scangle_it5.376
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1420.15
X-RAY DIFFRACTIONp_singtor_nbd0.1730.3
X-RAY DIFFRACTIONp_multtor_nbd0.2550.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1870.2
X-RAY DIFFRACTIONp_planar_tor7
X-RAY DIFFRACTIONp_staggered_tor19.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.520
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.176 / Rfactor Rfree: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS

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