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- PDB-1igp: X-RAY CRYSTALLOGRAPHIC STUDIES OF RECOMBINANT INORGANIC PYROPHOSP... -

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Basic information

Entry
Database: PDB / ID: 1igp
TitleX-RAY CRYSTALLOGRAPHIC STUDIES OF RECOMBINANT INORGANIC PYROPHOSPHATASE FROM ESCHERICHIA COLI
ComponentsINORGANIC PYROPHOSPHATASE
KeywordsACID 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
AuthorsOganessyan, V.Yu. / Avaeva, S.M. / Harutyunyan, E.H.
Citation
Journal: FEBS Lett. / Year: 1994
Title: X-ray crystallographic studies of recombinant inorganic pyrophosphatase from Escherichia coli.
Authors: Oganessyan, V.Y.u. / Kurilova, S.A. / Vorobyeva, N.N. / Nazarova, T.I. / Popov, A.N. / Lebedev, A.A. / Avaeva, S.M. / Harutyunyan, E.H.
#1: Journal: Bioorg.Khim. / Year: 1991
Title: Crystal Structure of Ferric Complex of the Yellow Lupin Leghemoglobin with Isoquinoline at 1.8 Angstroms Resolution
Authors: Safonova, T.N. / Teplyakov, A.V. / Obmolova, G.V. / Popov, A.N. / Kuranova, I.P. / Harutyunyan, E.G.
#2: Journal: Bioorg.Khim. / Year: 1988
Title: X-Ray Structure of Ferrous Complexes of the Yellow Lupin Leghemoglobin with Co and No at 1.8 Angstroms Resolution
Authors: Obmolova, G.V. / Safonova, T.N. / Teplyakov, A.V. / Popov, A.N. / Kuranova, I.P. / Harutyunyan, E.G. / Vainshtein, B.K.
#3: Journal: J.Appl.Math.Phys. / Year: 1988
Title: Cloning and Characterization of the Gene Encoding Inorganic Pyrophosphatase of Escherichia Coli K 12
Authors: Lahti, R. / Pitkaranta, T. / Valve, E. / Ilta, I. / Kukko-Kalske, E. / Heinonen, J.
History
DepositionAug 1, 1994Processing site: BNL
Revision 1.0Dec 20, 1994Provider: 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 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INORGANIC PYROPHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)19,5851
Polymers19,5851
Non-polymers00
Water2,342130
1
A: INORGANIC PYROPHOSPHATASE
x 6


Theoretical massNumber of molelcules
Total (without water)117,5126
Polymers117,5126
Non-polymers00
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 area13620 Å2
ΔGint-100 kcal/mol
Surface area39650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)110.400, 110.400, 76.800
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 12

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Components

#1: Protein INORGANIC PYROPHOSPHATASE


Mass: 19585.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A7A9, inorganic diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.3 Å3/Da / Density % sol: 46.47 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 9116 / % possible obs: 87 % / Observed criterion σ(I): 3 / Num. measured all: 26800 / Rmerge(I) obs: 0.063

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.22 / Highest resolution: 2.2 Å
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1379 0 0 130 1509
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.074

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