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- PDB-1ino: RECOMBINANT INORGANIC PYROPHOSPHATASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1ino
TitleRECOMBINANT INORGANIC PYROPHOSPHATASE FROM ESCHERICHIA COLI
ComponentsINORGANIC PYROPHOSPHATASE
KeywordsACID ANHYDRIDE HYDROLASE / METAL BINDING / MN2+ ION / COMPLEX
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.Yu. / Avaeva, S.M. / Harutyunyan, E.H.
CitationJournal: Febs Lett. / Year: 1995
Title: Mg2+ activation of Escherichia coli inorganic pyrophosphatase.
Authors: Avaeva, S.M. / Rodina, E.V. / Kurilova, S.A. / Nazarova, T.I. / Vorobyeva, N.N. / Harutyunyan, E.H. / VYu, Oganessyan
History
DepositionOct 3, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 4, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: INORGANIC PYROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6522
Polymers19,5971
Non-polymers551
Water2,612145
1
A: INORGANIC PYROPHOSPHATASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)117,91412
Polymers117,5846
Non-polymers3306
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 area15280 Å2
ΔGint-136 kcal/mol
Surface area38170 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
Components on special symmetry positions
IDModelComponents
11A-272-

HOH

21A-296-

HOH

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Components

#1: Protein INORGANIC PYROPHOSPHATASE / / PYROPHOSPHATE HYDROLASE


Mass: 19597.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Plasmid: PUC19 / Gene (production host): PYROPHOSPHATASE ESCHERICHIA COLI / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7A9, inorganic diphosphatase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 46.44 %
Crystal grow
*PLUS
Method: unknown

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorDetector: 2DIMENSION-GAS CAMERA/INSTITUTE OF CRYSTALLOGRAPHY,MOSCOW
Date: Oct 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 8948 / % possible obs: 97.4 % / Rmerge(I) obs: 0.08

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.2→12 Å / σ(F): 0 /
RfactorNum. reflection
obs0.16 42300
Displacement parametersBiso mean: 21.66 Å2
Refinement stepCycle: LAST / Resolution: 2.2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 1 145 1527
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0450.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0510.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1151.5
X-RAY DIFFRACTIONp_mcangle_it1.8592.2
X-RAY DIFFRACTIONp_scbond_it1.6822.2
X-RAY DIFFRACTIONp_scangle_it2.372.5
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1760.2
X-RAY DIFFRACTIONp_multtor_nbd0.2280.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1870.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor0.85610
X-RAY DIFFRACTIONp_staggered_tor22.77315
X-RAY DIFFRACTIONp_orthonormal_tor22.78245
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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