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- PDB-1mjy: STRUCTURE OF INORGANIC PYROPHOSPHATASE MUTANT D70N -

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Basic information

Entry
Database: PDB / ID: 1mjy
TitleSTRUCTURE OF INORGANIC PYROPHOSPHATASE MUTANT D70N
ComponentsINORGANIC PYROPHOSPHATASE
KeywordsHYDROLASE / ACID ANHYDRIDE HYDROLASE / MUTATION
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: 2.1 Å
AuthorsOganesyan, V. / Harutyunyan, E.H. / Avaeva, S.M. / Huber, R.
Citation
Journal: Biochemistry Mosc. / Year: 1998
Title: Three-dimensional structures of mutant forms of E. coli inorganic pyrophosphatase with Asp-->Asn single substitution in positions 42, 65, 70, and 97.
Authors: Avaeva, S.M. / Rodina, E.V. / Vorobyeva, N.N. / Kurilova, S.A. / Nazarova, T.I. / Sklyankina, V.A. / Oganessyan, V.Y. / Samygina, V.R. / Harutyunyan, E.H.
#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
DepositionFeb 8, 1997Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Nov 3, 2021Group: Database references / Other
Category: 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
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INORGANIC PYROPHOSPHATASE
B: INORGANIC PYROPHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)39,1692
Polymers39,1692
Non-polymers00
Water3,873215
1
A: INORGANIC PYROPHOSPHATASE
B: INORGANIC PYROPHOSPHATASE

A: INORGANIC PYROPHOSPHATASE
B: INORGANIC PYROPHOSPHATASE

A: INORGANIC PYROPHOSPHATASE
B: INORGANIC PYROPHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)117,5066
Polymers117,5066
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
Buried area13870 Å2
ΔGint-88 kcal/mol
Surface area38650 Å2
MethodPISA
2
A: INORGANIC PYROPHOSPHATASE
B: INORGANIC PYROPHOSPHATASE
x 6


Theoretical massNumber of molelcules
Total (without water)235,01212
Polymers235,01212
Non-polymers00
Water21612
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
MethodPQS
Unit cell
Length a, b, c (Å)104.483, 104.483, 172.953
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-280-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.484889, -0.873457, -0.044225), (-0.874425, 0.485124, 0.005979), (0.016232, 0.04157, -0.999004)
Vector: 57.14372, 30.63597, 123.31921)

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Components

#1: Protein INORGANIC PYROPHOSPHATASE / / PYROPHOSPHATE HYDROLASE


Mass: 19584.295 Da / Num. of mol.: 2 / Mutation: D70N
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 40 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Mpotassium phosphate11
21 %PEG200011
3ammonium chloride12

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 21273 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.085
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. all: 241153

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Processing

SoftwareName: REFMAC / Classification: refinement
RefinementResolution: 2.1→15 Å / σ(F): 1
Details: ESTIMATED COORD. ERROR 0.30 ANGSTROMS FINAL RMS COORD. SHIFT 0.002 ANGSTROMS
RfactorNum. reflection
Rfree0.231 -
Rwork0.164 -
obs-241153
Displacement parametersBiso mean: 30.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2760 0 0 215 2975
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0370.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.024
X-RAY DIFFRACTIONp_mcangle_it2.955
X-RAY DIFFRACTIONp_scbond_it5.716
X-RAY DIFFRACTIONp_scangle_it7.756
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1380.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.2570.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1570.3
X-RAY DIFFRACTIONp_planar_tor9.17
X-RAY DIFFRACTIONp_staggered_tor20.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor20.620
X-RAY DIFFRACTIONp_special_tor

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