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- PDB-1mjw: STRUCTURE OF INORGANIC PYROPHOSPHATASE MUTANT D42N -

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Basic information

Entry
Database: PDB / ID: 1mjw
TitleSTRUCTURE OF INORGANIC PYROPHOSPHATASE MUTANT D42N
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: 1.95 Å
AuthorsOganesyan, V. / Harutyunyan, E.H. / Avaeva, S.M. / Samygina, V.R. / 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 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3854
Polymers39,1932
Non-polymers1922
Water2,846158
1
A: INORGANIC PYROPHOSPHATASE
B: INORGANIC PYROPHOSPHATASE
hetero molecules

A: INORGANIC PYROPHOSPHATASE
B: INORGANIC PYROPHOSPHATASE
hetero molecules

A: INORGANIC PYROPHOSPHATASE
B: INORGANIC PYROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,15412
Polymers117,5786
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
Buried area14120 Å2
ΔGint-189 kcal/mol
Surface area40170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)110.300, 110.300, 154.600
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
11A-202-

HOH

21B-197-

HOH

31B-202-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.504235, -0.862655, 0.039672), (-0.86247, 0.505377, 0.027192), (-0.043507, -0.020505, -0.998843)
Vector: 163.58371, 93.82043, 74.20378)

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Components

#1: Protein INORGANIC PYROPHOSPHATASE / PYROPHOSPHATE HYDROLASE


Mass: 19596.348 Da / Num. of mol.: 2 / Mutation: D42N
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.31 Å3/Da / Density % sol: 40 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Avaeva, S., (1997) FEBS Lett., 410, 502.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTris-HCl1drop
235 %ammonium sulfate1drop
34 mg/mlprotein1drop
40.1 MTris-HCl1reservoir
545 %ammonium sulfate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 25910 / % possible obs: 97.5 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.08
Reflection
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 15 Å / Num. obs: 259100 / Num. measured all: 2581560 / Rmerge(I) obs: 0.057

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Processing

SoftwareName: REFMAC / Classification: refinement
RefinementResolution: 1.95→15 Å / σ(F): 1
Details: ESTIMATED COORD. ERROR 0.25 ANGSTROMS FINAL RMS COORD. SHIFT 0.002 ANGSTROMS
RfactorNum. reflection
Rfree0.266 -
Rwork0.191 -
obs-258156
Displacement parametersBiso mean: 34.25 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2762 0 10 158 2930
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.674
X-RAY DIFFRACTIONp_mcangle_it2.526
X-RAY DIFFRACTIONp_scbond_it3.296
X-RAY DIFFRACTIONp_scangle_it4.696
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1420.15
X-RAY DIFFRACTIONp_singtor_nbd0.1880.3
X-RAY DIFFRACTIONp_multtor_nbd0.2570.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1550.2
X-RAY DIFFRACTIONp_planar_tor8.27
X-RAY DIFFRACTIONp_staggered_tor21.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.120
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Num. reflection obs: 259100 / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS

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