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- PDB-1mjx: STRUCTURE OF INORGANIC PYROPHOSPHATASE MUTANT D65N -

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Basic information

Entry
Database: PDB / ID: 1mjx
TitleSTRUCTURE OF INORGANIC PYROPHOSPHATASE MUTANT D65N
ComponentsINORGANIC PYROPHOSPHATASE
KeywordsHYDROLASE / ACID ANHYDRIDE HYDROLASE / MUTATION
Function / homology
Function and homology information


triphosphatase activity / ec:3.6.1.1: / inorganic diphosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / zinc ion binding / membrane / cytosol
Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase / Inorganic pyrophosphatase signature.
Inorganic pyrophosphatase
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.15 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 8, 1997 / Release: Dec 3, 1997
RevisionDateData content typeGroupProviderType
1.0Dec 3, 1997Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance

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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
Water3,081171
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_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area14230 Å2
ΔGint-187 kcal/mol
Surface area40060 Å2
MethodPISA, PQS
Unit cell
γ
α
β
Length a, b, c (Å)110.200, 110.200, 155.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.471479, -0.878501, -0.077089), (-0.879794, 0.47457, -0.027308), (0.060574, 0.054948, -0.99665)
Vector: 63.38308, 35.65392, 133.19885)

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Components

#1: Protein/peptide INORGANIC PYROPHOSPHATASE / / PYROPHOSPHATE HYDROLASE


Mass: 19596.350 Da / Num. of mol.: 2 / Mutation: D65N
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, EC: 3.6.1.1
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O / Water

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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

Crystal-ID: 1

IDConc.Common nameSol-ID
10.1 MTris-HCldrop
235 %ammonium sulfatedrop
34 mg/mlproteindrop
40.1 MTris-HClreservoir
545 %ammonium sulfatereservoir

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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: 19966 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.116
Reflection
*PLUS
Highest resolution: 2.15 Å / Num. measured all: 264155

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Processing

SoftwareName: REFMAC / Classification: refinement
RefinementResolution: 2.15→15 Å / σ(F): 1
Details: ESTIMATED COORD. ERROR 0.30 ANGSTROMS FINAL RMS COORD. SHIFT 0.002 ANGSTROMS
RfactorNum. reflection
Rfree0.263 -
Rwork0.19 -
Obs-264155
Displacement parametersBiso mean: 34.21 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.15→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2762 0 10 171 2943
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal target
p_bond_d0.0140.02
p_angle_d0.0370.04
p_angle_deg
p_planar_d0.0380.05
p_hb_or_metal_coord
p_mcbond_it1.464
p_mcangle_it2.316
p_scbond_it2.86
p_scangle_it3.996
p_plane_restr
p_chiral_restr0.1320.15
p_singtor_nbd0.1860.3
p_multtor_nbd0.2510.3
p_xhyhbond_nbd
p_xyhbond_nbd0.170.3
p_planar_tor9.17
p_staggered_tor21.715
p_orthonormal_tor
p_transverse_tor21.520
p_special_tor

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