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- PDB-2au6: Crystal structure of catalytic intermediate of inorganic pyrophos... -

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Basic information

Entry
Database: PDB / ID: 2au6
TitleCrystal structure of catalytic intermediate of inorganic pyrophosphatase
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / intermediate / inorganic pyrophosphatase
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
FLUORIDE ION / : / PHOSPHATE ION / PYROPHOSPHATE 2- / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSamygina, V.R. / Popov, A.N. / Avaeva, S.M. / Bartunik, H.D.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Reversible inhibition of Escherichia coli inorganic pyrophosphatase by fluoride: trapped catalytic intermediates in cryo-crystallographic studies
Authors: Samygina, V.R. / Moiseev, V.M. / Rodina, E.V. / Vorobyeva, N.N. / Popov, A.N. / Kurilova, S.A. / Nazarova, T.I. / Avaeva, S.M. / Bartunik, H.D.
History
DepositionAug 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,30214
Polymers19,5851
Non-polymers71713
Water5,206289
1
A: Inorganic pyrophosphatase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)121,81384
Polymers117,5126
Non-polymers4,30278
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_676x-y+1,-y+2,-z+11
crystal symmetry operation6_766-x+2,-x+y+1,-z+11
Buried area25980 Å2
ΔGint-632 kcal/mol
Surface area35550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)110.805, 110.805, 73.576
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-205-

MN

21A-511-

HOH

31A-555-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Inorganic pyrophosphatase / Pyrophosphate phospho- hydrolase / PPase


Mass: 19585.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0A7A9, inorganic diphosphatase

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Non-polymers , 7 types, 302 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#7: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsPO4 AND POP ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.
Sequence detailsTHERE IS THR IN THE POSITION 85 ACCORDING TO: OGANESSYAN V.YU., KURILOVA S.A., VOROBEVA N.N., ...THERE IS THR IN THE POSITION 85 ACCORDING TO: OGANESSYAN V.YU., KURILOVA S.A., VOROBEVA N.N., NAZAROVA T.I., POPOV A.N., LEBEDEV A.A., AVAEVA S.M., HARUTYUNYAN E.H.(1994) FEBS LETT., 348, P301-304. ANALYSIS OF THE DENSITY MAP SHOWS THAT RESIDUE IN THIS POSITION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growpH: 5 / Details: pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 25, 2003 / Details: DOUBLE FOCUSSING X-RAY OPTICS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. all: 56152 / Num. obs: 56152 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 16.1
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.54 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→10 Å / Num. parameters: 16115 / Num. restraintsaints: 20688 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1568 2674 5 %RANDOM
Rwork0.1252 ---
obs0.1252 51086 94.8 %-
all-51086 --
Refine analyzeNum. disordered residues: 33 / Occupancy sum hydrogen: 1310.93 / Occupancy sum non hydrogen: 1604.36
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 0 25 289 1694
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.039
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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