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- PDB-1ygz: Crystal Structure of Inorganic Pyrophosphatase from Helicobacter ... -

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Basic information

Entry
Database: PDB / ID: 1ygz
TitleCrystal Structure of Inorganic Pyrophosphatase from Helicobacter pylori
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / 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 speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsWu, C.A. / Lokanath, N.K. / Kim, D.Y. / Park, H.J. / Hwang, H.Y. / Kim, S.T. / Suh, S.W. / Kim, K.K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of inorganic pyrophosphatase from Helicobacter pylori.
Authors: Wu, C.A. / Lokanath, N.K. / Kim, D.Y. / Park, H.J. / Hwang, H.Y. / Kim, S.T. / Suh, S.W. / Kim, K.K.
History
DepositionJan 6, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
C: Inorganic pyrophosphatase
D: Inorganic pyrophosphatase
E: Inorganic pyrophosphatase
F: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)116,9136
Polymers116,9136
Non-polymers00
Water8,035446
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Inorganic pyrophosphatase
F: Inorganic pyrophosphatase

E: Inorganic pyrophosphatase
F: Inorganic pyrophosphatase

E: Inorganic pyrophosphatase
F: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)116,9136
Polymers116,9136
Non-polymers00
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
Buried area14360 Å2
ΔGint-78 kcal/mol
Surface area37700 Å2
MethodPISA, PQS
3
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)116,9136
Polymers116,9136
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
MethodPQS
4
C: Inorganic pyrophosphatase
D: Inorganic pyrophosphatase

C: Inorganic pyrophosphatase
D: Inorganic pyrophosphatase

C: Inorganic pyrophosphatase
D: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)116,9136
Polymers116,9136
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
MethodPQS
Unit cell
Length a, b, c (Å)115.055, 115.055, 73.782
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

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


Mass: 19485.520 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P56153, inorganic diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8
Details: MPD, imidazole, magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 0.9797, 0.9799, 0.9740
DetectorType: MACSCIENCE / Detector: IMAGE PLATE
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97991
30.9741
ReflectionResolution: 2.6→30 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.5
Reflection shellResolution: 2.6→2.69 Å / % possible obs: 88.1 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.8 / % possible all: 88.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.6→20 Å / Cross valid method: THROUGHTOUT / σ(F): 0
Details: THIS IS A TWINNED STRUCTURE. THE TWINNING OPERATOR IS (H,K,L) -> (H,-H-K,-L) AND THE TWINNING FRACTION IS 0.5. THE R-FACTOR IS 0.203 AND THE R-FREE IS 0.262 WHEN THIS TWINNING OPERATOR IS USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 3117 9.3 %RANDOM
Rwork0.206 ---
all-33539 --
obs-33036 98.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.054 Å2-1.797 Å20 Å2
2--2.054 Å20 Å2
3----4.108 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8106 0 0 446 8552
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it4.923
X-RAY DIFFRACTIONc_mcangle_it7.11
X-RAY DIFFRACTIONc_scbond_it7.064
X-RAY DIFFRACTIONc_scangle_it9.049
LS refinement shellResolution: 2.6→2.69 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.2748 3053 -
Rfree-260 7.84 %
obs--92.04 %

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