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- PDB-1i74: STREPTOCOCCUS MUTANS INORGANIC PYROPHOSPHATASE -

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Basic information

Entry
Database: PDB / ID: 1i74
TitleSTREPTOCOCCUS MUTANS INORGANIC PYROPHOSPHATASE
ComponentsPROBABLE MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE
KeywordsHYDROLASE
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / manganese ion binding / cytoplasm
Similarity search - Function
Manganese-dependent inorganic pyrophosphatase, probable / DHHA2 domain / DHHA2 domain / DHHA2 domain superfamily / DHHA2 domain / DHHA2 / inorganic pyrophosphatase (n-terminal core) / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family ...Manganese-dependent inorganic pyrophosphatase, probable / DHHA2 domain / DHHA2 domain / DHHA2 domain superfamily / DHHA2 domain / DHHA2 / inorganic pyrophosphatase (n-terminal core) / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family / DHH phosphoesterase superfamily / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Probable manganese-dependent inorganic pyrophosphatase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsMerckel, M.C. / Fabrichniy, I.P. / Goldman, A. / Lahti, R. / Salminen, A.
CitationJournal: Structure / Year: 2001
Title: Crystal structure of Streptococcus mutans pyrophosphatase: a new fold for an old mechanism.
Authors: Merckel, M.C. / Fabrichniy, I.P. / Salminen, A. / Kalkkinen, N. / Baykov, A.A. / Lahti, R. / Goldman, A.
History
DepositionMar 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 600HETEROGEN The ligand names and their residue numbers in the PDB file are different from what is ...HETEROGEN The ligand names and their residue numbers in the PDB file are different from what is listed in the paper. Their correspondences are as follows: paper PDB file ----- --------- MN A 401 MN A 401 MN A 402 MN A 402 MG A 403 MG 403 SO4 A 404 SO4 404 SO4 A 405 SO4 405 HOH A 406 HOH 406 MN B 401 MN B 401 MN B 402 MN B 402 MG B 403 MG 1403 SO4 B 404 SO4 1404 SO4 B 405 SO4 1405 HOH B 406 HOH 1406

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROBABLE MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE
B: PROBABLE MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,72412
Polymers67,0722
Non-polymers65310
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-135 kcal/mol
Surface area24230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.600, 95.300, 95.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROBABLE MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE / PYROPHOSPHATE PHOSPHO-HYDROLASE / PPASE


Mass: 33535.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O68579, inorganic diphosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG MME 5000, (NH4)2(SO4), MgCl2, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
142 mg/mlprotein1drop
2150 mMTris-HCl1drop
315 mM1dropMgCl2
430 %PEG5000 MME1reservoir
5100 mMMES-NaOH1reservoir
6200 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X31 / Wavelength: 0.9050, 0.9767, 0.9774
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 2000
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9051
20.97671
30.97741
ReflectionResolution: 2.2→19.76 Å / Num. all: 130000 / Num. obs: 38000 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.5
Reflection shellResolution: 2.2→19.76 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.257 / % possible all: 91.6
Reflection
*PLUS
% possible obs: 99 % / Num. measured all: 130000

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→19.76 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.257 3247 Random
Rwork0.209 --
all-32539 -
obs-32539 -
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4686 0 26 364 5076
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.26 446 -
Rwork0.212 --
obs-4109 77.5 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / σ(F): 0 / Rfactor obs: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.212

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