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- PDB-2yf9: STRUCTURAL AND FUNCTIONAL INSIGHTS OF DR2231 PROTEIN, THE MAZG-LI... -

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Entry
Database: PDB / ID: 2yf9
TitleSTRUCTURAL AND FUNCTIONAL INSIGHTS OF DR2231 PROTEIN, THE MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE FROM DEINOCOCCUS RADIODURANS, NATIVE FORM
ComponentsMAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
KeywordsHYDROLASE / DIMERIC DUTPASE
Function / homology
Function and homology information


nucleoside triphosphate diphosphatase activity / metal ion binding
Similarity search - Function
putative ntp pyrophosphohydrolase like fold / putative ntp pyrophosphohydrolase like domain / NTP pyrophosphohydrolase-like domain superfamily / Phosphoribosyl-ATP pyrophosphohydrolase-like / Phosphoribosyl-ATP pyrophosphohydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HAD superfamily Cof-like phosphohydrolase
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsGoncalves, A.M.D. / De Sanctis, D. / Mcsweeney, S.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and Functional Insights Into Dr2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase from Deinococcus Radiodurans.
Authors: Goncalves, A.M.D. / Desanctis, D. / Mcsweeney, S.M.
History
DepositionApr 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Database references / Version format compliance
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8515
Polymers16,7091
Non-polymers1424
Water2,558142
1
A: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
hetero molecules

A: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,70110
Polymers33,4172
Non-polymers2848
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area7810 Å2
ΔGint-148.3 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.925, 62.925, 167.578
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2053-

HOH

21A-2087-

HOH

31A-2109-

HOH

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Components

#1: Protein MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE / DR2231


Mass: 16708.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Strain: R1 / Plasmid: PET151/D-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9RS96, nucleoside-triphosphate diphosphatase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.86 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 7
Details: 1.0 M LITHIUM CHLORIDE, 0.1 M CITRIC ACID, 5-10%(W/V) PEG 6000., pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97627
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 22, 2010 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 1.9→45.68 Å / Num. obs: 16383 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Biso Wilson estimate: 23.21 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.2 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YEU

2yeu


Resolution: 1.899→45.683 Å / SU ML: 0.22 / σ(F): 1.37 / Phase error: 17.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2252 843 5.2 %
Rwork0.1883 --
obs0.19 16305 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.991 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso mean: 25.38 Å2
Baniso -1Baniso -2Baniso -3
1-4.6289 Å20 Å20 Å2
2--4.6289 Å20 Å2
3----7.1559 Å2
Refinement stepCycle: LAST / Resolution: 1.899→45.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1088 0 4 142 1234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181139
X-RAY DIFFRACTIONf_angle_d1.0921550
X-RAY DIFFRACTIONf_dihedral_angle_d13.37434
X-RAY DIFFRACTIONf_chiral_restr0.09170
X-RAY DIFFRACTIONf_plane_restr0.007212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8987-2.01760.28921480.2252483X-RAY DIFFRACTION99
2.0176-2.17340.24991520.17562492X-RAY DIFFRACTION100
2.1734-2.39210.22511490.17212508X-RAY DIFFRACTION100
2.3921-2.73820.22911370.19362564X-RAY DIFFRACTION100
2.7382-3.44970.23331090.19092625X-RAY DIFFRACTION100
3.4497-45.6960.20051480.18652790X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 28.4473 Å / Origin y: 13.7702 Å / Origin z: 12.1328 Å
111213212223313233
T0.1125 Å20.0299 Å2-0.0032 Å2-0.084 Å2-0.0043 Å2--0.0962 Å2
L0.2074 °20.0838 °2-0.113 °2-0.1628 °20.1663 °2--0.4096 °2
S-0.0382 Å °-0.0258 Å °-0.0104 Å °0.0356 Å °0.0501 Å °-0.0164 Å °0.0089 Å °0.0513 Å °-0.0109 Å °
Refinement TLS groupSelection details: CHAIN A

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