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- PDB-2yvn: Crystal structure of NDX2 from thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 2yvn
TitleCrystal structure of NDX2 from thermus thermophilus HB8
ComponentsMutT/nudix family protein
KeywordsHYDROLASE / NUDIX PROTEIN / ADP-RIBOSE / FAD / THERMUS THERMOPHILUS / HYDROLAS / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


pyrophosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / nucleotide binding / metal ion binding / cytosol
Similarity search - Function
NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
MutT/nudix family protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsWakamatsu, T. / Nakagawa, N. / Kuramitsu, S. / Yokoyama, S. / Masui, R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Bacteriol. / Year: 2008
Title: Structural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8
Authors: Wakamatsu, T. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
History
DepositionApr 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MutT/nudix family protein


Theoretical massNumber of molelcules
Total (without water)20,3361
Polymers20,3361
Non-polymers00
Water1,820101
1
A: MutT/nudix family protein

A: MutT/nudix family protein


Theoretical massNumber of molelcules
Total (without water)40,6732
Polymers40,6732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area4640 Å2
ΔGint-35 kcal/mol
Surface area16190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)41.175, 101.201, 97.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein MutT/nudix family protein / NDX2


Mass: 20336.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: ndx2 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q5SJY9, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M MES (PH 6.5), 0.08M SODIUM ACETATE, 7%(W/V) PEG 8000, 10%(W/V) GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 29, 2005
RadiationMonochromator: TRANSPARENT DIAMOND DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. all: 19698 / Num. obs: 19698 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 9.6 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 37.2
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 5.8 / Num. unique all: 1931 / % possible all: 98.9

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YVM

2yvm


Resolution: 1.84→27.36 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1757 -RANDOM
Rwork0.224 ---
all-17840 --
obs-17840 98.3 %-
Displacement parametersBiso mean: 20.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.46 Å20 Å20 Å2
2---4.43 Å20 Å2
3----2.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.84→27.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1437 0 0 101 1538
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it1.05
X-RAY DIFFRACTIONc_mcangle_it1.72
X-RAY DIFFRACTIONc_scbond_it1.46
X-RAY DIFFRACTIONc_scangle_it2.24
LS refinement shellResolution: 1.84→1.96 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.288 289 -
Rwork0.249 --
obs--95.2 %

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