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- PDB-2yyh: Crystal structure of Nudix family protein from Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 2yyh
TitleCrystal structure of Nudix family protein from Aquifex aeolicus
Components8-OXO-dGTPase domain
KeywordsHYDROLASE / Nudix family protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


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
8-OXO-dGTPase domain (MutT domain)
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsNakagawa, N. / Kishishita, S. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of Nudix family protein from Aquifex aeolicus
Authors: Nakakaga, N. / Kishishita, S. / Yokoyama, S. / Kuramitsu, S.
History
DepositionApr 30, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 8-OXO-dGTPase domain
B: 8-OXO-dGTPase domain
C: 8-OXO-dGTPase domain
D: 8-OXO-dGTPase domain


Theoretical massNumber of molelcules
Total (without water)63,2194
Polymers63,2194
Non-polymers00
Water9,404522
1
A: 8-OXO-dGTPase domain
B: 8-OXO-dGTPase domain


Theoretical massNumber of molelcules
Total (without water)31,6102
Polymers31,6102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 8-OXO-dGTPase domain
D: 8-OXO-dGTPase domain


Theoretical massNumber of molelcules
Total (without water)31,6102
Polymers31,6102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.020, 34.336, 130.005
Angle α, β, γ (deg.)90.00, 106.06, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-283-

HOH

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Components

#1: Protein
8-OXO-dGTPase domain / MutT domain


Mass: 15804.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: mutT / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL-X / References: UniProt: O67435
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.07 Å3/Da / Density % sol: 40.54 % / Description: The file contains Friedel pairs.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 0.16M LiCl, 16% PEG3350, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97894, 0.9000, 0.97935
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: May 16, 2006 / Details: mirrors
RadiationMonochromator: Si II / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978941
20.91
30.979351
ReflectionResolution: 1.8→50 Å / Num. obs: 91555 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 2.75 % / Biso Wilson estimate: 13.6 Å2 / Rsym value: 0.042 / Net I/σ(I): 18
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 1.96 / Rsym value: 0.25 / % possible all: 91

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→39.5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 389621.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: the file contains Friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 4332 4.9 %RANDOM
Rwork0.211 ---
obs0.211 88647 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.2637 Å2 / ksol: 0.367316 e/Å3
Displacement parametersBiso mean: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å21.02 Å2
2--6.62 Å20 Å2
3----7.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4357 0 0 522 4879
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 648 5.2 %
Rwork0.3 11718 -
obs--78.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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