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- PDB-3i9x: Crystal structure of a mutT/nudix family protein from Listeria innocua -

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Basic information

Entry
Database: PDB / ID: 3i9x
TitleCrystal structure of a mutT/nudix family protein from Listeria innocua
ComponentsmutT/nudix family protein
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsBonanno, J.B. / Gilmore, M. / Bain, K.T. / Miller, S. / Romero, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a mutT/nudix family protein from Listeria innocua
Authors: Bonanno, J.B. / Gilmore, M. / Bain, K.T. / Miller, S. / Romero, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJul 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0172
Polymers20,9251
Non-polymers921
Water45025
1
A: mutT/nudix family protein
hetero molecules

A: mutT/nudix family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0334
Polymers41,8492
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area2200 Å2
ΔGint-8 kcal/mol
Surface area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.129, 96.129, 97.594
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

Detailspossible dimer

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Components

#1: Protein mutT/nudix family protein


Mass: 20924.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Gene: lin0490 / Plasmid: modified pET26 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92EH0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5
Details: 100mM Hepes pH 7.5, 4% glycerol, 1.3M tri-sodium citrate, vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 11, 2009
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.2→31.668 Å / Num. all: 14089 / Num. obs: 14075 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 42.4 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 26.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 43.3 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 9.9 / Num. unique all: 2001 / Rsym value: 0.449 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.295 / WRfactor Rwork: 0.239 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.813 / SU B: 5.018 / SU ML: 0.13 / SU R Cruickshank DPI: 0.191 / SU Rfree: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.191 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.276 685 4.9 %RANDOM
Rwork0.223 ---
obs0.225 14015 99.89 %-
all-14030 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 80.97 Å2 / Biso mean: 50.271 Å2 / Biso min: 31.29 Å2
Baniso -1Baniso -2Baniso -3
1--3.73 Å2-1.87 Å20 Å2
2---3.73 Å20 Å2
3---5.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1206 0 6 25 1237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221238
X-RAY DIFFRACTIONr_bond_other_d0.0020.02846
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.9951681
X-RAY DIFFRACTIONr_angle_other_deg0.99232073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7765156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.63924.71753
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36715204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.085157
X-RAY DIFFRACTIONr_chiral_restr0.0940.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211371
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02234
X-RAY DIFFRACTIONr_mcbond_it1.1221.5784
X-RAY DIFFRACTIONr_mcbond_other0.2151.5313
X-RAY DIFFRACTIONr_mcangle_it2.05621260
X-RAY DIFFRACTIONr_scbond_it2.6693454
X-RAY DIFFRACTIONr_scangle_it4.4084.5421
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 44 -
Rwork0.253 951 -
all-995 -
obs-951 100 %

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