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- PDB-2azw: Crystal structure of the MutT/nudix family protein from Enterococ... -

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Basic information

Entry
Database: PDB / ID: 2azw
TitleCrystal structure of the MutT/nudix family protein from Enterococcus faecalis
ComponentsMutT/nudix family protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MutT/nudix / Enterococcus faecalis / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / 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
: / MutT/nudix family protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsZhang, R. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The 1.9A crystal structure of the MutT/nudix family protein from Enterococcus faecalis
Authors: Zhang, R. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionSep 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: MutT/nudix family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2822
Polymers17,0441
Non-polymers2381
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.839, 90.839, 52.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThis protein may existed as monomer.

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Components

#1: Protein MutT/nudix family protein


Mass: 17044.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 29375717, UniProt: Q836H1*PLUS
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.19 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 6, 2005 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.9→64.28 Å / Num. all: 17434 / Num. obs: 17228 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 40.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3300 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→64.28 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.43 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.124
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22969 929 5.1 %RANDOM
Rwork0.19303 ---
all0.19479 17434 --
obs0.19479 17228 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.935 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2--0.58 Å20 Å2
3----1.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.04 Å0.026 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 1.9→64.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1188 0 16 160 1364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221235
X-RAY DIFFRACTIONr_angle_refined_deg1.0971.951674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5545144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.64623.38762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41415193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.104159
X-RAY DIFFRACTIONr_chiral_restr0.0780.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02953
X-RAY DIFFRACTIONr_nbd_refined0.1850.2541
X-RAY DIFFRACTIONr_nbtor_refined0.2990.2835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2145
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.226
X-RAY DIFFRACTIONr_mcbond_it0.7451.5744
X-RAY DIFFRACTIONr_mcangle_it1.20921168
X-RAY DIFFRACTIONr_scbond_it1.5893575
X-RAY DIFFRACTIONr_scangle_it2.4084.5506
LS refinement shellResolution: 1.9→1.932 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 62 -
Rwork0.244 1078 -
obs--85.91 %
Refinement TLS params.Method: refined / Origin x: 16.516 Å / Origin y: 33.96 Å / Origin z: 12.52 Å
111213212223313233
T-0.0521 Å20.086 Å20.0066 Å2--0.0274 Å2-0.0024 Å2---0.0655 Å2
L1.6277 °2-1.2929 °2-0.1907 °2-1.914 °20.367 °2--3.7925 °2
S0.1489 Å °0.1072 Å °0.0377 Å °-0.1941 Å °-0.0874 Å °-0.1544 Å °0.2894 Å °0.3522 Å °-0.0615 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 502 - 50
2X-RAY DIFFRACTION1AA51 - 9951 - 99
3X-RAY DIFFRACTION1AA100 - 148100 - 148

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