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- PDB-3hhj: Crystal structure of mutator mutT from Bartonella henselae -

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Basic information

Entry
Database: PDB / ID: 3hhj
TitleCrystal structure of mutator mutT from Bartonella henselae
ComponentsMutator mutT protein
KeywordsHYDROLASE / NIAID / SSGCID / deCODE / UW / SBRI / infectious diseases / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA repair / metal ion binding
Similarity search - Function
Mutator MutT / MutY, C-terminal / NUDIX domain / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Mutator mutT protein / Mutator mutT protein
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of a Nudix hydrolase (MutT) in the Mg(2+)-bound state from Bartonella henselae, the bacterium responsible for cat scratch fever.
Authors: Buchko, G.W. / Edwards, T.E. / Abendroth, J. / Arakaki, T.L. / Law, L. / Napuli, A.J. / Hewitt, S.N. / Van Voorhis, W.C. / Stewart, L.J. / Staker, B.L. / Myler, P.J.
History
DepositionMay 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 7, 2011Group: Database references
Revision 1.3Sep 21, 2011Group: Database references
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Mutator mutT protein
B: Mutator mutT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6614
Polymers35,6132
Non-polymers492
Water2,936163
1
A: Mutator mutT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8312
Polymers17,8061
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mutator mutT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8312
Polymers17,8061
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.500, 93.490, 43.880
Angle α, β, γ (deg.)90.000, 109.240, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Mutator mutT protein


Mass: 17806.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Expressed with an N-terminal hexahistidine tag and 3C cleavage site. Not cleaved prior to crystallization.
Source: (gene. exp.) Bartonella henselae (bacteria) / Strain: Houston-1 / Gene: mutT, BH02020 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6G5F4, UniProt: A0A0H3LW43*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Proplex sparse matrix screen condition B5, 0.1 M Hepes pH 7.5, 10% PEG 4000, 0.1M MgCl2, 20% Glycerol as cryo, 26.9 mg/mL Protein, crystal tracking ID 202117b5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 21194 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.598 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.71
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.06 / Num. measured obs: 3640 / Num. unique all: 1406 / Num. unique obs: 1406 / % possible all: 88.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 57.69 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.72 Å
Translation3 Å19.72 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FK9

3fk9


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.217 / WRfactor Rwork: 0.188 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.822 / SU B: 4.69 / SU ML: 0.123 / SU R Cruickshank DPI: 0.196 / SU Rfree: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1086 5.1 %RANDOM
Rwork0.202 ---
obs0.203 21194 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.34 Å2 / Biso mean: 30.479 Å2 / Biso min: 14.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å2-0.94 Å2
2---1.31 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2060 0 2 163 2225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222153
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.972931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3015269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67325104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18315360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.133158
X-RAY DIFFRACTIONr_chiral_restr0.1020.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211662
X-RAY DIFFRACTIONr_mcbond_it0.9771.51314
X-RAY DIFFRACTIONr_mcangle_it1.79122113
X-RAY DIFFRACTIONr_scbond_it2.2573839
X-RAY DIFFRACTIONr_scangle_it3.6664.5813
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 60 -
Rwork0.277 1344 -
all-1404 -
obs--88.14 %

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