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- PDB-4dyw: Crystal structure of MutT NUDIX hydrolase from Burkholderia pseud... -

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Basic information

Entry
Database: PDB / ID: 4dyw
TitleCrystal structure of MutT NUDIX hydrolase from Burkholderia pseudomallei
ComponentsMutT/NUDIX family protein
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / MutT / NUDIX hydrolase / nucleotide diphosphate X hydrolase
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
MutT/NUDIX family protein
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of MutT NUDIX hydrolase from Burkholderia pseudomallei
Authors: Edwards, T.E. / Clifton, M.C. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionFeb 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MutT/NUDIX family protein
B: MutT/NUDIX family protein


Theoretical massNumber of molelcules
Total (without water)34,6712
Polymers34,6712
Non-polymers00
Water97354
1
A: MutT/NUDIX family protein


Theoretical massNumber of molelcules
Total (without water)17,3361
Polymers17,3361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MutT/NUDIX family protein


Theoretical massNumber of molelcules
Total (without water)17,3361
Polymers17,3361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-18 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.040, 78.040, 113.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 5 - 133 / Label seq-ID: 26 - 154

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein MutT/NUDIX family protein


Mass: 17335.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_0547 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JWU2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 50.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: BupsA.00264.a.A1 PS01261 at 27 mg/mL against 0.2 M NaK Tartrate, 30% PEG 3350 PACT E9 focus screen with 20% ethylene glycol as cro-protectant, crystal tracking ID 230892e11, pH 7.0, VAPOR ...Details: BupsA.00264.a.A1 PS01261 at 27 mg/mL against 0.2 M NaK Tartrate, 30% PEG 3350 PACT E9 focus screen with 20% ethylene glycol as cro-protectant, crystal tracking ID 230892e11, pH 7.0, 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: 0.976484 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976484 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 12763 / Num. obs: 12669 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 51.427 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.52
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.5-2.570.5764.08578193099.7
2.57-2.640.4944.62555489399.7
2.64-2.710.3915.57535587199.8
2.71-2.80.3446.28526484299.6
2.8-2.890.2388.66516082799.6
2.89-2.990.2069.49493879599.7
2.99-3.10.13613.77469776399.9
3.1-3.230.11315.82466675499.7
3.23-3.370.08320.62439571999.7
3.37-3.540.06425.65401768699.6
3.54-3.730.04833.07367965198.9
3.73-3.950.03937.26348561898.7
3.95-4.230.0347.31337457699.7
4.23-4.560.02853.18322155099.6
4.56-50.02753.19288751399.8
5-5.590.02751.35263847099.2
5.59-6.460.02751.83242641399
6.46-7.910.02453.75211836399.5
7.91-11.180.0267.55164529499.7
11.180.01769.671714178.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å48.73 Å
Translation3 Å48.73 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HHJ

3hhj


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2215 / WRfactor Rwork: 0.1804 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8144 / SU B: 17.4 / SU ML: 0.189 / SU R Cruickshank DPI: 0.374 / SU Rfree: 0.2609 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.374 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 633 5 %RANDOM
Rwork0.2077 ---
obs0.2099 12668 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.6 Å2 / Biso mean: 45.9818 Å2 / Biso min: 24.49 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å20 Å2
2--1.99 Å20 Å2
3----3.97 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 0 54 2003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191997
X-RAY DIFFRACTIONr_bond_other_d0.0040.021326
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9592731
X-RAY DIFFRACTIONr_angle_other_deg1.13433225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9615256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93923.33387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19215295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9391517
X-RAY DIFFRACTIONr_chiral_restr0.0840.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212263
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02402
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRms dev position (Å)Weight position
11A3963X-RAY DIFFRACTION0.120.05
12B3963X-RAY DIFFRACTION0.120.05
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 39 -
Rwork0.319 779 -
all-818 -
obs--99.63 %
Refinement TLS params.

T23: -0.0179 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1861-0.0309-0.48010.1799-0.50133.263-0.01710.0086-0.03820.017-0.02760.02550.0263-0.03840.04470.0859-0.0396-0.00470.08020.026818.4438-15.231314.1893
20.84060.38260.76390.18060.48613.90940.0294-0.04140.00450.0112-0.03370.0046-0.0351-0.15570.00430.0820.0161-0.00150.06770.034817.7345-14.6136-14.075
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 133
2X-RAY DIFFRACTION1A201 - 228
3X-RAY DIFFRACTION2B5 - 133
4X-RAY DIFFRACTION2B201 - 226

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