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- PDB-4gk6: X-ray crystal structure of a hypothetical deoxyuridine 5-triphosp... -

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Basic information

Entry
Database: PDB / ID: 4gk6
TitleX-ray crystal structure of a hypothetical deoxyuridine 5-triphosphate nucleotidohydrolase from Mycobacterium abscessus
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionAug 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 13, 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 / 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 / _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: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4442
Polymers14,4081
Non-polymers351
Water2,846158
1
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3326
Polymers43,2253
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation10_656-y+1,z,-x+11
Buried area10460 Å2
ΔGint-72 kcal/mol
Surface area17140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.260, 98.260, 98.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-362-

HOH

21A-443-

HOH

31A-444-

HOH

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Components

#1: Protein Deoxyuridine 5'-triphosphate nucleotidohydrolase / dUTPase / dUTP pyrophosphatase


Mass: 14408.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / DSM 44196 / Gene: dut, MAB_3003c / Production host: Escherichia coli (E. coli) / References: UniProt: B1MCW0, dUTP diphosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.74 Å3/Da / Density % sol: 55.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1 M Lithium chloride, 0.1 M sodium acetate, 30% PEG 6000, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 19154 / Num. obs: 19154 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.707 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.65-1.690.5453.2786851420100
1.69-1.740.463.8984731374100
1.74-1.790.3724.8780541313100
1.79-1.840.296.179981294100
1.84-1.910.2267.637759125999.9
1.91-1.970.1769.837439120399.9
1.97-2.050.15510.6972911191100
2.05-2.130.12713.126871110899.9
2.13-2.220.107156626107699.9
2.22-2.330.09616.6364301042100
2.33-2.460.08718.186086989100
2.46-2.610.08218.965710928100
2.61-2.790.07421.15448891100
2.79-3.010.06423.865071831100
3.01-3.30.05627.224541753100
3.3-3.690.05129.644135702100
3.69-4.260.04431.743596606100
4.26-5.220.04333.513177522100
5.22-7.380.04530.77246841599.8
7.380.03833.45133323797.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1MQ7

1mq7


Resolution: 1.65→40.15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.601 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1807 986 5.1 %RANDOM
Rwork0.1586 ---
all0.1598 19154 --
obs0.1598 19154 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.92 Å2 / Biso mean: 15.774 Å2 / Biso min: 2.94 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 1 158 1151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191044
X-RAY DIFFRACTIONr_bond_other_d0.0010.021040
X-RAY DIFFRACTIONr_angle_refined_deg1.48621437
X-RAY DIFFRACTIONr_angle_other_deg0.74432398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5115151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.224.3941
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.47515171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.397159
X-RAY DIFFRACTIONr_chiral_restr0.0840.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211211
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02206
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 79 -
Rwork0.207 1341 -
all-1420 -
obs--100 %
Refinement TLS params.

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)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8794-0.7448-0.99471.35310.76991.3078-0.06190.1616-0.0359-0.04590.0305-0.0122-0.0801-0.08870.03140.1651-0.09410.00940.1767-0.01780.00417.524380.797852.4528
20.306-0.07760.08520.428-0.16150.8969-0.01950.09540.0133-0.0669-0.04970.026-0.17070.00580.06910.06680.0015-0.0070.05020.00760.05218.519786.472864.7011
30.2059-0.06950.21530.10630.07610.4999-0.00950.00370.0105-0.0106-0.0051-0.0054-0.0273-0.02290.01460.0667-0.00190.0050.0548-0.00840.056218.117679.962268.1916
41.02210.07810.73223.5914-0.80830.8367-0.0695-0.1012-0.083-0.16840.0904-0.03580.0228-0.1677-0.02090.049-0.0193-0.00860.0653-0.00730.062113.396271.856561.3531
50.2736-0.19690.13690.6887-0.04540.2363-0.01770.01390.014-0.01160.0110.0082-0.0226-0.04060.00670.06240.00770.0030.0474-0.00240.04517.607180.905870.0228
62.1563-0.42061.21011.55870.51791.0645-0.06660.0268-0.0065-0.00970.07840.0023-0.04110.0602-0.01180.08790.00290.00220.01850.00410.071427.163948.047481.3928
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 12
2X-RAY DIFFRACTION2A13 - 37
3X-RAY DIFFRACTION3A38 - 76
4X-RAY DIFFRACTION4A77 - 87
5X-RAY DIFFRACTION5A88 - 120
6X-RAY DIFFRACTION6A121 - 133

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