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- PDB-7n6s: Crystal Structure of deoxyuridine 5'-triphosphate nucleotidohydro... -

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Basic information

Entry
Database: PDB / ID: 7n6s
TitleCrystal Structure of deoxyuridine 5'-triphosphate nucleotidohydrolase from Rickettsia prowazekii str. Madrid E in complex with 2'-deoxyuridine 5'-monophoephate (dUMP)
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / SSGCID / Deoxyuridine 5'-triphosphate nucleotidohydrolase / dut / Rickettsia prowazekii / nucleotide metabolism / 2'-deoxyuridine 5'-monophoephate / dUMP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesRickettsia prowazekii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of deoxyuridine 5'-triphosphate nucleotidohydrolase from Rickettsia prowazekii str. Madrid E in complex with 2'-deoxyuridine 5'-monophoephate (dUMP)
Authors: Abendroth, J. / deBouver, N.D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJun 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
B: Deoxyuridine 5'-triphosphate nucleotidohydrolase
C: Deoxyuridine 5'-triphosphate nucleotidohydrolase
D: Deoxyuridine 5'-triphosphate nucleotidohydrolase
E: Deoxyuridine 5'-triphosphate nucleotidohydrolase
F: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,15312
Polymers98,3046
Non-polymers1,8496
Water11,962664
1
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
B: Deoxyuridine 5'-triphosphate nucleotidohydrolase
D: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0766
Polymers49,1523
Non-polymers9253
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12420 Å2
ΔGint-57 kcal/mol
Surface area17710 Å2
MethodPISA
2
C: Deoxyuridine 5'-triphosphate nucleotidohydrolase
E: Deoxyuridine 5'-triphosphate nucleotidohydrolase
F: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0766
Polymers49,1523
Non-polymers9253
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14390 Å2
ΔGint-65 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.720, 87.000, 183.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 16383.980 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia prowazekii (strain Madrid E) (bacteria)
Strain: Madrid E / Gene: dut, RP399 / Plasmid: RiprA.10050.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZDD2, dUTP diphosphatase
#2: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H13N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Anatrace / Calibre MCSG1 screen, condition H9: 100mM BisTris /HCl pH 5.5, 25% (w/V) PEG 3350: RiprA.10050.a.A1.PS00480 at 24mg/ml + 5mM dUMP / MgCl2: tray 320891 h9: cryo: 20% glycerol + compounds: puck bqq7-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 9, 2021
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 82624 / % possible obs: 99.8 % / Redundancy: 7.073 % / Biso Wilson estimate: 32.944 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.039 / Χ2: 0.941 / Net I/σ(I): 30.17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.85.9440.4853.2360080.8810.53399.9
1.8-1.846.6550.3554.6858780.9480.386100
1.84-1.97.1850.2786.3957400.9720.3100
1.9-1.967.0170.2597.7255680.9750.2899.3
1.96-2.027.1250.17110.2854000.9880.18599.9
2.02-2.097.3010.15312.6152120.9910.16599.8
2.09-2.177.3490.11116.3150260.9950.12100
2.17-2.267.2680.09820.0548280.9960.10599
2.26-2.367.3790.07523.8746990.9980.08199.8
2.36-2.477.2720.06228.0744770.9980.067100
2.47-2.617.2750.0523442670.9990.056100
2.61-2.777.4920.04440.7840340.9990.047100
2.77-2.967.3930.03450.2138490.9990.037100
2.96-3.27.0650.02758.86356010.0399.9
3.2-3.57.0360.02467.3328510.02699.8
3.5-3.917.2450.02177.08300610.02399.7
3.91-4.526.9460.01983.1264910.0299.9
4.52-5.537.0430.01786.73228010.018100
5.53-7.836.9890.01784.54180110.01999.9
7.83-506.3240.01588.05105710.01699.4

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Processing

Software
NameVersionClassification
PHENIX1.19 dev 4224refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
Cootmodel building
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 7n56, apo structure

7n56


Resolution: 1.75→45.83 Å / SU ML: 0.1974 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3886
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2053 2043 2.47 %0
Rwork0.1717 80568 --
obs0.1725 82611 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.66 Å2
Refinement stepCycle: LAST / Resolution: 1.75→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6384 0 120 664 7168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00776670
X-RAY DIFFRACTIONf_angle_d0.90519073
X-RAY DIFFRACTIONf_chiral_restr0.06421097
X-RAY DIFFRACTIONf_plane_restr0.00871187
X-RAY DIFFRACTIONf_dihedral_angle_d11.76672493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.30711400.25945259X-RAY DIFFRACTION99.85
1.79-1.840.25461510.21275290X-RAY DIFFRACTION99.96
1.84-1.890.24291260.18715352X-RAY DIFFRACTION99.93
1.89-1.940.2651340.22315277X-RAY DIFFRACTION99.25
1.94-20.22331310.19875272X-RAY DIFFRACTION99.87
2-2.070.23861310.19765319X-RAY DIFFRACTION99.85
2.07-2.160.26771330.18165359X-RAY DIFFRACTION99.98
2.16-2.260.22911410.1895291X-RAY DIFFRACTION99.31
2.26-2.380.23811370.18675350X-RAY DIFFRACTION99.65
2.38-2.520.24051400.18625371X-RAY DIFFRACTION100
2.52-2.720.24371260.18695387X-RAY DIFFRACTION99.95
2.72-2.990.22141490.17875408X-RAY DIFFRACTION100
2.99-3.430.16921170.1685433X-RAY DIFFRACTION99.87
3.43-4.310.18281620.14155458X-RAY DIFFRACTION99.82
4.31-45.830.14981250.14955742X-RAY DIFFRACTION99.86
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)
11.32620772358-0.08431121378730.5523107838081.193506667660.1309089102581.772882064110.0360755935560.01803633411180.000230263155602-0.0359136731693-0.007103730228440.152125520993-0.00728896122161-0.200112710350.01131237769470.0993622068790.002764113424270.02481131996470.1453422854770.02978276022980.19250875479820.313216948412.603272543520.8641618836
20.824919871544-0.6224091823070.07605039743561.589858688430.1085378058131.165728549860.04689087877690.0711455627198-0.0225298447399-0.0676729028788-0.0284148304392-0.03753761523290.1793988609480.191182696717-0.002334698860670.1018033388410.01024374205690.003845100881350.217930553213-0.0009714969433390.19220615861636.18942251336.0341305550919.7229378655
31.492014448910.09146834412350.3067347011862.18782329465-0.2978707215262.58035295351-0.03037187828910.0644576834791-0.08776024074040.12894425768-0.03346985708510.0212485254508-0.2227308270130.09139993584110.01602858695470.147127284851-0.0247476112413-0.0009984820361840.1203174744030.009341772446680.14020223052534.15400331315.7972083517562.2390295233
41.732388127010.744240677371-0.2105805974821.68856638394-0.410788076211.51958121020.0030704495925-0.0182259995057-0.02388509422530.0163828069574-0.0575008910024-0.168746132685-0.1802495660450.260611618940.04024948274460.1300613461540.01103833566840.01701535541210.1586668726860.03250118073560.18516121003835.100666210121.395096959817.477899114
51.257849012460.0269442485801-0.170352635112.05994268255-0.2611644007752.3335242548-0.02261821340920.1063871571060.1787285009710.0508342024769-0.0259913261512-0.00241023250587-0.6983757539960.1401796388730.04046664785090.373962241714-0.07744383453-0.03934224890460.2008536982960.02608885906130.17983727552335.147660402619.732256178360.8020932834
61.632944043270.3455615086730.3385463041762.54063201914-0.1085453953762.21840074662-0.0515810314624-0.1135964122980.03408576755110.547409726826-0.03006050903950.15370484575-0.546274497636-0.06008949939470.02701865292610.423013678063-0.01728557886740.02437181964290.154543669283-0.003577138535420.18095058489531.262515872414.388533041973.3221702601
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11(chain 'A' and resid 0 through 201)AA - B0 - 201
22(chain 'B' and resid 1 through 201)BC - D1 - 201
33(chain 'C' and resid 2 through 201)CE - F2 - 201
44(chain 'D' and resid 2 through 201)DG - H2 - 201
55(chain 'E' and resid 2 through 201)EI - J2 - 201
66(chain 'F' and resid 3 through 201)FK - L3 - 201

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