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- PDB-7syc: Crystal Structure of Nucleoside triphosphate pyrophosphohydrolase... -

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Basic information

Entry
Database: PDB / ID: 7syc
TitleCrystal Structure of Nucleoside triphosphate pyrophosphohydrolase from Klebsiella pneumoniae subsp. pneumoniae
Components7,8-dihydro-8-oxoguanine-triphosphatase
KeywordsHYDROLASE / SSGCID / DNA repair / nudix hydrolase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


8-oxo-dGTP diphosphatase / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA repair
Similarity search - Function
Mutator MutT / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
7,8-dihydro-8-oxoguanine-triphosphatase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Crystal Structure of Nucleoside triphosphate pyrophosphohydrolase from Klebsiella pneumoniae subsp. pneumoniae
Authors: DeBouver, N.D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 7,8-dihydro-8-oxoguanine-triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9292
Polymers15,9051
Non-polymers241
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.140, 67.140, 136.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-338-

HOH

21A-389-

HOH

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Components

#1: Protein 7,8-dihydro-8-oxoguanine-triphosphatase / 8-oxo-dGTP diphosphatase / 8-oxo-dGTP diphosphatase MutT


Mass: 15905.060 Da / Num. of mol.: 1 / Fragment: KlpnC.00264.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Gene: mutT, E3U38_03970, NCTC9504_05440, RJA_22585 / Plasmid: KlpnC.00264.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Y0Q4X2, 8-oxo-dGTP diphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: KlpnC.00264.a.B1.PW38992 [Barcode: 322156a9] [pin_id: llw0-5] [collection: aps21idf 9/23/2021] [crystallization conditions: MCSG1 A9 0.1M HEPES/NaOH, pH 7.5, 0.2M MgCl2, 25% (w/v) PEG 3350] [cryo: 10% EG]

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 21, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→44.19 Å / Num. obs: 12903 / % possible obs: 99.9 % / Redundancy: 13.577 % / Biso Wilson estimate: 39.3 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.046 / Χ2: 0.935 / Net I/σ(I): 32.73 / Num. measured all: 175186
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.0514.3460.5765.06132419239230.9480.598100
2.05-2.1114.0980.3767.68128869149140.9750.39100
2.11-2.1714.2540.3228.99125018778770.9820.334100
2.17-2.2414.2030.26510.78122578638630.9870.275100
2.24-2.3114.2420.21913.05116648198190.9930.227100
2.31-2.3914.10.17715.88113658068060.9950.183100
2.39-2.4814.0910.14419.47111047887880.9960.149100
2.48-2.5814.0330.11423.46105537527520.9980.118100
2.58-2.713.8410.08430.44100217247240.9990.088100
2.7-2.8313.6530.06638.0294076896890.9990.069100
2.83-2.9813.3390.05743.3488846666660.9990.06100
2.98-3.1613.2020.04850.2483836356350.9990.05100
3.16-3.3812.8110.0456.3276745995990.9990.042100
3.38-3.6512.8050.03862.7471585595590.9990.039100
3.65-412.7210.03166.38665352352310.032100
4-4.4712.6540.02971.26617548848810.031100
4.47-5.1612.6640.02772.12535742342310.028100
5.16-6.3212.290.02770.17453536936910.028100
6.32-8.9411.8750.02469.9236223063050.9990.02699.7
8.94-44.199.6460.02566.0917461911810.9990.02694.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20rc3_4406refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A6S

3a6s


Resolution: 2→44.19 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2406 1300 10.08 %
Rwork0.1979 11603 -
obs0.2024 12903 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.79 Å2 / Biso mean: 47.9441 Å2 / Biso min: 22.71 Å2
Refinement stepCycle: final / Resolution: 2→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 1 110 1077
Biso mean--55.03 50.63 -
Num. residues----122
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.080.26431350.254112601395100
2.08-2.170.28691430.216812461389100
2.18-2.290.24821240.219612651389100
2.29-2.430.27841330.225112761409100
2.43-2.620.27661320.249212791411100
2.62-2.880.26281490.221212631412100
2.88-3.30.25531500.21212971447100
3.3-4.160.22671600.171213141474100
4.16-44.190.22011740.17991403157799
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)
15.00552.7614-1.43845.0288-1.07832.58230.1071-0.2091-0.1444-0.010.22080.50240.4751-0.0946-0.22190.2912-0.018-0.08820.41580.15350.4096-29.692319.49082.5525
26.88312.6095-0.2962.77441.32823.5294-0.27511.57860.4369-0.8160.9135-0.414-0.37850.218-0.19840.26360.08080.040.58540.21080.3858-15.361736.0321-8.8077
36.16232.59-0.82948.3879-0.70958.013-0.09081.4974-1.4744-1.33690.02640.57810.6066-0.4863-0.15530.39210.0946-0.07510.9697-0.04240.4521-22.713926.2895-10.1932
47.42511.6888-4.16836.78133.07599.95810.08050.51-0.76891.0540.06-0.3942.1537-0.07020.4290.39510.0036-0.09020.33250.01750.522-21.23517.79716.5986
55.23571.2878-5.40894.3380.44226.4242-0.10910.1828-0.41180.02240.0403-1.18780.44290.375-0.11980.22970.0355-0.04370.45340.0570.5576-14.539422.65280.8175
60.85490.82660.59834.54611.32633.25330.4214-0.1820.63270.0548-0.11520.3014-0.2718-0.1091-0.21580.20230.04780.0030.45620.07120.3296-24.438229.99643.4429
74.48795.0626-0.2324.6850.45571.34660.0291-0.1884-0.3659-0.2294-0.1811-0.13140.2742-0.04430.11660.20010.0292-0.00880.41630.10420.3954-30.223824.1081.6513
88.04340.10282.36686.6989-1.79294.96370.18321.5505-0.9822-0.9727-0.2339-0.48640.58970.2445-0.01620.33970.03790.0890.7591-0.11610.4637-10.492126.6089-7.4831
99.1745-3.49363.62797.0247-1.32725.889-0.35072.94810.1884-0.9483-0.00540.8923-0.1157-1.05160.4860.3050.1115-0.03431.00320.30260.4192-18.3135.7261-13.6626
107.3272-0.19151.54552.6932-1.90588.5508-0.0861.49120.8611-0.4114-0.04560.4257-1.096-2.10210.08810.33340.1118-0.04960.960.12820.5716-28.934634.7503-8.2291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 11 )A-1 - 11
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 21 )A12 - 21
3X-RAY DIFFRACTION3chain 'A' and (resid 22 through 36 )A22 - 36
4X-RAY DIFFRACTION4chain 'A' and (resid 37 through 45 )A37 - 45
5X-RAY DIFFRACTION5chain 'A' and (resid 46 through 60 )A46 - 60
6X-RAY DIFFRACTION6chain 'A' and (resid 61 through 74 )A61 - 74
7X-RAY DIFFRACTION7chain 'A' and (resid 75 through 87 )A75 - 87
8X-RAY DIFFRACTION8chain 'A' and (resid 88 through 101 )A88 - 101
9X-RAY DIFFRACTION9chain 'A' and (resid 102 through 109 )A102 - 109
10X-RAY DIFFRACTION10chain 'A' and (resid 110 through 129 )A110 - 129

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