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- PDB-2pgs: Crystal structure of a putative deoxyguanosinetriphosphate tripho... -

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Basic information

Entry
Database: PDB / ID: 2pgs
TitleCrystal structure of a putative deoxyguanosinetriphosphate triphosphohydrolase from Pseudomonas syringae pv. phaseolicola 1448A
ComponentsPutative deoxyguanosinetriphosphate triphosphohydrolase
KeywordsHYDROLASE / Deoxyguanosinetriphosphate triphsphohydrolase / Pseudomonas syringae pv. phaseolicola 1448A / 10395g / PSI-2 / NYSGXRC / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


triphosphoric monoester hydrolase activity
Similarity search - Function
putative deoxyguanosinetriphosphate triphosphohydrolase fold / putative deoxyguanosinetriphosphate triphosphohydrolase like domain / eoxyguanosinetriphosphate triphosphohydrolase domain-like / eoxyguanosinetriphosphate triphosphohydrolase fold / Deoxyguanosinetriphosphate triphosphohydrolase, C-terminal / Deoxyguanosinetriphosphate triphosphohydrolase, central domain superfamily / dNTP triphosphohydrolase / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. ...putative deoxyguanosinetriphosphate triphosphohydrolase fold / putative deoxyguanosinetriphosphate triphosphohydrolase like domain / eoxyguanosinetriphosphate triphosphohydrolase domain-like / eoxyguanosinetriphosphate triphosphohydrolase fold / Deoxyguanosinetriphosphate triphosphohydrolase, C-terminal / Deoxyguanosinetriphosphate triphosphohydrolase, central domain superfamily / dNTP triphosphohydrolase / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Deoxyguanosinetriphosphate triphosphohydrolase, putative
Similarity search - Component
Biological speciesPseudomonas syringae pv. phaseolicola 1448A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsRao, K.N. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative deoxyguanosinetriphosphate triphosphohydrolase from Pseudomonas syringae pv. phaseolicola 1448A at 2.35 A resolution
Authors: Rao, K.N. / Burley, S.K. / Swaminathan, S.
History
DepositionApr 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative deoxyguanosinetriphosphate triphosphohydrolase


Theoretical massNumber of molelcules
Total (without water)51,2521
Polymers51,2521
Non-polymers00
Water88349
1
A: Putative deoxyguanosinetriphosphate triphosphohydrolase
x 6


Theoretical massNumber of molelcules
Total (without water)307,5136
Polymers307,5136
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area14780 Å2
ΔGint-85 kcal/mol
Surface area85890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.730, 103.730, 159.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Putative deoxyguanosinetriphosphate triphosphohydrolase


Mass: 51252.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. phaseolicola 1448A (bacteria)
Species: Pseudomonas savastanoi / Strain: 1448A, Race 6 / Gene: PSPPH_2088 / Production host: Escherichia coli (E. coli) / References: UniProt: Q48JX0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Sodium formate, PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2007 / Details: Mirrors
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. all: 22333 / Num. obs: 22333 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 24.5 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.4
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2081 / % possible all: 95.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
SHARPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.35→49.31 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 79922.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 619 2.9 %RANDOM
Rwork0.251 ---
obs0.251 21262 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.4847 Å2 / ksol: 0.357658 e/Å3
Displacement parametersBiso mean: 43.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å25.22 Å20 Å2
2--0.21 Å20 Å2
3----0.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.35→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3056 0 0 49 3105
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 92 2.8 %
Rwork0.291 3189 -
obs--92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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