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- PDB-1k7k: crystal structure of RdgB- inosine triphosphate pyrophosphatase f... -

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Basic information

Entry
Database: PDB / ID: 1k7k
Titlecrystal structure of RdgB- inosine triphosphate pyrophosphatase from E. coli
ComponentsHypothetical protein yggVHypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MAD / His-tag / large groove / disordered Se-Met / Putative ribosomal protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


XTP/dITP diphosphatase / purine nucleoside triphosphate catabolic process / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity / nucleotide binding ...XTP/dITP diphosphatase / purine nucleoside triphosphate catabolic process / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity / nucleotide binding / magnesium ion binding / protein homodimerization activity / cytosol / cytoplasm
Similarity search - Function
dITP/XTP pyrophosphatase / Ham1-like protein / Ham1 family / Inosine triphosphate pyrophosphatase-like / Maf protein - #10 / Maf protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
dITP/XTP pyrophosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsSanishvili, R. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Skarina, T. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli.
Authors: Savchenko, A. / Proudfoot, M. / Skarina, T. / Singer, A. / Litvinova, O. / Sanishvili, R. / Brown, G. / Chirgadze, N. / Yakunin, A.F.
History
DepositionOct 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein yggV


Theoretical massNumber of molelcules
Total (without water)23,8711
Polymers23,8711
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.180, 78.180, 80.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsMolecule is alongated, with dominant beta sheet extending throughout. There are additional beta strands at both ends of the beta sheet. Several alpha helices surround the ends of beta-sheet, leaving large groove on one side of the plane of the sheet.

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Components

#1: Protein Hypothetical protein yggV / Hypothesis


Mass: 23871.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P52061
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growMethod: vapor diffusion / pH: 5.8
Details: PEG4k, Am. Acetate, Na-Citrate, pH 5.8, VAPOR DIFFUSION
Temp details: ambient

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97937, 0.97918
SYNCHROTRONAPS 19-ID21.03321
Detector
TypeIDDetectorDateDetails
CUSTOM-MADE1CCDAug 21, 2001Double-crystal monochromator, mirror
CUSTOM-MADE2CCDSep 10, 2001Double-crystal monochromator, mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)MADMx-ray1
2SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979371
20.979181
31.033211
ReflectionResolution: 1.45→60 Å / Num. all: 40104 / Num. obs: 40104 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rsym value: 0.06
Reflection shellResolution: 1.45→1.5 Å / % possible all: 93.8

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Processing

Software
NameVersionClassification
CNSrefinement
REFMAC5refinement
d*TREKdata reduction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→55.09 Å / SU B: 2.585 / SU ML: 0.098 / SU Rfree: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.087 / Stereochemistry target values: REFMAC defaults / Details: used maximum likelihood method
RfactorNum. reflection% reflectionSelection details
Rfree0.23751 1875 5.1 %RANDOM
Rwork0.21135 ---
obs0.21261 35524 92.68 %-
Displacement parametersBiso mean: 16.815 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2---0.74 Å20 Å2
3---1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.5→55.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 0 255 1956
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_mcbond_it0.767
X-RAY DIFFRACTIONp_mcangle_it1.176
X-RAY DIFFRACTIONp_scbond_it2.125
X-RAY DIFFRACTIONp_scangle_it2.895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.5-1.5390.291270.25X-RAY DIFFRACTION295820
1.539-1.5810.2571150.229X-RAY DIFFRACTION285920
1.581-1.6270.2311230.224X-RAY DIFFRACTION281420
1.627-1.6770.2481030.215X-RAY DIFFRACTION269820
1.677-1.7320.2691210.218X-RAY DIFFRACTION263820
1.732-1.7930.2621280.223X-RAY DIFFRACTION254020
1.793-1.860.269990.223X-RAY DIFFRACTION246320
1.86-1.9360.2641240.22X-RAY DIFFRACTION237620
1.936-2.0220.3031130.215X-RAY DIFFRACTION228520
2.022-2.1210.3031300.219X-RAY DIFFRACTION221020
2.121-2.2350.241020.224X-RAY DIFFRACTION208620
2.235-2.370.2221060.213X-RAY DIFFRACTION197820
2.37-2.5340.202900.225X-RAY DIFFRACTION187020
2.534-2.7360.244870.219X-RAY DIFFRACTION175120
2.736-2.9970.278760.22X-RAY DIFFRACTION161320
2.997-3.3490.23800.229X-RAY DIFFRACTION148220
3.349-3.8650.202660.204X-RAY DIFFRACTION131020
3.865-4.7280.169520.179X-RAY DIFFRACTION113120
4.728-6.6630.23360.238X-RAY DIFFRACTION89720
6.663-55.9020.33180.25X-RAY DIFFRACTION55020

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