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- PDB-3rjz: X-ray crystal structure of the putative n-type atp pyrophosphatas... -

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Basic information

Entry
Database: PDB / ID: 3rjz
TitleX-ray crystal structure of the putative n-type atp pyrophosphatase from pyrococcus furiosus, the northeast structural genomics target pfr23
ComponentsN-type ATP pyrophosphatase superfamily
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / alpha-beta protein / n-type ATP pyrophosphatase
Function / homology
Function and homology information


diphthine-ammonia ligase activity / protein histidyl modification to diphthamide / ATP binding
Similarity search - Function
putative n-type atp pyrophosphatase, domain 2 / putative n-type atp pyrophosphatase, domain 2 / Diphthamide synthase domain / Uncharacterised protein MJ0570 / Uncharacterised protein MJ0570, ATP-binding / Diphthine--ammonia ligase/Uncharacterised protein MJ0570 / Diphthamide synthase / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Alpha-Beta Complex ...putative n-type atp pyrophosphatase, domain 2 / putative n-type atp pyrophosphatase, domain 2 / Diphthamide synthase domain / Uncharacterised protein MJ0570 / Uncharacterised protein MJ0570, ATP-binding / Diphthine--ammonia ligase/Uncharacterised protein MJ0570 / Diphthamide synthase / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-type ATP pyrophosphatase superfamily
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsForouhar, F. / Lee, I. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: A large conformational change in the putative ATP pyrophosphatase PF0828 induced by ATP binding.
Authors: Forouhar, F. / Saadat, N. / Hussain, M. / Seetharaman, J. / Lee, I. / Janjua, H. / Xiao, R. / Shastry, R. / Acton, T.B. / Montelione, G.T. / Tong, L.
History
DepositionApr 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
SupersessionJun 1, 2011ID: 1RU8
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 11, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-type ATP pyrophosphatase superfamily


Theoretical massNumber of molelcules
Total (without water)27,1071
Polymers27,1071
Non-polymers00
Water1,53185
1
A: N-type ATP pyrophosphatase superfamily

A: N-type ATP pyrophosphatase superfamily


Theoretical massNumber of molelcules
Total (without water)54,2152
Polymers54,2152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area1960 Å2
ΔGint-8 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.036, 85.036, 74.502
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein N-type ATP pyrophosphatase superfamily


Mass: 27107.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF0828 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8U2K6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, 5 mM DTT, and 0.02% NaN3. Reservoir solution: 380 mM K/NaTartrate, , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.92927 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 16, 2003 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92927 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 23183 / Num. obs: 23091 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.072 / Net I/σ(I): 26.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 6.1 / Num. unique all: 2300 / Rsym value: 0.22 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SnBthen SOLVE/RESOLVEphasing
CNS1.2 & XtalViewrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.93 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 267007.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1971 9.3 %RANDOM
Rwork0.239 ---
all0.242 23142 --
obs0.239 21129 91.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.7501 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 34.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.76 Å20 Å20 Å2
2--2.76 Å20 Å2
3----5.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1649 0 0 85 1734
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.68
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.297 150 8.6 %
Rwork0.227 1599 -
obs-1599 75.8 %

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