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- PDB-3rk0: X-ray crystal Structure of the putative N-type ATP pyrophosphatas... -

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Basic information

Entry
Database: PDB / ID: 3rk0
TitleX-ray crystal Structure of the putative N-type ATP pyrophosphatase (PF0828) in complex with AMP from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target PfR23
ComponentsN-type ATP pyrophosphatase superfamily
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / alpha-beta protein that binds ATP / possibly n-type ATP pyrophosphatase / AMP and ATP binding
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
ADENOSINE MONOPHOSPHATE / N-type ATP pyrophosphatase superfamily
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsForouhar, F. / Saadat, N. / Hussain, M. / Seetharaman, J. / Janjua, J. / Xiao, R. / Cunningham, K. / Ma, L. / Shastry, R. / Everett, J.K. ...Forouhar, F. / Saadat, N. / Hussain, M. / Seetharaman, J. / Janjua, J. / Xiao, R. / Cunningham, K. / Ma, L. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / 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: 3H7E
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 11, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-type ATP pyrophosphatase superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4552
Polymers27,1071
Non-polymers3471
Water99155
1
A: N-type ATP pyrophosphatase superfamily
hetero molecules

A: N-type ATP pyrophosphatase superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9094
Polymers54,2152
Non-polymers6942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4190 Å2
ΔGint-21 kcal/mol
Surface area20630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.201, 85.201, 74.249
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: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 291 K / Method: micro batch under oil / pH: 7.5
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, 5 mM DTT, 0.02% NaN3, and 10mM dephospho-coenzyme A. Reservoir solution: 20% (w/v) PEG3350 and 200mM magnesium formate., micro ...Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, 5 mM DTT, 0.02% NaN3, and 10mM dephospho-coenzyme A. Reservoir solution: 20% (w/v) PEG3350 and 200mM magnesium formate., micro batch under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97915 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 31, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 20451 / Num. obs: 20390 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.059 / Net I/σ(I): 46.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 15.1 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 8.2 / Num. unique all: 2031 / Rsym value: 0.341 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
COMOphasing
CNS1.2 & XtalViewrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RJZ

3rjz


Resolution: 2.4→19.94 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 382365.25 / 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
Rfree0.278 1789 9.6 %RANDOM
Rwork0.229 ---
all0.232 20396 --
obs0.229 18724 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.2879 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 47.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.47 Å20 Å20 Å2
2--2.47 Å20 Å2
3----4.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 23 55 1766
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.66
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.341 155 9.7 %
Rwork0.257 1446 -
obs-1446 78.9 %

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