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- PDB-1yxb: Crystal structure of Phosphoribosyl-ATP pyrophosphatase from Stre... -

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Basic information

Entry
Database: PDB / ID: 1yxb
TitleCrystal structure of Phosphoribosyl-ATP pyrophosphatase from Streptomyces coelicolor. NESG target RR8.
ComponentsPhosphoribosyl-ATP pyrophosphatase
KeywordsHYDROLASE / Phosphoribosyl-ATP pyrophosphatase / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


phosphoribosyl-ATP diphosphatase / phosphoribosyl-ATP diphosphatase activity / L-histidine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Phosphoribosyl-ATP pyrophosphohydrolase / Phosphoribosyl-ATP pyrophosphohydrolase-like / Phosphoribosyl-ATP pyrophosphohydrolase / MazG-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphoribosyl-ATP pyrophosphatase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsBenach, J. / Kuzin, A.P. / Forouhar, F. / Abashidze, M. / Vorobiev, S.M. / Rong, X. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of Phosphoribosyl-ATP pyrophosphatase from Streptomyces coelicolor. NESG target RR8.
Authors: Benach, J. / Kuzin, A.P. / Forouhar, F. / Abashidze, M. / Vorobiev, S.M. / Rong, X. / Acton, T.B. / Montelione, G.T. / Hunt, J.F.
History
DepositionFeb 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosyl-ATP pyrophosphatase
B: Phosphoribosyl-ATP pyrophosphatase
C: Phosphoribosyl-ATP pyrophosphatase
D: Phosphoribosyl-ATP pyrophosphatase
E: Phosphoribosyl-ATP pyrophosphatase
F: Phosphoribosyl-ATP pyrophosphatase
G: Phosphoribosyl-ATP pyrophosphatase
H: Phosphoribosyl-ATP pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)89,5288
Polymers89,5288
Non-polymers00
Water4,234235
1
A: Phosphoribosyl-ATP pyrophosphatase
B: Phosphoribosyl-ATP pyrophosphatase
C: Phosphoribosyl-ATP pyrophosphatase
D: Phosphoribosyl-ATP pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)44,7644
Polymers44,7644
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10260 Å2
ΔGint-94 kcal/mol
Surface area15230 Å2
MethodPISA
2
E: Phosphoribosyl-ATP pyrophosphatase
F: Phosphoribosyl-ATP pyrophosphatase
G: Phosphoribosyl-ATP pyrophosphatase
H: Phosphoribosyl-ATP pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)44,7644
Polymers44,7644
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10250 Å2
ΔGint-95 kcal/mol
Surface area15250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.904, 62.361, 76.620
Angle α, β, γ (deg.)79.21, 82.13, 75.42
Int Tables number1
Space group name H-MP1
Detailsthe a.u. contains two biological assemblies. tetramer A,B,C,D and tetramer E,F,G,H

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Components

#1: Protein
Phosphoribosyl-ATP pyrophosphatase / PRA-PH


Mass: 11190.965 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: hisE / Production host: Escherichia coli (E. coli) / Keywords: Phosphoribosyl-ATP pyrophosphatase
References: UniProt: Q9EWK0, phosphoribosyl-ATP diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.34 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97944 / Wavelength: 0.97944 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 21879 / Num. obs: 21879 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 50.7 Å2 / Rmerge(I) obs: 0.051
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.336 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→19.89 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 812830.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1138 5.2 %RANDOM
Rwork0.25 ---
obs0.25 21879 90.5 %-
all-21879 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.5663 Å2 / ksol: 0.24139 e/Å3
Displacement parametersBiso mean: 72.7 Å2
Baniso -1Baniso -2Baniso -3
1-10.1 Å21.21 Å2-6.94 Å2
2---0.83 Å2-14.32 Å2
3----9.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5248 0 0 235 5483
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_mcbond_it2.371.5
X-RAY DIFFRACTIONc_mcangle_it4.12
X-RAY DIFFRACTIONc_scbond_it3.732
X-RAY DIFFRACTIONc_scangle_it5.792.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 148 5 %
Rwork0.296 2802 -
obs--73.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PS_PARAM.PRO
X-RAY DIFFRACTION3PARAM19.SOL

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