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- PDB-3c90: The 1.25 A Resolution Structure of Phosphoribosyl-ATP Pyrophospho... -

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Basic information

Entry
Database: PDB / ID: 3c90
TitleThe 1.25 A Resolution Structure of Phosphoribosyl-ATP Pyrophosphohydrolase from Mycobacterium tuberculosis, crystal form II
ComponentsPhosphoribosyl-ATP pyrophosphatase
KeywordsHYDROLASE / alpha-helical / Amino-acid biosynthesis / Histidine biosynthesis / Structural Genomics / TB Structural Genomics Consortium / TBSGC / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


response to host iron concentration / phosphoribosyl-ATP diphosphatase / phosphoribosyl-ATP diphosphatase activity / L-histidine biosynthetic process / cell wall / peptidoglycan-based cell wall / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Phosphoribosyl-ATP pyrophosphohydrolase / MazG-like / Phosphoribosyl-ATP pyrophosphohydrolase-like / Phosphoribosyl-ATP pyrophosphohydrolase / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphoribosyl-ATP pyrophosphatase / Phosphoribosyl-ATP pyrophosphatase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsJavid-Majd, F. / Yang, D. / Ioerger, T.R. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: The 1.25 A resolution structure of phosphoribosyl-ATP pyrophosphohydrolase from Mycobacterium tuberculosis.
Authors: Javid-Majd, F. / Yang, D. / Ioerger, T.R. / Sacchettini, J.C.
History
DepositionFeb 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Phosphoribosyl-ATP pyrophosphatase
A: Phosphoribosyl-ATP pyrophosphatase
B: Phosphoribosyl-ATP pyrophosphatase
C: Phosphoribosyl-ATP pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)40,6174
Polymers40,6174
Non-polymers00
Water4,197233
1
X: Phosphoribosyl-ATP pyrophosphatase
A: Phosphoribosyl-ATP pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)20,3092
Polymers20,3092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-29.8 kcal/mol
Surface area8290 Å2
MethodPISA
2
B: Phosphoribosyl-ATP pyrophosphatase
C: Phosphoribosyl-ATP pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)20,3092
Polymers20,3092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-31 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.702, 43.119, 67.547
Angle α, β, γ (deg.)90.000, 96.430, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 10154.372 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: hisE, Rv2122c, MT2182, MTCY261.18 / Plasmid: pET23a(+) / Production host: Escherichia coli (E. coli)
References: UniProt: P0A5B1, UniProt: P9WMM9*PLUS, phosphoribosyl-ATP diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1M Sodium formate, 0.1M Sodium iodide, 0.1 mM Calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.54178 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Details: Osmic optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 31912 / % possible obs: 98.9 %

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0000refinement
PDB_EXTRACT3.004data extraction
NONIUS/MACSCIENCEdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Y6X

1y6x


Resolution: 1.79→33.56 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.393 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1605 5.1 %RANDOM
Rwork0.207 ---
obs0.209 31690 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.448 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-0.25 Å2
2--0.81 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.79→33.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2708 0 0 233 2941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212748
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.9633720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0995344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99624.375128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28215480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7841520
X-RAY DIFFRACTIONr_chiral_restr0.0780.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022044
X-RAY DIFFRACTIONr_nbd_refined0.2150.21402
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2201
X-RAY DIFFRACTIONr_metal_ion_refined0.0660.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.2105
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4780.221
X-RAY DIFFRACTIONr_mcbond_it0.7611.51756
X-RAY DIFFRACTIONr_mcangle_it1.22722720
X-RAY DIFFRACTIONr_scbond_it231121
X-RAY DIFFRACTIONr_scangle_it3.2744.51000
LS refinement shellResolution: 1.79→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.423 109
Rwork0.354 2088
all-2197

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