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- PDB-1y6x: The 1.25 A resolution structure of phosphoribosyl-ATP pyrophospho... -

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Basic information

Entry
Database: PDB / ID: 1y6x
TitleThe 1.25 A resolution structure of phosphoribosyl-ATP pyrophosphohydrolase from Mycobacterium tuberculosis
ComponentsPhosphoribosyl-ATP pyrophosphatase
KeywordsHYDROLASE / helical bundle / phosphoribosyl-ATP / histidine / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


response to host iron concentration / phosphoribosyl-ATP diphosphatase / phosphoribosyl-ATP diphosphatase activity / cell wall / L-histidine biosynthetic process / 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 / SYNCHROTRON / MAD / Resolution: 1.25 Å
AuthorsJavid-Majd, F. / 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
DepositionDec 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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

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Assembly

Deposited unit
A: Phosphoribosyl-ATP pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)10,3321
Polymers10,3321
Non-polymers00
Water2,720151
1
A: Phosphoribosyl-ATP pyrophosphatase

A: Phosphoribosyl-ATP pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)20,6652
Polymers20,6652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
2
A: Phosphoribosyl-ATP pyrophosphatase

A: Phosphoribosyl-ATP pyrophosphatase

A: Phosphoribosyl-ATP pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)30,9973
Polymers30,9973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area10050 Å2
ΔGint-84 kcal/mol
Surface area14340 Å2
MethodPISA
3
A: Phosphoribosyl-ATP pyrophosphatase

A: Phosphoribosyl-ATP pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)20,6652
Polymers20,6652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)37.925, 62.597, 67.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-164-

HOH

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Components

#1: Protein Phosphoribosyl-ATP pyrophosphatase / PRA-PH / PRATP-PH / phosphoribosyl-ATP pyrophosphohydrolase


Mass: 10332.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: Rv37 / Gene: hisE / Plasmid: pET23a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-plysS
References: UniProt: P0A5B1, UniProt: P9WMM9*PLUS, phosphoribosyl-ATP diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.5 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium citrate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1.0037, 0.9802,0.9799, 0.9572
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 2, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00371
20.98021
30.97991
40.95721
ReflectionResolution: 1.1→45.64 Å / Num. obs: 24294 / % possible obs: 100 %

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.25→45.64 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.591 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.063 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20747 1042 5.2 %RANDOM
Rwork0.18336 ---
all0.18458 20798 --
obs-19181 97.24 %-
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: 11.028 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.25→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms677 0 0 151 828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022687
X-RAY DIFFRACTIONr_bond_other_d0.0010.02640
X-RAY DIFFRACTIONr_angle_refined_deg0.9851.97930
X-RAY DIFFRACTIONr_angle_other_deg0.71531479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.475586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03524.37532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.36815120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.649155
X-RAY DIFFRACTIONr_chiral_restr0.0530.2108
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02766
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02137
X-RAY DIFFRACTIONr_nbd_refined0.220.2163
X-RAY DIFFRACTIONr_nbd_other0.1560.2612
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2351
X-RAY DIFFRACTIONr_nbtor_other0.0840.2380
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2114
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.242
X-RAY DIFFRACTIONr_mcbond_it0.7861.5541
X-RAY DIFFRACTIONr_mcbond_other0.2311.5181
X-RAY DIFFRACTIONr_mcangle_it1.0042680
X-RAY DIFFRACTIONr_scbond_it1.743288
X-RAY DIFFRACTIONr_scangle_it2.4874.5250
X-RAY DIFFRACTIONr_rigid_bond_restr1.33731568
X-RAY DIFFRACTIONr_sphericity_free2.1323151
X-RAY DIFFRACTIONr_sphericity_bonded1.31931317
LS refinement shellResolution: 1.25→1.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 44 -
Rwork0.227 903 -
obs--88.84 %

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