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- PDB-1yvw: Crystal structure of Phosphoribosyl-ATP pyrophosphohydrolase from... -

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Basic information

Entry
Database: PDB / ID: 1yvw
TitleCrystal structure of Phosphoribosyl-ATP pyrophosphohydrolase from Bacillus cereus. NESGC target BcR13.
ComponentsPhosphoribosyl-ATP pyrophosphatase
KeywordsHYDROLASE / HELIX BUNDLE / HISTIDINE BIOSYNTHESIS / 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 / MazG-like / Phosphoribosyl-ATP pyrophosphohydrolase-like / Phosphoribosyl-ATP pyrophosphohydrolase / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphoribosyl-ATP pyrophosphatase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsBenach, J. / Kuzin, A.P. / Forouhar, F. / Abashidze, M. / Vorobiev, S.M. / Shastry, R. / 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 pyrophosphohydrolase from Bacillus cereus at 2.6 A resolution.
Authors: Benach, J. / Kuzin, A.P. / Forouhar, F. / Abashidze, M. / Vorobiev, S.M. / Shastry, R. / Rong, X. / Acton, T.B. / Montelione, G.T. / Hunt, J.F.
History
DepositionFeb 16, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,7134
Polymers54,7134
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10760 Å2
ΔGint-110 kcal/mol
Surface area15570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.959, 81.959, 222.978
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Detailsthe a.u. contains the putative biological assembly

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Components

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


Mass: 13678.231 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: hisE / Production host: Escherichia coli (E. coli)
References: UniProt: Q81G00, phosphoribosyl-ATP diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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 Å3/Da / Density % sol: 38.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 3.5 M NaFormate, 50mM NaAcetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97927 / Wavelength: 0.97927 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: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 14016 / Num. obs: 14016 / % possible obs: 80 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 58.1 Å2 / Rmerge(I) obs: 0.067
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.32 / % possible all: 80

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→29.06 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2783848.82 / 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
Rfree0.263 708 5.1 %RANDOM
Rwork0.244 ---
all0.244 14016 --
obs0.244 14016 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.4166 Å2 / ksol: 0.327497 e/Å3
Displacement parametersBiso mean: 56.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å22.82 Å20 Å2
2--0.53 Å20 Å2
3----1.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2988 0 0 169 3157
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.661.5
X-RAY DIFFRACTIONc_mcangle_it4.622
X-RAY DIFFRACTIONc_scbond_it5.622
X-RAY DIFFRACTIONc_scangle_it8.82.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 101 4.6 %
Rwork0.264 2088 -
obs--93.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PS_PARAM.PROPROTEIN.TOP
X-RAY DIFFRACTION2PARAM19.SOL

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