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- PDB-5zmi: Crystal structure of APRT from Y. pseudotuberculosis in complex w... -

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Basic information

Entry
Database: PDB / ID: 5zmi
TitleCrystal structure of APRT from Y. pseudotuberculosis in complex with adenine.
ComponentsAdenine phosphoribosyltransferase
KeywordsTRANSFERASE / adenine phosphoribosyltransferase / adenine
Function / homology
Function and homology information


adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / AMP salvage / purine ribonucleoside salvage / cytosol
Similarity search - Function
: / Adenine phosphoribosyl transferase / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENINE / Adenine phosphoribosyltransferase
Similarity search - Component
Biological speciesYersinia pseudotuberculosis IP 32953 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPavithra, G.C. / Fox, G.C. / Ramagopal, U.A.
CitationJournal: To be published
Title: Crystal structure of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis
Authors: Pavithra, G.C. / Ramagopal, U.A.
History
DepositionApr 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
A: Adenine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3243
Polymers20,1661
Non-polymers1582
Water18010
1
A: Adenine phosphoribosyltransferase
hetero molecules

A: Adenine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6486
Polymers40,3322
Non-polymers3164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3680 Å2
ΔGint-31 kcal/mol
Surface area14770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.958, 78.650, 53.679
Angle α, β, γ (deg.)90.000, 115.200, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Adenine phosphoribosyltransferase / APRT


Mass: 20165.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis IP 32953 (bacteria)
Strain: IP32953 / Gene: YPTB0991 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q66DQ2, adenine phosphoribosyltransferase
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.79 Å3/Da / Density % sol: 55.95 % / Mosaicity: 0.68 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG4000, 0.1M Tris-Hcl pH 8.5, 0.2M Sodium Acetate with 5mM adenine and 5% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.05→48.57 Å / Num. obs: 13665 / % possible obs: 98.1 % / Redundancy: 2.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.034 / Rrim(I) all: 0.061 / Net I/σ(I): 9.9
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.49 / Num. unique obs: 1026 / CC1/2: 0.731 / Rpim(I) all: 0.375 / Rrim(I) all: 0.62 / % possible all: 94.8

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MB6

4mb6


Resolution: 2.05→48.57 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 11.233 / SU ML: 0.136 / SU R Cruickshank DPI: 0.1654 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.155
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 651 4.8 %RANDOM
Rwork0.1855 ---
obs0.1876 13011 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 102.09 Å2 / Biso mean: 58.491 Å2 / Biso min: 36.35 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å2-0.78 Å2
2---1.79 Å20 Å2
3---0.53 Å2
Refinement stepCycle: final / Resolution: 2.05→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1343 0 11 10 1364
Biso mean--65.72 49.45 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191378
X-RAY DIFFRACTIONr_bond_other_d0.0010.021321
X-RAY DIFFRACTIONr_angle_refined_deg1.58921872
X-RAY DIFFRACTIONr_angle_other_deg0.70833056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2425177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70124.11851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82315229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.741157
X-RAY DIFFRACTIONr_chiral_restr0.0850.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211519
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02267
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 44 -
Rwork0.287 930 -
all-974 -
obs--94.29 %
Refinement TLS params.Method: refined / Origin x: 21.0714 Å / Origin y: -0.1791 Å / Origin z: 7.3287 Å
111213212223313233
T0.158 Å2-0.0494 Å20.0774 Å2-0.1965 Å2-0.0565 Å2--0.0584 Å2
L1.5642 °20.0565 °2-0.7315 °2-0.7239 °2-0.4273 °2--1.0966 °2
S0.2726 Å °-0.1039 Å °0.0724 Å °0.1614 Å °-0.1874 Å °0.1839 Å °-0.1049 Å °-0.0742 Å °-0.0852 Å °

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