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- PDB-5zoc: Crystal structure of APRT from Y. pseudotuberculosis with bound a... -

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Basic information

Entry
Database: PDB / ID: 5zoc
TitleCrystal structure of APRT from Y. pseudotuberculosis with bound adenine (C2 space group).
ComponentsAdenine phosphoribosyltransferase
KeywordsTRANSFERASE / adenine phosphoribosyltransferase / Yersinia pseudotuberculosis / 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 / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsPavithra, G.C. / Ramagopal, U.A.
CitationJournal: To be published
Title: Crystal structure of APRT from Y. pseudotuberculosis with bound adenine (C2 space group).
Authors: Pavithra, G.C. / Ramagopal, U.A.
History
DepositionApr 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 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

Downloads & links

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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
Water79344
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 area3700 Å2
ΔGint-30 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.714, 77.873, 54.074
Angle α, β, γ (deg.)90.000, 112.610, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-332-

HOH

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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: apt, 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.: 44 / 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: 2.83 Å3/Da / Density % sol: 56.53 % / Mosaicity: 0.673 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG3350, 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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5417 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 15046 / % possible obs: 95.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.017 / Rrim(I) all: 0.039 / Χ2: 0.875 / Net I/σ(I): 42.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.013.40.1495120.9920.0850.1730.79763.9
2.01-2.053.80.1455910.9910.0780.1650.79876.7
2.05-2.094.30.1166650.9940.0590.1310.80186.3
2.09-2.1350.1157850.9950.0550.1270.91198.7
2.13-2.185.30.1097710.9950.0510.1210.944100
2.18-2.235.30.0967820.9950.0450.1070.965100
2.23-2.295.30.0867780.9970.040.0950.966100
2.29-2.355.40.0717890.9970.0330.0780.976100
2.35-2.425.40.0667710.9970.0310.0730.999100
2.42-2.495.40.0567730.9980.0260.0620.996100
2.49-2.585.40.0477900.9980.0210.0510.953100
2.58-2.695.30.0437860.9980.020.0470.938100
2.69-2.815.40.047640.9990.0180.0440.928100
2.81-2.965.30.0357860.9980.0160.0390.87199.7
2.96-3.145.30.0317890.9990.0140.0340.77899.6
3.14-3.395.20.0317860.9980.0150.0340.76299.4
3.39-3.7350.0337820.9960.0160.0360.76699.1
3.73-4.264.80.0337720.9950.0170.0380.74898.6
4.26-5.374.60.0337790.9950.0180.0380.73897.4
5.371-504.70.037950.9970.0150.0340.66598.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MB6

4mb6


Resolution: 1.98→49.92 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.046 / SU ML: 0.108 / SU R Cruickshank DPI: 0.1693 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.151
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 704 4.8 %RANDOM
Rwork0.1984 ---
obs0.1999 13968 93.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.05 Å2 / Biso mean: 31.64 Å2 / Biso min: 10.81 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å2-0 Å2-0.37 Å2
2--0.25 Å2-0 Å2
3---1.59 Å2
Refinement stepCycle: final / Resolution: 1.98→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1343 0 11 44 1398
Biso mean--34.92 29.37 -
Num. residues----177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191408
X-RAY DIFFRACTIONr_bond_other_d00.021332
X-RAY DIFFRACTIONr_angle_refined_deg1.1791.9971920
X-RAY DIFFRACTIONr_angle_other_deg0.59133092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8845184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33124.28656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36215234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.84157
X-RAY DIFFRACTIONr_chiral_restr0.0650.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211579
X-RAY DIFFRACTIONr_gen_planes_other00.02275
LS refinement shellResolution: 1.981→2.032 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 32 -
Rwork0.261 553 -
all-585 -
obs--49.79 %
Refinement TLS params.Method: refined / Origin x: 21.307 Å / Origin y: -0.884 Å / Origin z: 7.837 Å
111213212223313233
T0.1959 Å20.0036 Å20.0585 Å2-0.0686 Å20.0017 Å2--0.0329 Å2
L2.2728 °20.0389 °2-1.4398 °2-1.1449 °2-0.479 °2--4.316 °2
S0.1992 Å °0.0081 Å °0.1274 Å °0.2443 Å °-0.0031 Å °0.1559 Å °-0.1431 Å °-0.3924 Å °-0.1961 Å °

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