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- PDB-5yw2: Crystal structure of Adenine phosphoribosyltransferase from Franc... -

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Basic information

Entry
Database: PDB / ID: 5yw2
TitleCrystal structure of Adenine phosphoribosyltransferase from Francisella tularensis.
ComponentsAdenine phosphoribosyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


adenine binding / adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / AMP salvage / purine ribonucleoside salvage / AMP binding / cytoplasm
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 phosphoribosyltransferase / Adenine phosphoribosyltransferase
Similarity search - Component
Biological speciesFrancisella tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsPavithra, G.C. / Ramagopal, U.A.
CitationJournal: FEBS J. / Year: 2018
Title: Crystal structures of APRT from Francisella tularensis - an N-H···N hydrogen bond imparts adenine specificity in adenine phosporibosyltransferases.
Authors: Pavithra, G.C. / Ramagopal, U.A.
History
DepositionNov 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenine phosphoribosyltransferase
C: Adenine phosphoribosyltransferase
B: Adenine phosphoribosyltransferase
D: Adenine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,87818
Polymers77,1614
Non-polymers71614
Water1,06359
1
A: Adenine phosphoribosyltransferase
B: Adenine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9399
Polymers38,5812
Non-polymers3587
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-101 kcal/mol
Surface area15080 Å2
MethodPISA
2
C: Adenine phosphoribosyltransferase
D: Adenine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9399
Polymers38,5812
Non-polymers3587
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-103 kcal/mol
Surface area15490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.168, 82.147, 170.119
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Details1. Density close to residue Arg63 is modeled as chlorine ion in all the four chains based only on the experimental density and the environment. 2. Disordered density near PRPP binding site cannot be modeled.

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Components

#1: Protein
Adenine phosphoribosyltransferase / APRT


Mass: 19290.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis (bacteria) / Gene: apt / Plasmid: LIC-PET30A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0E2ZLA9, UniProt: Q5NII9*PLUS, adenine phosphoribosyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.45 Å3/Da / Density % sol: 49.85 % / Mosaicity: 0.443 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Magnesium chloride, 0.1M HEPES:NaOH pH 7.5, 25% PEG 3350, cryo 0.5M Lithium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.28→35.36 Å / Num. obs: 35141 / % possible obs: 99.3 % / Redundancy: 9 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.029 / Rrim(I) all: 0.084 / Χ2: 0.916 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.28-2.329.20.97117150.930.3320.714100
2.32-2.369.10.62817620.9230.2170.6911000.665
2.36-2.419.20.54317150.9410.1860.7071000.575
2.41-2.469.10.49417760.9450.170.6951000.523
2.46-2.519.20.40817150.9780.140.7041000.432
2.51-2.579.10.33517480.9830.1150.7391000.355
2.57-2.639.20.28817090.9760.0990.7681000.305
2.63-2.79.10.24117800.9830.0830.7661000.255
2.7-2.789.20.18117280.9920.0630.821000.192
2.78-2.879.10.15417580.9940.0530.8241000.163
2.87-2.989.10.13717660.9950.0470.8951000.145
2.98-3.099.10.10517380.9970.0360.9321000.111
3.09-3.249.10.08717680.9970.031.0351000.093
3.24-3.4190.07117820.9980.0251.0651000.075
3.41-3.628.70.06315770.9980.0221.22890.067
3.62-3.98.30.07117450.9970.0251.22398.40.075
3.9-4.298.90.06317890.9980.0221.1241000.066
4.29-4.918.80.06618200.9970.0231.3381000.07
4.91-6.198.70.05318190.9980.0191.0661000.057
6.19-35.3680.03719310.9990.0141.072990.04

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MB6

4mb6


Resolution: 2.28→35.36 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / SU B: 16.872 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25875 1729 4.9 %RANDOM
Rwork0.20195 ---
obs0.20481 33294 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.396 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--3.13 Å2-0 Å2
3----3.05 Å2
Refinement stepCycle: 1 / Resolution: 2.28→35.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5358 0 30 59 5447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0195512
X-RAY DIFFRACTIONr_bond_other_d0.0020.025438
X-RAY DIFFRACTIONr_angle_refined_deg2.06827464
X-RAY DIFFRACTIONr_angle_other_deg1.081312592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8595719
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51124.757206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.29315970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4641527
X-RAY DIFFRACTIONr_chiral_restr0.1150.2883
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216085
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021034
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2963.152870
X-RAY DIFFRACTIONr_mcbond_other2.2933.1492869
X-RAY DIFFRACTIONr_mcangle_it3.7654.7043588
X-RAY DIFFRACTIONr_mcangle_other3.7654.7063589
X-RAY DIFFRACTIONr_scbond_it2.5543.4722642
X-RAY DIFFRACTIONr_scbond_other2.553.4692638
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2155.0493869
X-RAY DIFFRACTIONr_long_range_B_refined6.05836.0745568
X-RAY DIFFRACTIONr_long_range_B_other6.02935.9845555
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.283→2.342 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 127 -
Rwork0.302 2418 -
obs--98.26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.38080.1133-0.02160.09460.16040.5455-0.11560.03540.24110.02010.02390.00850.1495-0.11040.09160.1279-0.041-0.01740.1009-0.05170.207821.25210.139412.6367
20.6233-0.36580.84890.72380.41242.787-0.16780.4623-0.11840.147-0.07160.2889-0.15780.96940.23940.092-0.05250.02840.4955-0.0360.131342.14694.385857.2626
31.54860.0322-0.6450.18640.30460.9276-0.0927-0.15910.1250.02980.0692-0.01790.18080.17210.02350.1560.0486-0.00550.0765-0.06330.199942.9514-3.883817.5007
40.59110.01750.43980.651-0.29262.44970.10920.0163-0.09580.01240.03920.02970.2836-0.1846-0.14840.18430.0129-0.04240.068-0.02320.149422.2601-5.011462.4538
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 302
2X-RAY DIFFRACTION2C-3 - 302
3X-RAY DIFFRACTION3B-2 - 302
4X-RAY DIFFRACTION4D-2 - 302

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