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- PDB-4x44: Crystal Structure of Mutant R89Q of human Adenine phosphoribosylt... -

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Basic information

Entry
Database: PDB / ID: 4x44
TitleCrystal Structure of Mutant R89Q of human Adenine phosphoribosyltransferase
ComponentsAdenine phosphoribosyltransferase
KeywordsTRANSFERASE / APRT
Function / homology
Function and homology information


Defective APRT disrupts adenine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / grooming behavior / Purine salvage / GMP salvage / IMP salvage / AMP salvage ...Defective APRT disrupts adenine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / grooming behavior / Purine salvage / GMP salvage / IMP salvage / AMP salvage / purine ribonucleoside salvage / AMP binding / secretory granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / cytoplasm / 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
ADENOSINE MONOPHOSPHATE / Adenine phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0535 Å
AuthorsPimenta, A. / Pereira, H.M. / Mercaldi, G. / Thiemann, O.H.
CitationJournal: To Be Published
Title: Crystal Structure of Mutant R89Q of human Adenine phosphoribosyltransferase
Authors: Pimenta, A. / Pereira, H.M. / Mercaldi, G. / Thiemann, O.H.
History
DepositionDec 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)20,1364
Polymers19,6011
Non-polymers5353
Water3,855214
1
A: Adenine phosphoribosyltransferase
hetero molecules

A: Adenine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2728
Polymers39,2012
Non-polymers1,0716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area5310 Å2
ΔGint-61 kcal/mol
Surface area14460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.493, 59.493, 109.772
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1175-

HOH

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Components

#1: Protein Adenine phosphoribosyltransferase / APRT


Mass: 19600.662 Da / Num. of mol.: 1 / Mutation: R89Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APRT / Plasmid: pet29a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P07741, adenine phosphoribosyltransferase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25.5% PEG 4000, 85mM Tris pH 8.5, 170mM Sodium acetate, 15% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.458 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 2.053→52.305 Å / Num. all: 12943 / Num. obs: 12943 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.058 / Rrim(I) all: 0.149 / Rsym value: 0.137 / Net I/av σ(I): 5.034 / Net I/σ(I): 12.9 / Num. measured all: 85146
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.053-2.166.60.4781.51196218070.20.4783.7100
2.16-2.296.60.3721166717600.1550.374.9100
2.29-2.456.70.3062.41092216360.1280.3066100
2.45-2.656.70.2313.21031615490.0960.2318.5100
2.65-2.96.70.1824.1948314220.0760.18210.8100
2.9-3.246.60.1186.2866113030.0490.11815.6100
3.24-3.746.60.0957769911600.040.09521100
3.74-4.586.50.06510.2654910040.0280.06526.9100
4.58-6.486.30.05710.850998030.0240.05730.7100
6.48-54.8865.60.04613.127884990.0210.04632.799.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.2.25data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.0535→52.305 Å / FOM work R set: 0.8731 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 628 4.87 %Random selection
Rwork0.17 12261 --
obs0.1716 12889 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.13 Å2 / Biso mean: 20.23 Å2 / Biso min: 7.91 Å2
Refinement stepCycle: final / Resolution: 2.0535→52.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 34 214 1600
Biso mean--26.39 32.02 -
Num. residues----177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021414
X-RAY DIFFRACTIONf_angle_d0.6611920
X-RAY DIFFRACTIONf_chiral_restr0.045216
X-RAY DIFFRACTIONf_plane_restr0.003244
X-RAY DIFFRACTIONf_dihedral_angle_d14.536539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0535-2.26010.25891440.19932953X-RAY DIFFRACTION99
2.2601-2.58720.23691590.18423024X-RAY DIFFRACTION100
2.5872-3.25950.21741590.17353050X-RAY DIFFRACTION100
3.2595-52.320.16521660.15263234X-RAY DIFFRACTION100
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)
13.26080.71040.15123.56410.08694.0435-0.1049-0.3385-0.56080.281-0.0891-0.22080.30570.17530.09420.15880.00920.02870.16720.05620.2203-8.9058-14.522435.2639
22.6165-0.0197-0.54542.3180.17712.0516-0.0693-0.03030.11790.0762-0.00390.2138-0.0781-0.10810.06370.09140.00820.01130.130.0210.1123-17.7092-1.359236.731
30.36120.3910.57621.03420.89735.29110.04210.0335-0.0553-0.0255-0.11430.01310.34540.2245-0.02250.1290.03530.0190.1010.01490.138-3.8224-11.771723.9115
42.265-0.9669-0.90872.57470.49692.86820.04770.0185-0.12640.025-0.0551-0.0478-0.00670.06410.03610.1192-0.01520.00640.09340.02160.1292-3.663-1.804420.0445
51.045-0.82950.52472.65-0.60831.2919-0.0934-0.12730.20810.17970.0871-0.0972-0.14360.06380.03640.0999-0.01690.0020.1227-0.00470.1347-6.31989.600817.6422
61.89480.659-0.02252.3853-0.62062.09180.0554-0.3522-0.03260.20170.15090.39-0.1073-0.1758-0.13180.15460.04140.02140.18920.02840.1866-19.30279.880116.3553
70.7925-0.07740.11981.5522-0.71762.0573-0.01630.0322-0.0001-0.12590.0730.01470.16860.1204-0.0750.10810.0004-0.01090.08860.00390.1187-11.44991.972112.9393
81.60180.21-0.90161.3302-0.50091.9703-0.11480.0893-0.1339-0.18780.07710.23130.2829-0.2660.0210.137-0.0119-0.01960.1268-0.00420.1472-17.5304-6.082217.2136
90.75980.20970.2562.3579-1.16974.89050.0315-0.0245-0.1754-0.14160.07560.15020.1365-0.4317-0.08120.1308-0.0056-0.0170.1292-0.01660.1072-17.4892-10.357521.986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 12 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 35 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 54 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 55 through 79 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 80 through 95 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 96 through 113 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 114 through 146 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 147 through 168 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 169 through 180 )A0

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