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- PDB-1mzv: Crystal Structure of Adenine Phosphoribosyltransferase (APRT) Fro... -

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Basic information

Entry
Database: PDB / ID: 1mzv
TitleCrystal Structure of Adenine Phosphoribosyltransferase (APRT) From Leishmania tarentolae
ComponentsAdenine Phosphoribosyltransferase
KeywordsTRANSFERASE / alpha/beta structure
Function / homology
Function and homology information


adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / purine ribonucleoside salvage / nucleotide binding / cytoplasm
Similarity search - Function
: / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / PHOSPHATE ION / adenine phosphoribosyltransferase
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsThiemann, O.H. / Silva, M. / Oliva, G. / Silva, C.H.T.P. / Iulek, J.
CitationJournal: Biochim.Biophys.Acta / Year: 2004
Title: Crystal structure of adenine phosphoribosyltransferase from Leishmania tarentolae: potential implications for APRT catalytic mechanism.
Authors: Silva, M. / Silva, C.H.T.P. / Iulek, J. / Oliva, G. / Thiemann, O.H.
History
DepositionOct 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)26,3563
Polymers25,9141
Non-polymers4422
Water4,197233
1
A: Adenine Phosphoribosyltransferase
hetero molecules

A: Adenine Phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7126
Polymers51,8282
Non-polymers8844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area4980 Å2
ΔGint-39 kcal/mol
Surface area18400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.538, 64.538, 234.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operation: y-x, y, 1/2-z

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Components

#1: Protein Adenine Phosphoribosyltransferase


Mass: 25913.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania tarentolae (eukaryote) / Plasmid: pET29(+) / Production host: Escherichia coli (E. coli)
References: UniProt: O77103, adenine phosphoribosyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 277 K / pH: 7
Details: MOPS 100 mM, 22% isopropanol, Protein at 8 mg/ml, pH 7.00, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
22 mMAMP1drop
3100 mMMOPS1reservoirpH7.0
422 %isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.38
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 2.2→28.27 Å / Num. obs: 15513 / % possible obs: 99.5 % / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.24 Å / % possible all: 93.1
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / Num. obs: 14724 / % possible obs: 99.5 % / Num. measured all: 229639 / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.08refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QB7

1qb7


Resolution: 2.2→28.27 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 789 5.1 %RANDOM
Rwork0.181 ---
obs0.183 14724 99.5 %-
all-15513 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.16 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å21.01 Å20 Å2
2--2.01 Å20 Å2
3----3.02 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 28 233 1911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211710
X-RAY DIFFRACTIONr_bond_other_d0.0020.021598
X-RAY DIFFRACTIONr_angle_refined_deg1.4942.0012317
X-RAY DIFFRACTIONr_angle_other_deg0.87133708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6195215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9922.98567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.76715293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5771514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021871
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02337
X-RAY DIFFRACTIONr_nbd_refined0.220.2375
X-RAY DIFFRACTIONr_nbd_other0.250.21897
X-RAY DIFFRACTIONr_nbtor_other0.0860.2951
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.2177
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3680.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2740.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6531.51070
X-RAY DIFFRACTIONr_mcangle_it1.23121722
X-RAY DIFFRACTIONr_scbond_it1.9523640
X-RAY DIFFRACTIONr_scangle_it3.2514.5595
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.278 58
Rwork0.229 986
Refinement TLS params.Method: refined / Origin x: 8.3269 Å / Origin y: 31.2102 Å / Origin z: 68.421 Å
111213212223313233
T0.1567 Å20.02 Å2-0.154 Å2-0.0033 Å2-0.0197 Å2--0.1514 Å2
L1.9834 °2-0.2831 °22.4906 °2-1.5704 °20.1629 °2--5.8951 °2
S-0.2356 Å °0.0148 Å °0.1499 Å °0.1496 Å °0.1159 Å °-0.1258 Å °-0.3365 Å °0.3358 Å °0.1198 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2172 - 217
2X-RAY DIFFRACTION1AC3011
3X-RAY DIFFRACTION1AB4011
4X-RAY DIFFRACTION1AD402 - 6341 - 233
Refinement
*PLUS
Rfactor Rfree: 0.2178 / Rfactor Rwork: 0.1809
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.494

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