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- PDB-4ga4: Crystal structure of AMP phosphorylase N-terminal deletion mutant -

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Basic information

Entry
Database: PDB / ID: 4ga4
TitleCrystal structure of AMP phosphorylase N-terminal deletion mutant
ComponentsPutative thymidine phosphorylase
KeywordsTRANSFERASE / phosphorolysis
Function / homology
Function and homology information


AMP phosphorylase / pyrimidine deoxyribonucleoside metabolic process / pentosyltransferase activity / thymidine phosphorylase activity / pyrimidine nucleobase metabolic process / 1,4-alpha-oligoglucan phosphorylase activity / AMP catabolic process / AMP binding / phosphate ion binding / cytosol
Similarity search - Function
Thymidine phosphorylase/AMP phosphorylase / AMP phosphorylase / Pyrimidine nucleoside phosphorylase-like, C-terminal domain / Thymidine/pyrimidine-nucleoside phosphorylase / Pyrimidine nucleoside phosphorylase, C-terminal / Pyrimidine-nucleoside phosphorylase, conserved site / Pyrimidine nucleoside phosphorylase-like, C-terminal domain superfamily / Pyrimidine nucleoside phosphorylase C-terminal domain / Thymidine and pyrimidine-nucleoside phosphorylases signature. / Pyrimidine nucleoside phosphorylase C-terminal domain ...Thymidine phosphorylase/AMP phosphorylase / AMP phosphorylase / Pyrimidine nucleoside phosphorylase-like, C-terminal domain / Thymidine/pyrimidine-nucleoside phosphorylase / Pyrimidine nucleoside phosphorylase, C-terminal / Pyrimidine-nucleoside phosphorylase, conserved site / Pyrimidine nucleoside phosphorylase-like, C-terminal domain superfamily / Pyrimidine nucleoside phosphorylase C-terminal domain / Thymidine and pyrimidine-nucleoside phosphorylases signature. / Pyrimidine nucleoside phosphorylase C-terminal domain / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C / Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / Glycosyl transferase family 3, N-terminal domain / Glycosyl transferase family 3, N-terminal domain superfamily / Glycosyl transferase family, helical bundle domain / Glycosyl transferase, family 3 / Glycosyl transferase family, a/b domain / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain superfamily / Aldehyde Oxidoreductase; domain 3 / Alpha-Beta Complex / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / AMP phosphorylase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å
AuthorsNishitani, Y. / Aono, R. / Nakamura, A. / Sato, T. / Atomi, H. / Imanaka, T. / Miki, K.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization
Authors: Nishitani, Y. / Aono, R. / Nakamura, A. / Sato, T. / Atomi, H. / Imanaka, T. / Miki, K.
History
DepositionJul 25, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Nov 8, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Putative thymidine phosphorylase
B: Putative thymidine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1364
Polymers93,9462
Non-polymers1902
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-31 kcal/mol
Surface area33520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.122, 166.122, 93.439
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Putative thymidine phosphorylase / TdRPase


Mass: 46973.176 Da / Num. of mol.: 2 / Fragment: UNP residues 85-503
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: deoA / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: Q5JCX3, thymidine phosphorylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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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: 3.96 Å3/Da / Density % sol: 68.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate tribasic dihydrate, 1.65M 1,6-hexanediol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.51→50 Å / Num. obs: 18550 / % possible obs: 100 %
Reflection shellResolution: 3.51→3.64 Å / Mean I/σ(I) obs: 5.9 / Rsym value: 0.398 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DSJ

2dsj


Resolution: 3.51→50 Å / Occupancy max: 1 / Occupancy min: 1
RfactorNum. reflection% reflectionSelection details
Rfree0.322 943 5.1 %RANDOM
Rwork0.272 ---
obs-18500 --
Solvent computationBsol: 38.8262 Å2
Displacement parametersBiso max: 198.83 Å2 / Biso mean: 79.5859 Å2 / Biso min: 25.78 Å2
Baniso -1Baniso -2Baniso -3
1-3.825 Å20 Å20 Å2
2--3.825 Å20 Å2
3----7.65 Å2
Refinement stepCycle: LAST / Resolution: 3.51→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5670 0 10 0 5680
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.7
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param

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