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- PDB-4ga5: Crystal structure of AMP phosphorylase C-terminal deletion mutant... -

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Basic information

Entry
Database: PDB / ID: 4ga5
TitleCrystal structure of AMP phosphorylase C-terminal deletion mutant in the apo-form
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
Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 - #50 / 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. ...Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 - #50 / 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 / 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 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Aldehyde Oxidoreductase; domain 3 / Alpha-Beta Complex / Up-down Bundle / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Putative thymidine phosphorylase
A: Putative thymidine phosphorylase
C: Putative thymidine phosphorylase
D: Putative thymidine phosphorylase
E: Putative thymidine phosphorylase
F: Putative thymidine phosphorylase
G: Putative thymidine phosphorylase
H: Putative thymidine phosphorylase


Theoretical massNumber of molelcules
Total (without water)438,4808
Polymers438,4808
Non-polymers00
Water00
1
B: Putative thymidine phosphorylase
F: Putative thymidine phosphorylase


Theoretical massNumber of molelcules
Total (without water)109,6202
Polymers109,6202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-24 kcal/mol
Surface area36810 Å2
MethodPISA
2
A: Putative thymidine phosphorylase

E: Putative thymidine phosphorylase


Theoretical massNumber of molelcules
Total (without water)109,6202
Polymers109,6202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
Buried area3230 Å2
ΔGint-27 kcal/mol
Surface area36850 Å2
MethodPISA
3
C: Putative thymidine phosphorylase
G: Putative thymidine phosphorylase


Theoretical massNumber of molelcules
Total (without water)109,6202
Polymers109,6202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-26 kcal/mol
Surface area37120 Å2
MethodPISA
4
D: Putative thymidine phosphorylase
H: Putative thymidine phosphorylase


Theoretical massNumber of molelcules
Total (without water)109,6202
Polymers109,6202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-26 kcal/mol
Surface area37070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.330, 249.482, 162.369
Angle α, β, γ (deg.)90.00, 110.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Putative thymidine phosphorylase / TdRPase


Mass: 54810.012 Da / Num. of mol.: 8 / Fragment: UNP residues 1-493
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

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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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M citrate-NaOH, 12% (w/v) PEG 4000, 5% (v/v) ethylene glycol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 73009 / % possible obs: 99.8 %
Reflection shellResolution: 3.25→3.37 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.401 / % possible all: 99.9

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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 4GA4

4ga4


Resolution: 3.25→50 Å / Occupancy max: 1 / Occupancy min: 1
RfactorNum. reflection% reflectionSelection details
Rfree0.289 3649 5 %RANDOM
Rwork0.261 ---
obs-72460 --
Solvent computationBsol: 56.9525 Å2
Displacement parametersBiso max: 251.77 Å2 / Biso mean: 59.173 Å2 / Biso min: 5.8 Å2
Baniso -1Baniso -2Baniso -3
1--6.704 Å20 Å2-0.827 Å2
2--3.096 Å20 Å2
3---3.608 Å2
Refinement stepCycle: LAST / Resolution: 3.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26752 0 0 0 26752
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param

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