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- PDB-4ga6: Crystal structure of AMP phosphorylase C-terminal deletion mutant... -

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Basic information

Entry
Database: PDB / ID: 4ga6
TitleCrystal structure of AMP phosphorylase C-terminal deletion mutant in complex with substrates
ComponentsPutative thymidine phosphorylase
KeywordsTRANSFERASE / phosphorolysis
Function / homology
Function and homology information


AMP phosphorylase / pyrimidine deoxyribonucleoside metabolic process / pentosyltransferase 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
ADENOSINE MONOPHOSPHATE / AMP phosphorylase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)110,6998
Polymers109,6202
Non-polymers1,0796
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-103 kcal/mol
Surface area35230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.177, 87.915, 105.549
Angle α, β, γ (deg.)90.00, 98.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative thymidine phosphorylase / / TdRPase


Mass: 54810.012 Da / Num. of mol.: 2 / 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
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1M phosphate-citrate, 20% (w/v) PEG 1000, 50mM Li2SO4, 0.2M guanidine-HCl, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 46007 / % possible obs: 98.9 %
Reflection shellResolution: 2.21→2.29 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.396 / % possible all: 97.3

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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 4GA5

4ga5


Resolution: 2.21→50 Å / Occupancy max: 1 / Occupancy min: 1
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2310 5 %RANDOM
Rwork0.214 ---
obs-45875 --
Solvent computationBsol: 66.2054 Å2
Displacement parametersBiso max: 69.99 Å2 / Biso mean: 31.6645 Å2 / Biso min: 9.81 Å2
Baniso -1Baniso -2Baniso -3
1-8.285 Å20 Å2-4.299 Å2
2---5.524 Å20 Å2
3----2.761 Å2
Refinement stepCycle: LAST / Resolution: 2.21→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7007 0 66 373 7446
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_mcbond_it1.7251.5
X-RAY DIFFRACTIONc_scbond_it2.9712
X-RAY DIFFRACTIONc_mcangle_it2.5662
X-RAY DIFFRACTIONc_scangle_it4.0992.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2amp_xplor_par.txt
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4water_rep.param

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