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- PDB-1cg6: STRUCTURE OF HUMAN 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE ... -

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Basic information

Entry
Database: PDB / ID: 1cg6
TitleSTRUCTURE OF HUMAN 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE COMPLEXED WITH 5'-DEOXY-5'-METHYLTHIOADENOSINE AND SULFATE AT 1.7 A RESOLUTION
ComponentsPROTEIN (5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE)
KeywordsTRANSFERASE / METHYLTHIOADENOSINE PHOSPHORYLASE / PURINE NUCLEOSIDE PHOSPHORYLASE / PURINE SALVAGE / METHYLTHIOADENOSINE / SULFATE
Function / homology
Function and homology information


Methionine salvage pathway / S-methyl-5'-thioadenosine phosphorylase / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / purine ribonucleoside salvage / nucleobase-containing compound metabolic process / response to testosterone / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / methylation ...Methionine salvage pathway / S-methyl-5'-thioadenosine phosphorylase / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / purine ribonucleoside salvage / nucleobase-containing compound metabolic process / response to testosterone / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / methylation / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
Methylthioadenosine phosphorylase (MTAP) / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-DEOXY-5'-METHYLTHIOADENOSINE / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.7 Å
AuthorsAppleby, T.C. / Erion, M.D. / Ealick, S.E.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: The structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase at 1.7 A resolution provides insights into substrate binding and catalysis.
Authors: Appleby, T.C. / Erion, M.D. / Ealick, S.E.
History
DepositionMar 27, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 5, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: PROTEIN (5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6703
Polymers31,2771
Non-polymers3932
Water2,756153
1
A: PROTEIN (5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE)
hetero molecules

A: PROTEIN (5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE)
hetero molecules

A: PROTEIN (5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0119
Polymers93,8313
Non-polymers1,1806
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area9350 Å2
ΔGint-122 kcal/mol
Surface area30010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.830, 122.830, 45.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Cell settingtrigonal
Space group name H-MP321

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Components

#1: Protein PROTEIN (5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE) / E.C.2.4.2.28 / MTA PHOSPHORYLASE / MTAP


Mass: 31277.053 Da / Num. of mol.: 1 / Mutation: ILE56VAL
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH 5'-DEOXY-5'-METHYLTHIOADENOSINE AND SULFATE
Source: (gene. exp.) Homo sapiens (human) / Tissue: PLACENTA
Description: MTAP CDNA WAS ISOLATED FROM A HUMAN PLACENTA CDNA LIBRARY AND EXPRESSED IN E. COLI
Cellular location: CYTOPLASM / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q13126, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 3 Å3/Da / Density % sol: 59 %
Crystal growpH: 7.4
Details: 12% (W/V) PEG 6000, 25% (V/V) ETHYLENE GLYCOL, 0.2M TRIS-HCL PH 7.8, 0.002M DTT, pH 7.4
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %PEG80001drop
20.1 MHEPES1drop
38 %ethylene glycol1drop
412 %(w/v)PEG60001reservoir
525 %(v/v)ethylene glycol1reservoir
6200 mMTris-HCl1reservoir
72 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.919
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 42292 / % possible obs: 96.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 18.5 Å2 / Rsym value: 5.3 / Net I/σ(I): 9.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6 % / Mean I/σ(I) obs: 6.5 / Rsym value: 10.6 / % possible all: 93.2
Reflection
*PLUS
Num. measured all: 393633 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 93.2 % / Rmerge(I) obs: 0.106

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.7→8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4174 10.1 %RANDOM
Rwork0.202 ---
obs-41325 96.6 %-
Displacement parametersBiso mean: 21.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.218 Å0.2 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 25 153 2244
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.249
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.17
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.7→1.78 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.299 467 9.6 %
Rwork0.287 4388 -
obs--92.6 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10.1 % / Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.17
LS refinement shell
*PLUS
Rfactor Rfree: 0.299 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.287

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