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- PDB-1cb0: STRUCTURE OF HUMAN 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE ... -

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Basic information

Entry
Database: PDB / ID: 1cb0
TitleSTRUCTURE OF HUMAN 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE AT 1.7 A RESOLUTION
ComponentsPROTEIN (5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE)
KeywordsTRANSFERASE / METHYLTHIOADENOSINE PHOSPHORYLASE / PURINE NUCLEOSIDE PHOSPHORYLASE / PURINE SALVAGE / ADENINE
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 / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / 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 / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / 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
ADENINE / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 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
DepositionFeb 26, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,4122
Polymers31,2771
Non-polymers1351
Water3,117173
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)94,2376
Polymers93,8313
Non-polymers4053
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 area7690 Å2
ΔGint-37 kcal/mol
Surface area29850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.760, 120.760, 44.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Cell settingtrigonal
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-361-

HOH

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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
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-ADE / ADENINE / Adenine


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: pH 7.4
Components of the solutions
IDNameCrystal-IDSol-ID
1ETHYLENE GLYCOL11
2PEG 600011
3TRIS BUFFER11
4DTT11
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: Nov 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: 39479 / % possible obs: 93.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 16 Å2 / Rsym value: 0.045 / Net I/σ(I): 12.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 8.1 / Rsym value: 0.078 / % possible all: 83.7
Reflection
*PLUS
Num. measured all: 276082 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 83.7 % / Rmerge(I) obs: 0.078

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Processing

Software
NameVersionClassification
MADSYSphasing
SHELXmodel building
MLPHAREphasing
X-PLOR3.843refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
Details: RESIDUES 282 AND 283 WERE NOT SEEN IN THE ELECTRON DENSITY MAPS DUE TO DISORDER
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3806 10 %RANDOM
Rwork0.181 ---
obs-38017 92.8 %-
Displacement parametersBiso mean: 17.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 10 173 2249
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.258
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.18
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: 0.013 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.265 425 10.2 %
Rwork0.243 3733 -
obs--82.3 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.18

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