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- PDB-3ozd: Crystal Structure of human 5'-deoxy-5'-methyladenosine phosphoryl... -

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Basic information

Entry
Database: PDB / ID: 3ozd
TitleCrystal Structure of human 5'-deoxy-5'-methyladenosine phosphorylase in complex with pCl-phenylthioDADMeImmA
ComponentsS-methyl-5'-thioadenosine phosphorylase
KeywordsTRANSFERASE / 5'-methylthioadenosine / phosphorylase / MTAP / pCl-phenylthioDADMeImmA
Function / homology
Function and homology information


Methionine salvage pathway / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5'-thioadenosine phosphorylase / 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 / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5'-thioadenosine phosphorylase / 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
Chem-4CT / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsHo, M. / Guan, R. / Almo, S.C. / Schramm, V.L.
CitationJournal: to be published
Title: Crystal Structure of human 5'-deoxy-5'-methyladenosine phosphorylase
Authors: Ho, M. / Guan, R. / Almo, S.C. / Schramm, V.L.
History
DepositionSep 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: S-methyl-5'-thioadenosine phosphorylase
B: S-methyl-5'-thioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3344
Polymers62,5542
Non-polymers7802
Water1,892105
1
A: S-methyl-5'-thioadenosine phosphorylase
hetero molecules

A: S-methyl-5'-thioadenosine phosphorylase
hetero molecules

A: S-methyl-5'-thioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0016
Polymers93,8313
Non-polymers1,1703
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6760 Å2
ΔGint-47 kcal/mol
Surface area30960 Å2
MethodPISA
2
B: S-methyl-5'-thioadenosine phosphorylase
hetero molecules

B: S-methyl-5'-thioadenosine phosphorylase
hetero molecules

B: S-methyl-5'-thioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0016
Polymers93,8313
Non-polymers1,1703
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 area6930 Å2
ΔGint-41 kcal/mol
Surface area31040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.539, 121.539, 87.661
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-286-

HOH

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Components

#1: Protein S-methyl-5'-thioadenosine phosphorylase / 5'-methylthioadenosine phosphorylase / MTA phosphorylase / MTAPase


Mass: 31277.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTAP, MSAP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q13126, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical ChemComp-4CT / (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-chlorophenyl)sulfanyl]methyl}pyrrolidin-3-ol


Mass: 389.902 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20ClN5OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2M NaCl, 0.1M sodium acetate, pH 4.6, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorDetector: CCD / Date: Mar 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.482
11h+k,-k,-l20.518
ReflectionResolution: 2.1→20 Å / Num. obs: 42831 / % possible obs: 99.5 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.124 / Χ2: 1.014 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.178.50.83643110.9541100
2.17-2.268.70.64642600.9681100
2.26-2.368.80.51742830.991100
2.36-2.498.90.42542771.041199.8
2.49-2.648.90.28942761.043199.8
2.64-2.8590.20442771.051199.5
2.85-3.139.10.14642650.989199.4
3.13-3.599.10.142831.064199.3
3.59-4.518.80.07842880.986199.4
4.51-208.70.07343111.049198

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.908 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 7.103 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2565 2189 5.1 %RANDOM
Rwork0.1995 ---
obs0.2023 42748 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.65 Å2 / Biso mean: 35.7552 Å2 / Biso min: 3.48 Å2
Baniso -1Baniso -2Baniso -3
1--3.47 Å20 Å20 Å2
2---3.47 Å20 Å2
3---6.94 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4224 0 52 105 4381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224386
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9775949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0725550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83924.023174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.54515780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9881527
X-RAY DIFFRACTIONr_chiral_restr0.0990.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213221
X-RAY DIFFRACTIONr_mcbond_it0.8211.52725
X-RAY DIFFRACTIONr_mcangle_it1.41924430
X-RAY DIFFRACTIONr_scbond_it2.20731661
X-RAY DIFFRACTIONr_scangle_it3.3854.51516
LS refinement shellResolution: 2.1→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 159 -
Rwork0.208 2929 -
all-3088 -
obs--98.25 %

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