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

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Basic information

Entry
Database: PDB / ID: 3ozc
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 / 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
Chem-4CT / PHOSPHATE ION / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,7623
Polymers31,2771
Non-polymers4852
Water1,20767
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)95,2869
Polymers93,8313
Non-polymers1,4556
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area7340 Å2
ΔGint-81 kcal/mol
Surface area30390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.252, 123.252, 44.879
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-286-

HOH

21A-289-

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.: 1
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.: 1 / Source method: obtained synthetically / Formula: C18H20ClN5OS
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2M NaCl, 0.1M phosphate buffer, 10% PEG 8000, pH 6.2, 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, L10.487
11h+k,-k,-l20.513
ReflectionResolution: 1.93→50 Å / Num. obs: 29552 / % possible obs: 99.5 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.077 / Χ2: 0.967 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.93-270.37627540.825194.8
2-2.087.10.2929410.8991100
2.08-2.177.20.20829480.9091100
2.17-2.297.20.16229500.9761100
2.29-2.437.30.13229730.9691100
2.43-2.627.30.129581.0311100
2.62-2.887.40.07729450.9841100
2.88-3.37.40.06229930.9661100
3.3-4.167.20.05829911.0891100
4.16-507.10.04730991.005199.7

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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: 1.93→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 2.604 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1541 1562 5.3 %RANDOM
Rwork0.1305 ---
obs0.1318 29481 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 46.55 Å2 / Biso mean: 21.5879 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--3.2 Å20 Å20 Å2
2---3.2 Å20 Å2
3---6.4 Å2
Refinement stepCycle: LAST / Resolution: 1.93→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2112 0 31 67 2210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222186
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9792963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8995272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22724.0786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95915387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7841513
X-RAY DIFFRACTIONr_chiral_restr0.090.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211600
X-RAY DIFFRACTIONr_mcbond_it0.7791.51358
X-RAY DIFFRACTIONr_mcangle_it1.41822206
X-RAY DIFFRACTIONr_scbond_it2.3433828
X-RAY DIFFRACTIONr_scangle_it3.8784.5757
LS refinement shellResolution: 1.932→1.982 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 125 -
Rwork0.161 2003 -
all-2128 -
obs--97.7 %

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