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- PDB-9jd2: Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylas... -

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Basic information

Entry
Database: PDB / ID: 9jd2
TitleCrystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 353K
ComponentsS-methyl-5'-thioadenosine phosphorylase
KeywordsTRANSFERASE / MTAP / complex / phosphorylase
Function / homology
Function and homology information


S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / purine ribonucleoside salvage / cytosol
Similarity search - Function
Methylthioadenosine phosphorylase (MTAP) / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily
Similarity search - Domain/homology
5'-DEOXY-5'-METHYLTHIOADENOSINE / PHOSPHATE ION / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesAeropyrum pernix K1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsIizuka, Y. / Kikuchi, M. / Yamauchi, T. / Tsunoda, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 353K
Authors: Iizuka, Y. / Kikuchi, M. / Yamauchi, T. / Tsunoda, M.
History
DepositionAug 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1703
Polymers30,7771
Non-polymers3922
Water84747
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)93,5099
Polymers92,3323
Non-polymers1,1776
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area10530 Å2
ΔGint-75 kcal/mol
Surface area27480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.048, 79.048, 233.48
Angle α, β, γ (deg.)90, 90, 120
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 30777.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first M and second F are missing in the uploaded structure because the electron density could not be observed.
Source: (gene. exp.) Aeropyrum pernix K1 (archaea) / Gene: mtnP, APE_1885 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9YAQ8, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


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


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.28 Å3/Da / Density % sol: 46.172 %
Crystal growTemperature: 293.2 K / Method: counter-diffusion / pH: 5.4
Details: The mixture of protein solution and agarose was filled into a glass capillary, and the capillary was immersed in the reservoir solution for crystallization. The composition of the reservoir ...Details: The mixture of protein solution and agarose was filled into a glass capillary, and the capillary was immersed in the reservoir solution for crystallization. The composition of the reservoir solution was as follows.15%(v/v)PEG#200,0.1 M phosphate citrate pH 5.4, 5 mM MTA

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Data collection

DiffractionMean temperature: 353 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→39.52 Å / Num. obs: 36182 / % possible obs: 100 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.069 / Rrim(I) all: 0.157 / Χ2: 0.85 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.87-39.5280.0325.82590.9990.0150.0330.397.4
1.62-1.65102.5451.117630.3441.2462.8380.93100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.77)refinement
Cootmodel building
MOLREPphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WTA

1wta


Resolution: 1.62→38.944 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.973 / SU B: 3.878 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.08 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1676 1820 5.03 %
Rwork0.1228 34362 -
all0.125 --
obs-36182 99.953 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.651 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0.155 Å20 Å2
2---0.31 Å20 Å2
3---1.005 Å2
Refinement stepCycle: LAST / Resolution: 1.62→38.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 25 47 2214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122245
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162116
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.8193064
X-RAY DIFFRACTIONr_angle_other_deg0.5911.7594854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9035278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.261526
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.01851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92510356
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.21610101
X-RAY DIFFRACTIONr_chiral_restr0.0870.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022710
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
X-RAY DIFFRACTIONr_nbd_refined0.2170.2348
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.21778
X-RAY DIFFRACTIONr_nbtor_refined0.180.21103
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21162
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.249
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2330.212
X-RAY DIFFRACTIONr_nbd_other0.2180.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1750.28
X-RAY DIFFRACTIONr_mcbond_it7.2182.4041103
X-RAY DIFFRACTIONr_mcbond_other7.2172.4041103
X-RAY DIFFRACTIONr_mcangle_it10.8414.3231381
X-RAY DIFFRACTIONr_mcangle_other10.8384.3231382
X-RAY DIFFRACTIONr_scbond_it10.9583.0981142
X-RAY DIFFRACTIONr_scbond_other10.9573.0971142
X-RAY DIFFRACTIONr_scangle_it16.3175.3881682
X-RAY DIFFRACTIONr_scangle_other16.3125.3861683
X-RAY DIFFRACTIONr_lrange_it20.20724.4852336
X-RAY DIFFRACTIONr_lrange_other20.20324.4912337
X-RAY DIFFRACTIONr_rigid_bond_restr4.18734361
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.62-1.6620.3221310.28924860.29126170.9350.9441000.283
1.662-1.7070.3051380.27124480.27325860.9280.9541000.262
1.707-1.7570.3171220.25623970.25925190.9380.961000.243
1.757-1.8110.2591200.20922840.21224040.9590.9741000.193
1.811-1.870.2131130.1722650.17223780.9730.9821000.149
1.87-1.9360.1781300.1321570.13322870.9820.9891000.109
1.936-2.0080.1431130.11820870.1222010.9880.99299.95460.1
2.008-2.090.1641090.11420270.11621360.9870.9931000.099
2.09-2.1830.173990.10619360.10920350.9830.9941000.094
2.183-2.2890.1431030.09918480.10119520.9870.99699.94880.09
2.289-2.4120.141930.09517750.09718680.9880.9961000.089
2.412-2.5580.184790.09817070.10217870.9820.99599.9440.092
2.558-2.7340.149690.11216040.11416750.9870.99299.88060.112
2.734-2.9520.149770.10814540.1115310.9870.9931000.111
2.952-3.2320.134740.10613780.10714520.9890.9931000.113
3.232-3.610.12640.09612550.09713190.9910.9941000.107
3.61-4.1630.121480.09211180.09311660.9920.9951000.109
4.163-5.0840.136530.0979420.0999960.990.99599.89960.123
5.084-7.1290.204540.1277430.1327970.9830.9931000.16
7.129-38.9440.177310.1494510.1514880.9840.98698.77050.209

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