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- PDB-2pyw: Structure of A. thaliana 5-methylthioribose kinase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2pyw
TitleStructure of A. thaliana 5-methylthioribose kinase in complex with ADP and MTR
ComponentsUncharacterized protein
KeywordsTRANSFERASE / 5-methylthioribose kinase / plant methionine recycling / refolding
Function / homology
Function and homology information


S-methyl-5-thioribose kinase / S-methyl-5-thioribose kinase activity / L-methionine salvage from methylthioadenosine / ATP binding / identical protein binding / cytosol
Similarity search - Function
Methylthioribose kinase / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 5-S-methyl-5-thio-alpha-D-ribofuranose / Methylthioribose kinase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKu, S.Y.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: Structure of A. thaliana 5-methylthioribose kinase in complex with ADP and MTR reveals a more occluded active site than its bacterial homolog
Authors: Ku, S.Y. / Cornell, K.A. / Howell, P.L.
History
DepositionMay 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,97918
Polymers96,2612
Non-polymers1,71816
Water14,016778
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-77 kcal/mol
Surface area30070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)162.460, 82.240, 91.080
Angle α, β, γ (deg.)90.00, 117.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Uncharacterized protein / At1g49820/F10F5_1


Mass: 48130.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: F10F5.1 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9C6D2, S-methyl-5-thioribose kinase
#4: Sugar ChemComp-SR1 / 5-S-methyl-5-thio-alpha-D-ribofuranose / 5-S-methyl-5-thio-alpha-D-ribose / 5-S-methyl-5-thio-D-ribose / 5-S-methyl-5-thio-ribose


Type: D-saccharide, alpha linking / Mass: 180.222 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O4S
IdentifierTypeProgram
a-D-Ribf5SMeIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 792 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 778 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 29, 2003 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→80.58 Å / Num. all: 83556 / Num. obs: 82470 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.38 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 16.9
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 4.8 / % possible all: 90.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OLC

2olc


Resolution: 1.9→80.58 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.451 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19723 4105 5 %RANDOM
Rwork0.16303 ---
all0.16475 83556 --
obs0.16475 78352 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.312 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-0.27 Å2
2--0.72 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.9→80.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6650 0 103 778 7531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226895
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9659322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9075825
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04223.664333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.901151181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6731548
X-RAY DIFFRACTIONr_chiral_restr0.0950.21020
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025197
X-RAY DIFFRACTIONr_nbd_refined0.1950.23446
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24777
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2713
X-RAY DIFFRACTIONr_metal_ion_refined0.0680.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3170.227
X-RAY DIFFRACTIONr_mcbond_it0.8191.54290
X-RAY DIFFRACTIONr_mcangle_it1.19626632
X-RAY DIFFRACTIONr_scbond_it2.09833029
X-RAY DIFFRACTIONr_scangle_it3.1994.52690
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 268 -
Rwork0.206 5146 -
obs--88.44 %

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