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- PDB-4h0u: Crystal structure of thymidylate synthase from Corynebacterium gl... -

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Basic information

Entry
Database: PDB / ID: 4h0u
TitleCrystal structure of thymidylate synthase from Corynebacterium glutamicum in complex with dUMP
ComponentsThymidylate synthase
KeywordsTRANSFERASE / nucleotide / dUMP
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytoplasm
Similarity search - Function
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsWang, W.C. / Chang, C.M.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of thymidylate synthase from Corynebacterium glutamicum in complex with dUMP
Authors: Wang, W.C. / Chang, C.M.
History
DepositionSep 10, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Thymidylate synthase
B: Thymidylate synthase
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,2768
Polymers121,0434
Non-polymers1,2334
Water1,33374
1
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1384
Polymers60,5222
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-22 kcal/mol
Surface area21230 Å2
MethodPISA
2
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1384
Polymers60,5222
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-23 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.042, 87.815, 165.747
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Thymidylate synthase / TS / TSase


Mass: 30260.863 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: cg0966, Cgl0844, thyA / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q8NS38, thymidylate synthase
#2: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.29 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M magnesium chloride, 0.1M Tris-HCl, 21% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 27894 / % possible obs: 99.9 % / Redundancy: 8 % / Rmerge(I) obs: 0.115
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 5.08 / Num. unique all: 2911 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H0R

4h0r


Resolution: 2.75→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.899 / SU B: 12.743 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24112 1516 5.2 %RANDOM
Rwork0.18653 ---
obs0.18934 27894 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.959 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2--0.64 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8264 0 80 74 8418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0218580
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.94811686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.22851018
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77724.467441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.363151349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5761546
X-RAY DIFFRACTIONr_chiral_restr0.1030.21231
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216694
X-RAY DIFFRACTIONr_mcbond_it0.7531.55104
X-RAY DIFFRACTIONr_mcangle_it1.45228225
X-RAY DIFFRACTIONr_scbond_it2.06733476
X-RAY DIFFRACTIONr_scangle_it3.4174.53461
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 101 -
Rwork0.226 2021 -
obs--99.44 %

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