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- PDB-4h0r: Crystal structure of thymidylate synthase from Corynebacterium gl... -

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Basic information

Entry
Database: PDB / ID: 4h0r
TitleCrystal structure of thymidylate synthase from Corynebacterium glutamicum
ComponentsThymidylate synthase
KeywordsTRANSFERASE / nucleotide / dUMP
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytosol
Similarity search - Function
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Thymidylate synthase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChang, C.M. / Wang, W.C.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of thymidylate synthase from Corynebacterium glutamicum
Authors: Chang, C.M. / Wang, W.C.
History
DepositionSep 10, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 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 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thymidylate synthase
B: Thymidylate synthase


Theoretical massNumber of molelcules
Total (without water)60,5222
Polymers60,5222
Non-polymers00
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-14 kcal/mol
Surface area21600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.464, 67.220, 78.120
Angle α, β, γ (deg.)90.000, 91.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thymidylate synthase / TS / TSase


Mass: 30260.863 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.28 Å3/Da / Density % sol: 45.94 % / Mosaicity: 0.51 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M magnesium chloride, 0.1M Tris-HCl, 24% 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: 2.3→30 Å / Num. obs: 24054 / % possible obs: 99.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.079 / Χ2: 1.082 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.383.20.42623071.208195.7
2.38-2.483.50.37423691.181199.5
2.48-2.593.70.30324311.133199.9
2.59-2.733.80.21723871.111199.9
2.73-2.93.80.1524131.119199.7
2.9-3.123.70.09924061.026199.7
3.12-3.433.70.06824090.995199.5
3.43-3.933.70.05724291.067199.7
3.93-4.953.70.05424210.974199.3
4.95-303.50.03724821.046199.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TSC

2tsc


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.687 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.387 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 1196 5 %RANDOM
Rwork0.1833 ---
obs0.1857 23991 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 81.26 Å2 / Biso mean: 31.3245 Å2 / Biso min: 10.63 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å20 Å2-0.2 Å2
2---0.98 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4154 0 0 196 4350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0214271
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9365815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5015513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51224.505222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.27315677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.0951523
X-RAY DIFFRACTIONr_chiral_restr0.1210.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213351
X-RAY DIFFRACTIONr_mcbond_it1.1061.52568
X-RAY DIFFRACTIONr_mcangle_it2.02924141
X-RAY DIFFRACTIONr_scbond_it3.16931703
X-RAY DIFFRACTIONr_scangle_it4.9164.51674
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 85 -
Rwork0.238 1536 -
all-1621 -
obs--93.27 %

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