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- PDB-6cdz: E. coli thymidylate synthase mutant I264Am -

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Basic information

Entry
Database: PDB / ID: 6cdz
TitleE. coli thymidylate synthase mutant I264Am
ComponentsThymidylate synthase
KeywordsTRANSFERASE
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / response to radiation / regulation of translation / methylation / magnesium ion binding / protein homodimerization activity / RNA binding / cytosol
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
10-PROPARGYL-5,8-DIDEAZAFOLIC ACID / 2'-deoxy-5'-uridylic acid / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFiner-moore, J.S. / Lee, T.T. / Stroud, R.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA-41323 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA63081 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM024485 United States
Citation
Journal: Biochemistry / Year: 2018
Title: A Single Mutation Traps a Half-Sites Reactive Enzyme in Midstream, Explaining Asymmetry in Hydride Transfer.
Authors: Finer-Moore, J.S. / Lee, T.T. / Stroud, R.M.
#1: Journal: Biochemistry / Year: 2000
Title: Effects of subunit occupancy on partitioning of an intermediate in thymidylate synthase mutants.
Authors: Variath, P. / Liu, Y. / Lee, T.T. / Stroud, R.M. / Santi, D.V.
History
DepositionFeb 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4666
Polymers60,8932
Non-polymers1,5734
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-20 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.658, 80.451, 94.080
Angle α, β, γ (deg.)90.00, 103.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thymidylate synthase / / TSase


Mass: 30446.510 Da / Num. of mol.: 2 / Fragment: residues 1-263
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: thyA, b2827, JW2795 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A884, thymidylate synthase
#2: Chemical ChemComp-CB3 / 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID


Mass: 477.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H23N5O6
#3: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P
#4: Chemical ChemComp-UMC / 2'-deoxy-5'-uridylic acid


Mass: 310.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O8P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES, 200 mM NH4Ac, 5mM DTT, 32% PEG 4000 (W/V)
PH range: 8.0-8.3

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 11, 2000
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 16256 / % possible obs: 84.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 10.5
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 720 / % possible all: 76.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1KCE

1kce


Resolution: 2.4→17 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.13
RfactorNum. reflection% reflectionSelection details
Rfree0.229 853 5.25 %andom
Rwork0.1803 ---
obs0.183 16238 84.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4290 0 110 162 4562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034562
X-RAY DIFFRACTIONf_angle_d0.6026206
X-RAY DIFFRACTIONf_dihedral_angle_d13.4712657
X-RAY DIFFRACTIONf_chiral_restr0.04639
X-RAY DIFFRACTIONf_plane_restr0.003805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4002-2.55010.31891120.25282416X-RAY DIFFRACTION80
2.5501-2.74630.29011380.23652409X-RAY DIFFRACTION80
2.7463-3.02130.2941380.22932454X-RAY DIFFRACTION81
3.0213-3.45540.28831460.20252488X-RAY DIFFRACTION82
3.4554-4.34170.19321360.15322635X-RAY DIFFRACTION86
4.3417-17.15980.17191830.13922983X-RAY DIFFRACTION97

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