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- PDB-2g8x: Escherichia coli Y209W apoprotein -

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Basic information

Entry
Database: PDB / ID: 2g8x
TitleEscherichia coli Y209W apoprotein
Componentsthymidylate synthase
KeywordsTRANSFERASE / beta sheet / alpha/beta protein / DTT
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
CARBONATE ION / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / PHOSPHATE ION / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsLee, T.T. / Finer-Moore, J.S. / Stroud, R.M.
CitationJournal: TO BE PUBLISHED
Title: The role of protein dynamics in thymidylate synthase catalysis: Variants of conserved dUMP-binding Tyr-261
Authors: Newby, Z. / Lee, T.T. / Morse, R.J. / Liu, L. / Liu, Y. / Venkatraman, P. / Santi, D.V. / Finer-Moore, J.S. / Stroud, R.M.
History
DepositionMar 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)61,8449
Polymers61,1652
Non-polymers6787
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-35 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.610, 79.690, 92.240
Angle α, β, γ (deg.)90.00, 103.86, 90.00
Int Tables number5
Space group name H-MC121
DetailsChains A and B constitute the biological homodimer

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Components

#1: Protein thymidylate synthase / / TS / TSase


Mass: 30582.697 Da / Num. of mol.: 2 / Mutation: Y209W, N-terminus is carbamylated
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ThyA / Production host: Escherichia coli (E. coli) / Strain (production host): chi2913recA / References: UniProt: P0A884, thymidylate synthase
#2: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 1.94 Å3/Da / Density % sol: 36.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 7.8mg/ml protein, 25mM KPO4, pH 7.5, and 5mM DTT equilibrated against a well buffer containing 28% PEG 4K, 100 mM Tris-Cl, pH 8.9, 200mM sodium acetate and 5mM DTT, VAPOR DIFFUSION, HANGING ...Details: 7.8mg/ml protein, 25mM KPO4, pH 7.5, and 5mM DTT equilibrated against a well buffer containing 28% PEG 4K, 100 mM Tris-Cl, pH 8.9, 200mM sodium acetate and 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2001
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.83→30.7 Å / Num. all: 41273 / Num. obs: 41273 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 28.1
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2073 / % possible all: 98.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1TJS

1tjs


Resolution: 1.83→30.7 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2091436.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: His-51 and Cys-146 in chain A are in two conformations in the crystal
RfactorNum. reflection% reflectionSelection details
Rfree0.202 2076 5 %RANDOM
Rwork0.164 ---
all0.166 41153 --
obs0.166 41153 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.5412 Å2 / ksol: 0.425534 e/Å3
Displacement parametersBiso mean: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å28.6 Å2
2---5.39 Å20 Å2
3---4.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.83→30.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4276 0 38 348 4662
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d1.55
X-RAY DIFFRACTIONc_mcbond_it0.991.5
X-RAY DIFFRACTIONc_mcangle_it1.62
X-RAY DIFFRACTIONc_scbond_it2.442
X-RAY DIFFRACTIONc_scangle_it3.342.5
LS refinement shellResolution: 1.83→1.91 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 256 5.1 %
Rwork0.225 4773 -
obs-5029 99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3param.po4carbonate.topo
X-RAY DIFFRACTION4carbonate.paramtopo.formic
X-RAY DIFFRACTION5dtt_odt_gcl.paramdtt_odt_gcl.top

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