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- PDB-1bid: E. COLI THYMIDYLATE SYNTHASE COMPLEXED WITH DUMP -

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Basic information

Entry
Database: PDB / ID: 1bid
TitleE. COLI THYMIDYLATE SYNTHASE COMPLEXED WITH DUMP
ComponentsTHYMIDYLATE SYNTHASE
KeywordsMETHYLTRANSFERASE / TRANSFERASE (METHYLTRANSFERASE) / SUBSTRATE MODULES
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, 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
2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.2 Å
AuthorsStout, T.J. / Sage, C.R. / Stroud, R.M.
CitationJournal: Structure / Year: 1998
Title: The additivity of substrate fragments in enzyme-ligand binding.
Authors: Stout, T.J. / Sage, C.R. / Stroud, R.M.
History
DepositionJun 27, 1997Processing site: BNL
Revision 1.0Jul 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8522
Polymers30,5441
Non-polymers3081
Water2,036113
1
A: THYMIDYLATE SYNTHASE
hetero molecules

A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7044
Polymers61,0872
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555x,-y,-z+1/21
Buried area6160 Å2
ΔGint-22 kcal/mol
Surface area20660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)133.060, 133.060, 133.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-772-

HOH

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Components

#1: Protein THYMIDYLATE SYNTHASE / TS / THYMIDYLATE SYNTHETASE


Mass: 30543.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: CHI-2913 / Gene: THYA / Plasmid: PTHYA-WT / Cell line (production host): CHI-2913 / Gene (production host): THYA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A884, thymidylate synthase
#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.3 Å3/Da / Density % sol: 58.1 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.8
Details: CRYSTALLIZATION EXPERIMENTS WERE CONDUCTED IN HANGING DROPS CONTAINING 4.2 MG/ML E. COLI TS, 0.38 MM DUMP, 3.8 MM DTT, AND 1.2 M (NH4)2SO4, AT PH 7.8 (20 MM KPO4) SUSPENDED OVER A WELL ...Details: CRYSTALLIZATION EXPERIMENTS WERE CONDUCTED IN HANGING DROPS CONTAINING 4.2 MG/ML E. COLI TS, 0.38 MM DUMP, 3.8 MM DTT, AND 1.2 M (NH4)2SO4, AT PH 7.8 (20 MM KPO4) SUSPENDED OVER A WELL SOLUTION CONTAINING 2.4 M (NH4)2SO4 AND 1.0 MM DTT., vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.2 mg/mlprotein1drop
20.38 mMdUMP1drop
33.8 mMdithiothreitol1drop
41.2 Mammonium sulfate1drop
520 mMpotassium phosphate1drop
62.4 Mammonium sulfate1reservoir
71.0 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 23029 / % possible obs: 96.9 % / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 17.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.319 / % possible all: 91.5
Reflection
*PLUS
Num. measured all: 92187

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Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1TJS

1tjs


Resolution: 2.2→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1862 9.8 %SHELLS
Rwork0.172 ---
obs0.172 18908 96.5 %-
Displacement parametersBiso mean: 27.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 20 113 2286
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.19
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.491.5
X-RAY DIFFRACTIONx_mcangle_it3.742
X-RAY DIFFRACTIONx_scbond_it3.812
X-RAY DIFFRACTIONx_scangle_it5.812.5
LS refinement shellResolution: 2.2→2.33 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 279 9 %
Rwork0.238 2809 -
obs--95.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM.PO4TOPO2.PO4
X-RAY DIFFRACTION4PARAMED.LIGTOPO.FORMIC
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.19

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