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- PDB-1bq1: E. COLI THYMIDYLATE SYNTHASE MUTANT N177A IN COMPLEX WITH CB3717 ... -

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Basic information

Entry
Database: PDB / ID: 1bq1
TitleE. COLI THYMIDYLATE SYNTHASE MUTANT N177A IN COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)
ComponentsTHYMIDYLATE SYNTHASE
KeywordsTRANSFERASE / ACTIVE SITE MUTANT / REACTION INTERMEDIATE
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
10-PROPARGYL-5,8-DIDEAZAFOLIC ACID / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsReyes, C.L. / Sage, C.R. / Rutenber, E.E. / Finer-Moore, J.S. / Stroud, R.M.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Inactivity of N229A thymidylate synthase due to water-mediated effects: isolating a late stage in methyl transfer.
Authors: Reyes, C.L. / Sage, C.R. / Rutenber, E.E. / Nissen, R.M. / Finer-Moore, J.S. / Stroud, R.M.
History
DepositionAug 20, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Nov 3, 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)62,6056
Polymers61,0332
Non-polymers1,5714
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-23 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.221, 127.221, 68.178
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999813, -0.01879, 0.004533), (0.015378, -0.631165, 0.775496), (-0.01171, 0.775421, 0.631336)
Vector: 61.82514, 22.17302, -10.6411)

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Components

#1: Protein THYMIDYLATE SYNTHASE


Mass: 30516.643 Da / Num. of mol.: 2 / Mutation: N177A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: X2913 / Gene: THYA / Plasmid: PTHYA-N177A / 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.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-CB3 / 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID


Mass: 477.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H23N5O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 52.4 %
Crystal growpH: 7 / Details: pH 7
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mM1dropK2PO4
230 mg/mlTS1drop
315 mMdUMP1drop
410 mMCB37171drop
5100 mM1dropMgCl2
6100 mMdithiothreitol1drop
72.2-2.26 Mammonium sulfate1drop
82.5 Mammonium sulphate1reservoir
920 mMKPO41reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS II / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 9, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 23346 / % possible obs: 87.7 % / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.4
Reflection shellHighest resolution: 2.4 Å / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.5 / % possible all: 73.8
Reflection
*PLUS
Num. measured all: 160471
Reflection shell
*PLUS
% possible obs: 73.8 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→7 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1993 9.9 %RANDOM
Rwork0.152 ---
obs0.152 20033 86.3 %-
Displacement parametersBiso mean: 21.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.21 Å
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4300 0 110 228 4638
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.37
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.971.5
X-RAY DIFFRACTIONx_mcangle_it4.412
X-RAY DIFFRACTIONx_scbond_it3.571.5
X-RAY DIFFRACTIONx_scangle_it5.22
LS refinement shellResolution: 2.5→2.65 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.29 323 10.3 %
Rwork0.208 2820 -
obs--80.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1SAGEE58Q_PARAM19X.PROSAGEE58Q_TOPH19X.PRO
X-RAY DIFFRACTION2SAGEE58Q_PARAM11.WATSAGEE58Q_TOPH11.WAT
X-RAY DIFFRACTION3SAGEE58Q_PARAMED.LIGSAGEE58Q_TOPO_COV.DUMP
X-RAY DIFFRACTION4SAGEE58Q_TOPO.CB3
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.37
LS refinement shell
*PLUS
Rfactor Rfree: 0.333 / Rfactor obs: 0.241

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