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- PDB-1zpr: E. COLI THYMIDYLATE SYNTHASE MUTANT E58Q IN COMPLEX WITH CB3717 A... -

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Basic information

Entry
Database: PDB / ID: 1zpr
TitleE. COLI THYMIDYLATE SYNTHASE MUTANT E58Q 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 / Resolution: 2.5 Å
AuthorsSage, C.R. / Stout, T.J. / Rutenber, E.E. / Stroud, R.M.
Citation
Journal: Biochemistry / Year: 1996
Title: An essential role for water in an enzyme reaction mechanism: the crystal structure of the thymidylate synthase mutant E58Q.
Authors: Sage, C.R. / Rutenber, E.E. / Stout, T.J. / Stroud, R.M.
#1: Journal: Biochemistry / Year: 1990
Title: Structure, Multiple Site Binding, and Segmental Accommodation in Thymidylate Synthase on Binding Dump and an Anti-Folate
Authors: Montfort, W.R. / Perry, K.M. / Fauman, E.B. / Finer-Moore, J.S. / Maley, G.F. / Hardy, L. / Maley, F. / Stroud, R.M.
History
DepositionOct 15, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 1.4Nov 20, 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)62,6896
Polymers61,1172
Non-polymers1,5714
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-23 kcal/mol
Surface area19120 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

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Components

#1: Protein THYMIDYLATE SYNTHASE


Mass: 30558.678 Da / Num. of mol.: 2 / Mutation: E58Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: X2913 / Plasmid: PTHYA-E58Q / 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.: 178 / 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: 2.6 Å3/Da / Density % sol: 52.4 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-9 mg/mlprotein1drop
220 mMpotassium phosphate1drop
32.3 Mammonium sulfate1drop
4100 mMdUMP1drop
54.78 mMCB37171drop
6beta-mercaptoethanol1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Date: Jan 9, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 23346 / % possible obs: 93.8 % / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.085
Reflection
*PLUS
Num. measured all: 200624

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 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. atoms4306 0 110 178 4594
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
X-RAY DIFFRACTION5SAGEE58Q_TOPO.FORMIC
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: 0.29

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