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- PDB-1njc: THYMIDYLATE SYNTHASE, MUTATION, N229D WITH 2'-DEOXYCYTIDINE 5'-MO... -

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Basic information

Entry
Database: PDB / ID: 1njc
TitleTHYMIDYLATE SYNTHASE, MUTATION, N229D WITH 2'-DEOXYCYTIDINE 5'-MONOPHOSPHATE (DCMP)
ComponentsTHYMIDYLATE SYNTHASE
KeywordsTRANSFERASE (METHYLTRANSFERASE) / TRANSFERASE / METHYLTRANSFERASE / NUCLEOTIDE BIOSYNTHESIS
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / 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'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsFiner-Moore, J. / Stroud, R.M.
Citation
Journal: Biochemistry / Year: 1996
Title: Partitioning roles of side chains in affinity, orientation, and catalysis with structures for mutant complexes: asparagine-229 in thymidylate synthase.
Authors: Finer-Moore, J.S. / Liu, L. / Schafmeister, C.E. / Birdsall, D.L. / Mau, T. / Santi, D.V. / Stroud, R.M.
#1: Journal: Faseb J. / Year: 1993
Title: Stereochemistry of a Multistep/Bipartite Methyl Transfer Reaction: Thymidylate Synthase
Authors: Stroud, R.M. / Finer-Moore, J.S.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Refined Structures of Substrate-Bound and Phosphate-Bound Thymidylate Synthase from Lactobacillus Casei
Authors: Finer-Moore, J. / Fauman, E.B. / Foster, P.G. / Perry, K.M. / Santi, D.V. / Stroud, R.M.
#3: Journal: Biochemistry / Year: 1993
Title: Exclusion of 2'-Deoxycytidine 5'-Monophosphate by Asparagine 229 of Thymidylate Synthase
Authors: Liu, L. / Santi, D.V.
#4: Journal: Biochemistry / Year: 1992
Title: Mutation of Asparagine 229 to Aspartate in Thymidylate Synthase Converts the Enzyme to a Deoxycytidylate Methylase
Authors: Liu, L. / Santi, D.V.
History
DepositionJan 23, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: 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 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9392
Polymers36,6311
Non-polymers3071
Water1,54986
1
A: THYMIDYLATE SYNTHASE
hetero molecules

A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8774
Polymers73,2632
Non-polymers6142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area5890 Å2
ΔGint-24 kcal/mol
Surface area26100 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.200, 79.200, 229.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-400-

HOH

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Components

#1: Protein THYMIDYLATE SYNTHASE


Mass: 36631.438 Da / Num. of mol.: 1 / Mutation: N229D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Description: PURCHASED FROM SIGMA / Gene: N229D MUTANT OF CLONED L. CASE / Plasmid: PKPTSD / Gene (production host): N229D MUTANT OF CLONED L. CASEI TS / Production host: Escherichia coli (E. coli)
Strain (production host): STRAIN CHI-2913 (WHICH LACKS A THYMIDYLATE SYNTHASE GENE)
References: UniProt: P00469, thymidylate synthase
#2: Chemical ChemComp-DCM / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE


Mass: 307.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 55 %
Crystal growpH: 7 / Details: pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.5-6.0 mg/mlprotein1drop
22-20 mMdCMP1drop
340 mMpotassium phosphate1drop
41 mMDTT1drop
51-2 %satammonium sulfate1drop
640 mMphosphate1reservoir
7DTT1reservoir
8EDTA1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 5, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 14050 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.104
Reflection
*PLUS
Num. measured all: 41508

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.5→50 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.184 --
obs0.184 11363 77 %
Displacement parametersBiso mean: 29.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 20 86 2699
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM11.DNATOPH11.DNA
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 7 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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