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- PDB-1jmf: CONTRIBUTIONS OF ORIENTATION AND HYDROGEN BONDING TO CATALYSIS IN... -

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Basic information

Entry
Database: PDB / ID: 1jmf
TitleCONTRIBUTIONS OF ORIENTATION AND HYDROGEN BONDING TO CATALYSIS IN ASN-229 MUTANTS OF THYMIDYLATE SYNTHASE
ComponentsTHYMIDYLATE SYNTHASE
KeywordsTRANSFERASE / METHYLTRANSFERASE
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytoplasm
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
2'-DEOXYURIDINE 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: J.Mol.Biol. / Year: 1998
Title: Contributions of orientation and hydrogen bonding to catalysis in Asn229 mutants of thymidylate synthase.
Authors: Finer-Moore, J.S. / Liu, L. / Birdsall, D.L. / Brem, R. / Apfeld, J. / Santi, D.V. / Stroud, R.M.
#1: 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.
#2: Journal: Faseb J. / Year: 1993
Title: Stereochemistry of a Multistep/Bipartite Methyl Transfer Reaction: Thymidylate Synthase
Authors: Stroud, R.M. / Finer-Moore, J.S.
#3: 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.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Asparagine 229 in Thymidylate Synthase Contributes to, But is not Essential for, Catalysis
Authors: Liu, L. / Santi, D.V.
History
DepositionSep 13, 1997Processing site: BNL
Revision 1.0Jan 28, 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 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 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)36,8962
Polymers36,5871
Non-polymers3081
Water1,33374
1
A: THYMIDYLATE SYNTHASE
hetero molecules

A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7914
Polymers73,1752
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area5790 Å2
ΔGint-32 kcal/mol
Surface area26190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.500, 78.500, 230.300
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-331-

HOH

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Components

#1: Protein THYMIDYLATE SYNTHASE /


Mass: 36587.430 Da / Num. of mol.: 1 / Mutation: N229A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Gene: N229A MUTANT OF CLONED L. CASE / Plasmid: PSCTS9 / Gene (production host): N229A MUTANT OF CLONED L. CASEI TS / Production host: Escherichia coli (E. coli)
Strain (production host): CHI-2913, LACKING A THYMIDYLATE SYNTHASE GENE
References: UniProt: P00469, thymidylate synthase
#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


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


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.8 Å3/Da / Density % sol: 55 %
Crystal growpH: 7.4 / Details: pH 7.4
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.5-6.0 mg/mlprotein1drop
22-20 mMdUMP1drop
340 mMpotassium phosphate1drop
41 mMDTT1drop
51-2 %satammonium sulfate1drop
6DTT1reservoir
7EDTA1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 12620 / % possible obs: 80 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.097
Reflection
*PLUS
Num. measured all: 46753

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
R-AXISIIdata reduction
X-PLORphasing
RefinementResolution: 2.5→7 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.27 --
Rwork0.198 --
obs0.198 11830 72 %
Displacement parametersBiso mean: 22 Å2
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2590 0 20 74 2684
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
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 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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