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- PDB-3b5b: Crystal structure of the thymidylate synthase k48q -

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Basic information

Entry
Database: PDB / ID: 3b5b
TitleCrystal structure of the thymidylate synthase k48q
ComponentsThymidylate synthase
KeywordsTRANSFERASE / Thymidylate synthase / 5-NO2-DUMP / Substrate Anologue / Methyltransferase / Nucleotide biosynthesis / Repressor / RNA-binding / Translation regulation
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/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
FORMIC ACID / 2'-DEOXY-5-NITROURIDINE 5'-(DIHYDROGEN PHOSPHATE) / 2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSotelo-Mundo, R.R. / Arreola, R. / Maley, F. / Montfort, W.R.
CitationJournal: Int.J.Biochem.Cell Biol. / Year: 2008
Title: Role of an invariant lysine residue in folate binding on Escherichia coli thymidylate synthase: Calorimetric and crystallographic analysis of the K48Q mutant.
Authors: Arvizu-Flores, A.A. / Sugich-Miranda, R. / Arreola, R. / Garcia-Orozco, K.D. / Velazquez-Contreras, E.F. / Montfort, W.R. / Maley, F. / Sotelo-Mundo, R.R.
History
DepositionOct 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Oct 20, 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_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 1.6Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thymidylate synthase
B: Thymidylate synthase
A: FORMIC ACID
B: FORMIC ACID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8306
Polymers61,0292
Non-polymers8004
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.370, 127.370, 67.840
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Thymidylate synthase / / TS / TSase


Mass: 30514.604 Da / Num. of mol.: 2 / Mutation: Q48K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21 (bacteria) / Species: Escherichia coli / Strain: bl21List of strains of Escherichia coli / Gene: thyA / Plasmid: pet17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): bl21 / References: UniProt: P0A884, thymidylate synthase
#2: Chemical ChemComp-NDU / 2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE


Type: DNA linking / Mass: 355.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O10P
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-NDN / 2'-DEOXY-5-NITROURIDINE 5'-(DIHYDROGEN PHOSPHATE) / [(2R,3S,5R)-3-HYDROXY-5-(5-NITRO-2,4-DIOXO-PYRIMIDIN-1-YL)OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE


Type: DNA linking / Mass: 353.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N3O10P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mM potassium phosphate buffer, 4 mM DTT and increments in ammonium sulfate from 2.05 to 2.6 M, pH 7.5 to 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Nov 22, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→35.52 Å / Num. all: 19482 / Num. obs: 19482 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 44.35 Å2 / Rsym value: 0.092 / Net I/σ(I): 12.3
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 2783 / Rsym value: 0.4 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
REFMACrefinement
PDB_EXTRACT3data extraction
MADNESSdata collection
PROCORdata reduction
Agrovatadata scaling
ROTAVATAdata scaling
TRUNCATEdata scaling
X-PLORphasing
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY: 1FFL, 1FWM

1ffl

1fwm


Resolution: 2.7→25.55 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1987704.625 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.234 837 4.9 %RANDOM
Rwork0.193 ---
all-19482 --
obs-16931 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.401 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 31.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.38 Å20 Å20 Å2
2---2.38 Å20 Å2
3---4.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.7→25.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4300 0 52 52 4404
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 131 4.3 %
Rwork0.3 2722 -
all-2844 -
obs--92.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ligand.parligand.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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