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- PDB-2l28: Solution structure of lactobacillus casei dihydrofolate reductase... -

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Basic information

Entry
Database: PDB / ID: 2l28
TitleSolution structure of lactobacillus casei dihydrofolate reductase apo-form, 25 conformers
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / DHFR / antifolates / co-operative binding
Function / homology
Function and homology information


response to methotrexate / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / folic acid metabolic process / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to antibiotic / cytosol
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Dihydrofolate reductase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsPolshakov, V.I. / Birdsall, B. / Feeney, J.
CitationJournal: Biochemistry / Year: 2011
Title: NMR Structures of Apo L. casei Dihydrofolate Reductase and Its Complexes with Trimethoprim and NADPH: Contributions to Positive Cooperative Binding from Ligand-Induced Refolding, ...Title: NMR Structures of Apo L. casei Dihydrofolate Reductase and Its Complexes with Trimethoprim and NADPH: Contributions to Positive Cooperative Binding from Ligand-Induced Refolding, Conformational Changes, and Interligand Hydrophobic Interactions.
Authors: Feeney, J. / Birdsall, B. / Kovalevskaya, N.V. / Smurnyy, Y.D. / Navarro Peran, E.M. / Polshakov, V.I.
History
DepositionAug 13, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrofolate reductase


Theoretical massNumber of molelcules
Total (without water)18,3321
Polymers18,3321
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Dihydrofolate reductase /


Mass: 18331.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Gene: folA, dhfR / Plasmid: PMT702 / Production host: Escherichia coli (E. coli) / Strain (production host): NF1 / References: UniProt: P00381, dihydrofolate reductase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
1332D 1H-15N HSQC
1422D 1H-13C HSQC
1523D HNCO
1623D HNCA
1723D HN(CO)CA
1823D HN(CA)CB
1923D (H)CCH-TOCSY
11033D HNHA
11133D HNHB
11233D 1H-15N NOESY
11323D 1H-13C NOESY
11432D 15N-rejected NOESY
11542D IPAP
11612D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM entity-1, 100 mM potassium chloride-2, 50 mM potassium phosphate-3, 0.1 % sodium azide-4, 100% D2O100% D2O
21 mM [U-99% 13C; U-99% 15N] entity-5, 100 mM potassium chloride-6, 50 mM potassium phosphate-7, 0.1 % sodium azide-8, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-99% 15N] entity-9, 100 mM potassium chloride-10, 50 mM potassium phosphate-11, 0.1 % sodium azide-12, 95% H2O/5% D2O95% H2O/5% D2O
41 mM [U-99% 15N] entity-13, 100 mM potassium chloride-14, 50 mM potassium phosphate-15, 0.1 % sodium azide-16, 5 % DMPC/DHPC-17, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMentity-11
100 mMpotassium chloride-21
50 mMpotassium phosphate-31
0.1 %sodium azide-41
1 mMentity-5[U-99% 13C; U-99% 15N]2
100 mMpotassium chloride-62
50 mMpotassium phosphate-72
0.1 %sodium azide-82
1 mMentity-9[U-99% 15N]3
100 mMpotassium chloride-103
50 mMpotassium phosphate-113
0.1 %sodium azide-123
1 mMentity-13[U-99% 15N]4
100 mMpotassium chloride-144
50 mMpotassium phosphate-154
0.1 %sodium azide-164
5 %DMPC/DHPC-174
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Bruker AvanceBrukerAVANCE6003
Varian UnityPlusVarianUNITYPLUS5004

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Variancollection
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
AnglesearchPolshakov VI & Feeney J.geometry optimization
NMRestPolshakov VIdata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ProcheckNMRLaskowski and MacArthurdata analysis
Insight II2000Accelrys Software Inc.data analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 25

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