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- PDB-1bzf: NMR SOLUTION STRUCTURE AND DYNAMICS OF THE COMPLEX OF LACTOBACILL... -

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Basic information

Entry
Database: PDB / ID: 1bzf
TitleNMR SOLUTION STRUCTURE AND DYNAMICS OF THE COMPLEX OF LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE WITH THE NEW LIPOPHILIC ANTIFOLATE DRUG TRIMETREXATE, 22 STRUCTURES
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / INHIBITOR-ENZYME COMPLEX
Function / homology
Function and homology information


response to methotrexate / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to antibiotic
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
TRIMETREXATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsPolshakov, V.I. / Birdsall, B. / Frenkiel, T.A. / Gargaro, A.R. / Feeney, J.
Citation
Journal: Protein Sci. / Year: 1999
Title: Structure and dynamics in solution of the complex of Lactobacillus casei dihydrofolate reductase with the new lipophilic antifolate drug trimetrexate.
Authors: Polshakov, V.I. / Birdsall, B. / Frenkiel, T.A. / Gargaro, A.R. / Feeney, J.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: The Solution Structure of the Complex of Lactobacillus Casei Dihydrofolate Reductase with Methotrexate
Authors: Gargaro, A.R. / Soteriou, A. / Frenkiel, T.A. / Bauer, C.J. / Birdsall, B. / Polshakov, V.I. / Barsukov, I.L. / Roberts, G.C. / Feeney, J.
History
DepositionOct 28, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7022
Polymers18,3321
Non-polymers3701
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)22 / 22NO NOE VIOLATION MORE THAN 0.1 ANGSTROM; NO DIHEDRAL ANGLE VIOLATION MORE THAN 3 DEGREES
RepresentativeModel #19

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Components

#1: Protein DIHYDROFOLATE REDUCTASE / / DHFR


Mass: 18331.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Plasmid: PMT702 / Production host: Escherichia coli (E. coli) / Strain (production host): NF1 / References: UniProt: P00381, dihydrofolate reductase
#2: Chemical ChemComp-TMQ / TRIMETREXATE / Trimetrexate


Mass: 370.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24N5O3 / Comment: inhibitor*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121NOESY
131ROESY
141HNHA
151HNHB
161HSQC
1713D-1H/15N-TOCSY-HMQC
1813D-1H/ 15N-ROESY-HMQC
1913D-1H/15N-NOESY-HMQC
11011D-NOE DIFFERENCE

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Sample preparation

DetailsContents: 90% H2O/10% D2O, 100% D2O
Sample conditionsIonic strength: 550 mM / pH: 6.5 / Pressure: 1 atm / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: NO NOE VIOLATION MORE THAN 0.1 ANGSTROM; NO DIHEDRAL ANGLE VIOLATION MORE THAN 3 DEGREES
Conformers calculated total number: 22 / Conformers submitted total number: 22

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