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Basic information

Entry
Database: PDB / ID: 1tdr
TitleEXPRESSION, CHARACTERIZATION, AND CRYSTALLOGRAPHIC ANALYSIS OF TELLUROMETHIONYL DIHYDROFOLATE REDUCTASE
ComponentsTELLUROMETHIONYL DIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / folic acid metabolic process / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / folic acid metabolic process / dihydrofolate reductase activity / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / 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
METHOTREXATE / TELLURIUM / Dihydrofolate reductase / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsLewinski, K. / Lebioda, L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Expression, characterization and crystallographic analysis of telluromethionyl dihydrofolate reductase.
Authors: Boles, J.O. / Lewinski, K. / Kunckle, M.G. / Hatada, M. / Lebioda, L. / Dunlap, R.B. / Odom, J.D.
#1: Journal: Nat.Struct.Biol. / Year: 1994
Title: Bio-Incorporation of Telluromethionine Into Buried Residues of Dihydrofolate Reductase
Authors: Boles, J.O. / Lewinski, K. / Kunkle, M. / Odom, J.D. / Dunlap, R.B. / Lebioda, L. / Hatada, M.
History
DepositionApr 13, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / 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 / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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: TELLUROMETHIONYL DIHYDROFOLATE REDUCTASE
B: TELLUROMETHIONYL DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,57111
Polymers36,0412
Non-polymers1,5309
Water6,125340
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.000, 93.000, 74.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Atom site foot note1: GLY A 95 - GLY A 96 OMEGA = 359.20 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: GLY B 95 - GLY B 96 OMEGA = 359.75 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein TELLUROMETHIONYL DIHYDROFOLATE REDUCTASE


Mass: 18020.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
References: UniProt: P00379, UniProt: P0ABQ4*PLUS, dihydrofolate reductase

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Non-polymers , 5 types, 349 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MTX / METHOTREXATE / Methotrexate


Mass: 454.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N8O5 / Comment: chemotherapy*YM
#4: Chemical
ChemComp-TE / TELLURIUM / Tellurium


Mass: 127.600 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Te
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.58 Å3/Da / Density % sol: 52.27 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %2-propanol1reservoir
220 %PEG40001reservoir
30.1 Msodium HEPES1reservoirpH7.5
45 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.98 Å
DetectorDetector: CCD / Date: Oct 24, 1992
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionNum. obs: 11234 / % possible obs: 88 % / Redundancy: 4.35 % / Rmerge(I) obs: 0.068
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. measured all: 48880 / Rmerge(I) obs: 0.065

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Processing

Software
NameClassification
MADNESdata collection
PROCORdata collection
PROLSQrefinement
MADNESdata reduction
PROCORdata reduction
RefinementResolution: 2.5→16 Å / σ(F): 0
Details: ATOM SD OF MET 42 AND ATOM SD OF MET 92 HAVE BEEN PARTIALLY CHEMICALLY SUBSTITUTED BY TELLURIUM. COORDINATES ARE GIVEN FOR BOTH SD AND TE IN THIS ENTRY, WITH PARTIAL OCCUPANCIES. NOTE THAT ...Details: ATOM SD OF MET 42 AND ATOM SD OF MET 92 HAVE BEEN PARTIALLY CHEMICALLY SUBSTITUTED BY TELLURIUM. COORDINATES ARE GIVEN FOR BOTH SD AND TE IN THIS ENTRY, WITH PARTIAL OCCUPANCIES. NOTE THAT IT IS NOT POSSIBLE FOR BOTH SD AND TE TO BE PRESENT SIMULTANEOUSLY IN ONE RESIDUE. ATOMS SD MET 42 AND SD MET 92 ARE PRESENTED AS PART OF RESIDUES 42 AND 92, RESPECTIVELY. THE TELLURIUM ATOMS ARE PRESENTED AS HET GROUPS AT THE END OF THE CHAIN.
RfactorNum. reflection
obs0.124 10732
Refinement stepCycle: LAST / Resolution: 2.5→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 73 340 2944
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0590.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.060.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9281.5
X-RAY DIFFRACTIONp_mcangle_it1.5561
X-RAY DIFFRACTIONp_scbond_it1.6181.5
X-RAY DIFFRACTIONp_scangle_it2.6922
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.1830.15
X-RAY DIFFRACTIONp_singtor_nbd0.2220.3
X-RAY DIFFRACTIONp_multtor_nbd0.2330.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.20.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.33
X-RAY DIFFRACTIONp_staggered_tor22.115
X-RAY DIFFRACTIONp_orthonormal_tor2420
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.124
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_planar_d0.062
X-RAY DIFFRACTIONp_chiral_restr0.178

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