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- PDB-1dra: CRYSTAL STRUCTURE OF UNLIGANDED ESCHERICHIA COLI DIHYDROFOLATE RE... -

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Basic information

Entry
Database: PDB / ID: 1dra
TitleCRYSTAL STRUCTURE OF UNLIGANDED ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE. LIGAND-INDUCED CONFORMATIONAL CHANGES AND COOPERATIVITY IN BINDING
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / NADP+ binding / folic acid biosynthetic process / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / NADP+ binding / folic acid biosynthetic process / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
METHOTREXATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsOatley, S.J. / Kraut, J.
Citation
Journal: Biochemistry / Year: 1991
Title: Crystal structure of unliganded Escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in binding.
Authors: Bystroff, C. / Kraut, J.
#1: Journal: Biochemistry / Year: 1990
Title: Crystal Structures of Escherichia Coli Dihydrofolate Reductase: The Nadp+ Holoenzyme and the Folate Nadp+ Ternary Complex. Substrate Binding and a Model for the Transition State
Authors: Bystroff, C. / Oatley, S.J. / Kraut, J.
#2: Journal: Biochemistry / Year: 1990
Title: Crystal Structures of Recombinant Human Dihydrofolate Reductase Complexed with Folate and 5-Deazafolate
Authors: Davies II, J.F. / Delcamp, T.J. / Prendergast, N.J. / Ashford, V.A. / Freisheim, J.H. / Kraut, J.
#3: Journal: Science / Year: 1986
Title: Functional Role of Aspartic Acid-27 in Dihydrofolate Reductase Revealed by Mutagenesis
Authors: Howell, E.E. / Villafranca, J.E. / Warren, M.S. / Oatley, S.J. / Kraut, J.
#4: Journal: J.Biol.Chem. / Year: 1982
Title: Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined at 1.7 Angstroms Resolution. I. General Features and Binding of Methotrexate
Authors: Bolin, J.T. / Filman, D.J. / Matthews, D.A. / Hamlin, R.C. / Kraut, J.
#5: Journal: J.Biol.Chem. / Year: 1982
Title: Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined at 1.7 Angstroms Resolution. II. Environment of Bound Nadph and Implications for Catalysis
Authors: Filman, D.J. / Bolin, J.T. / Matthews, D.A. / Kraut, J.
History
DepositionNov 6, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: DIHYDROFOLATE REDUCTASE
B: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0897
Polymers36,0692
Non-polymers1,0205
Water7,674426
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.790, 92.790, 74.060
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 ANGLE = 2.684 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: GLY B 95 - GLY B 96 OMEGA ANGLE = 2.555 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.92567, -0.3718, 0.07002), (-0.32949, 0.70125, -0.63221), (0.18596, -0.60829, -0.77163)
Vector: 59.28485, 47.33741, 96.52642)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*.

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Components

#1: Protein DIHYDROFOLATE REDUCTASE


Mass: 18034.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0ABQ4, dihydrofolate reductase
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 454.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N8O5
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
124 mg/mlprotein1dropunliganded
250 mMsodium/potassium phthalate1drop
350 %(w/w)PEG60001drop
425 %PEG60001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→5 Å
Details: DURING THE REFINEMENT THE CALCIUM ION (DESIGNATED CA) AND THE TWO CHLORIDE IONS (DESIGNATED CL) WERE MODELED AS OXYGEN ATOMS.
RfactorNum. reflection
obs0.153 26188
Refinement stepCycle: LAST / Resolution: 1.9→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 69 426 3005
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.015
X-RAY DIFFRACTIONp_angle_d0.0320.027
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.2862
X-RAY DIFFRACTIONp_mcangle_it3.4343
X-RAY DIFFRACTIONp_scbond_it3.1222
X-RAY DIFFRACTIONp_scangle_it5.0253
X-RAY DIFFRACTIONp_plane_restr0.0120.015
X-RAY DIFFRACTIONp_chiral_restr0.210.2
X-RAY DIFFRACTIONp_singtor_nbd0.1970.5
X-RAY DIFFRACTIONp_multtor_nbd0.2240.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2060.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.810
X-RAY DIFFRACTIONp_staggered_tor17.415
X-RAY DIFFRACTIONp_orthonormal_tor18.715
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 5 Å / Num. reflection obs: 26188 / Rfactor obs: 0.153
Solvent computation
*PLUS
Displacement parameters
*PLUS

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