PDB Short entry for 2HQP HEADER OXIDOREDUCTASE 19-JUL-06 2HQP TITLE SOLUTION STRUCTURE OF L.CASEI DIHYDROFOLATE REDUCTASE COMPLEXED WITH TITLE 2 NADPH, 32 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DHFR; COMPND 5 EC: 1.5.1.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS CASEI; SOURCE 3 ORGANISM_TAXID: 1582; SOURCE 4 GENE: FOLA, DHFR; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: NF1; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMT702 KEYWDS OXIDOREDUCTASE, DHFR EXPDTA SOLUTION NMR NUMMDL 32 AUTHOR V.I.POLSHAKOV,B.BIRDSALL REVDAT 3 09-MAR-22 2HQP 1 REMARK REVDAT 2 24-FEB-09 2HQP 1 VERSN REVDAT 1 05-JUN-07 2HQP 0 JRNL AUTH Y.SMURNYY,N.KOVALEVSKAYA,B.BIRDSALL,V.I.POLSHAKOV,J.FEENEY JRNL TITL STRUCTURAL INSIGHTS INTO COOPERATIVE EFFECTS OF LIGAND JRNL TITL 2 BINDING TO L. CASEI DIHYDROFOLATE REDUTASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1, XPLOR-NIH 3.11, CNS 1.0, ARIA 2.0A REMARK 3 AUTHORS : VARIAN INC (VNMR), CLORE (XPLOR-NIH), BRUNGER REMARK 3 (CNS), NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANNEALING FROM 1000K DOWN TO 0K WITH REMARK 3 25K STEP, 10PS OF DYNAMICS AT EACH STEP REMARK 4 REMARK 4 2HQP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUL-06. REMARK 100 THE DEPOSITION ID IS D_1000038648. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 100MM KCL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5MM DHFR-15N/NADPH, 50MM REMARK 210 PHOSPHATE BUFFER, 5% DMPC/DHPC, REMARK 210 90% H2O, 10% D2O; 1MM DHFR-15N/ REMARK 210 NADPH, 50MM PHOSPHATE BUFFER, REMARK 210 100% H2O; 1MM DHFR-15N/NADPH, REMARK 210 50MM PHOSPHATE BUFFER, 90% H2O, REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 2D REMARK 210 NOESY; COSY; 2D 15N-REJECTED REMARK 210 NOESY; IPAP REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; UNITY; UNITYPLUS; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 1998-2001, SPARKY 3.8 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 32 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 32 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 PHE A 49 102.81 -41.60 REMARK 500 1 PRO A 53 -167.85 -78.96 REMARK 500 1 HIS A 89 74.49 -110.45 REMARK 500 1 ALA A 97 64.01 -105.42 REMARK 500 2 ASP A 16 75.59 -152.73 REMARK 500 2 LEU A 23 75.22 -107.86 REMARK 500 2 PHE A 49 105.62 -45.88 REMARK 500 2 LYS A 51 72.19 -119.71 REMARK 500 2 ALA A 97 68.97 -104.24 REMARK 500 3 LYS A 15 -74.92 -68.89 REMARK 500 3 PHE A 49 104.48 -44.84 REMARK 500 3 PRO A 55 177.93 -59.49 REMARK 500 3 ALA A 97 60.86 -104.70 REMARK 500 4 LYS A 15 50.81 -97.09 REMARK 500 4 PHE A 49 105.07 -47.30 REMARK 500 4 LEU A 54 83.31 68.61 REMARK 500 4 ALA A 97 75.65 -100.17 REMARK 500 5 PHE A 49 100.92 -44.33 REMARK 500 5 LYS A 51 70.21 -112.32 REMARK 500 5 PRO A 53 -162.09 -79.02 REMARK 500 5 PRO A 55 64.68 -67.45 REMARK 500 5 ALA A 97 57.54 -104.89 REMARK 500 6 LYS A 15 -69.51 -95.41 REMARK 500 6 PHE A 49 101.85 -42.34 REMARK 500 6 PRO A 53 -164.05 -75.65 REMARK 500 6 THR A 58 79.71 -68.89 REMARK 500 6 HIS A 89 71.62 -107.06 REMARK 500 6 ALA A 97 73.17 -101.37 REMARK 500 7 PHE A 49 105.29 -47.10 REMARK 500 7 PRO A 53 -167.48 -76.41 REMARK 500 7 THR A 58 78.30 -68.47 REMARK 500 7 HIS A 89 70.61 -107.40 REMARK 500 7 ALA A 97 71.80 -102.20 REMARK 500 8 ASP A 16 32.50 -140.87 REMARK 500 8 PHE A 49 103.00 -42.65 REMARK 500 8 GLU A 56 31.15 74.62 REMARK 500 8 ALA A 97 69.90 -104.39 REMARK 500 9 PHE A 49 100.24 -38.87 REMARK 500 9 ALA A 97 72.91 -102.14 REMARK 500 10 ASP A 16 91.92 72.37 REMARK 500 10 PHE A 49 100.13 -42.34 REMARK 500 10 LYS A 51 69.89 -112.62 REMARK 500 10 PRO A 53 -159.83 -81.21 REMARK 500 10 ALA A 97 71.83 -103.97 REMARK 500 11 ASP A 16 78.47 -179.75 REMARK 500 11 PHE A 49 99.65 -42.11 REMARK 500 11 ALA A 97 68.59 -103.58 REMARK 500 12 LYS A 15 -76.38 -74.58 REMARK 500 12 PHE A 49 102.46 -47.12 REMARK 500 12 ALA A 97 71.53 -104.55 REMARK 500 REMARK 500 THIS ENTRY HAS 120 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP A 170 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LUD RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE SAME PROTEIN COMPLEXED WITH TRIMETHOPRIM REMARK 900 AND NADPH REMARK 900 RELATED ID: 1YHO RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH REMARK 900 TRIMETHOPRIM AND NADPH REMARK 900 RELATED ID: 3DFR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE SAME PROTEIN COMPLEXED WITH NADPH AND REMARK 900 METHOTREXATE REMARK 900 RELATED ID: 2HM9 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE SAME PROTEIN COMPLEXED WITH TRIMETHOPRIM DBREF 2HQP A 1 162 UNP P00381 DYR_LACCA 1 162 SEQRES 1 A 162 THR ALA PHE LEU TRP ALA GLN ASP ARG ASP GLY LEU ILE SEQRES 2 A 162 GLY LYS ASP GLY HIS LEU PRO TRP HIS LEU PRO ASP ASP SEQRES 3 A 162 LEU HIS TYR PHE ARG ALA GLN THR VAL GLY LYS ILE MET SEQRES 4 A 162 VAL VAL GLY ARG ARG THR TYR GLU SER PHE PRO LYS ARG SEQRES 5 A 162 PRO LEU PRO GLU ARG THR ASN VAL VAL LEU THR HIS GLN SEQRES 6 A 162 GLU ASP TYR GLN ALA GLN GLY ALA VAL VAL VAL HIS ASP SEQRES 7 A 162 VAL ALA ALA VAL PHE ALA TYR ALA LYS GLN HIS PRO ASP SEQRES 8 A 162 GLN GLU LEU VAL ILE ALA GLY GLY ALA GLN ILE PHE THR SEQRES 9 A 162 ALA PHE LYS ASP ASP VAL ASP THR LEU LEU VAL THR ARG SEQRES 10 A 162 LEU ALA GLY SER PHE GLU GLY ASP THR LYS MET ILE PRO SEQRES 11 A 162 LEU ASN TRP ASP ASP PHE THR LYS VAL SER SER ARG THR SEQRES 12 A 162 VAL GLU ASP THR ASN PRO ALA LEU THR HIS THR TYR GLU SEQRES 13 A 162 VAL TRP GLN LYS LYS ALA HET NDP A 170 74 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE FORMUL 2 NDP C21 H30 N7 O17 P3 HELIX 1 1 LEU A 23 THR A 34 1 12 HELIX 2 2 ARG A 43 GLU A 47 1 5 HELIX 3 3 ASP A 78 HIS A 89 1 12 HELIX 4 4 GLY A 99 PHE A 106 1 8 SHEET 1 A 8 VAL A 74 VAL A 76 0 SHEET 2 A 8 THR A 58 LEU A 62 1 N VAL A 61 O VAL A 76 SHEET 3 A 8 ILE A 38 GLY A 42 1 N VAL A 41 O LEU A 62 SHEET 4 A 8 LEU A 94 ILE A 96 1 O VAL A 95 N ILE A 38 SHEET 5 A 8 ALA A 2 ASP A 8 1 N ALA A 2 O LEU A 94 SHEET 6 A 8 THR A 112 LEU A 118 1 O LEU A 114 N PHE A 3 SHEET 7 A 8 HIS A 153 LYS A 160 -1 O TRP A 158 N LEU A 113 SHEET 8 A 8 PHE A 136 VAL A 144 -1 N ARG A 142 O TYR A 155 SHEET 1 B 2 LEU A 12 GLY A 14 0 SHEET 2 B 2 THR A 126 LYS A 127 -1 O THR A 126 N ILE A 13 CISPEP 1 ARG A 52 PRO A 53 1 0.08 CISPEP 2 GLY A 98 GLY A 99 1 0.16 CISPEP 3 ARG A 52 PRO A 53 2 -0.12 CISPEP 4 GLY A 98 GLY A 99 2 0.01 CISPEP 5 ARG A 52 PRO A 53 3 -0.64 CISPEP 6 GLY A 98 GLY A 99 3 0.06 CISPEP 7 ARG A 52 PRO A 53 4 0.56 CISPEP 8 GLY A 98 GLY A 99 4 -0.90 CISPEP 9 ARG A 52 PRO A 53 5 0.74 CISPEP 10 GLY A 98 GLY A 99 5 0.87 CISPEP 11 ARG A 52 PRO A 53 6 -0.36 CISPEP 12 GLY A 98 GLY A 99 6 0.79 CISPEP 13 ARG A 52 PRO A 53 7 0.64 CISPEP 14 GLY A 98 GLY A 99 7 -0.47 CISPEP 15 ARG A 52 PRO A 53 8 0.04 CISPEP 16 GLY A 98 GLY A 99 8 1.14 CISPEP 17 ARG A 52 PRO A 53 9 -0.21 CISPEP 18 GLY A 98 GLY A 99 9 0.54 CISPEP 19 ARG A 52 PRO A 53 10 0.25 CISPEP 20 GLY A 98 GLY A 99 10 -0.30 CISPEP 21 ARG A 52 PRO A 53 11 -0.13 CISPEP 22 GLY A 98 GLY A 99 11 0.45 CISPEP 23 ARG A 52 PRO A 53 12 0.35 CISPEP 24 GLY A 98 GLY A 99 12 0.76 CISPEP 25 ARG A 52 PRO A 53 13 0.00 CISPEP 26 GLY A 98 GLY A 99 13 0.27 CISPEP 27 ARG A 52 PRO A 53 14 0.36 CISPEP 28 GLY A 98 GLY A 99 14 0.28 CISPEP 29 ARG A 52 PRO A 53 15 -0.09 CISPEP 30 GLY A 98 GLY A 99 15 1.58 CISPEP 31 ARG A 52 PRO A 53 16 -0.29 CISPEP 32 GLY A 98 GLY A 99 16 0.35 CISPEP 33 ARG A 52 PRO A 53 17 -0.88 CISPEP 34 GLY A 98 GLY A 99 17 -0.37 CISPEP 35 ARG A 52 PRO A 53 18 0.02 CISPEP 36 GLY A 98 GLY A 99 18 0.86 CISPEP 37 ARG A 52 PRO A 53 19 -0.43 CISPEP 38 GLY A 98 GLY A 99 19 0.18 CISPEP 39 ARG A 52 PRO A 53 20 -0.19 CISPEP 40 GLY A 98 GLY A 99 20 0.22 CISPEP 41 ARG A 52 PRO A 53 21 -0.22 CISPEP 42 GLY A 98 GLY A 99 21 0.25 CISPEP 43 ARG A 52 PRO A 53 22 -0.35 CISPEP 44 GLY A 98 GLY A 99 22 -1.27 CISPEP 45 ARG A 52 PRO A 53 23 0.30 CISPEP 46 GLY A 98 GLY A 99 23 -0.13 CISPEP 47 ARG A 52 PRO A 53 24 0.05 CISPEP 48 GLY A 98 GLY A 99 24 0.48 CISPEP 49 ARG A 52 PRO A 53 25 0.87 CISPEP 50 GLY A 98 GLY A 99 25 -0.90 CISPEP 51 ARG A 52 PRO A 53 26 -0.20 CISPEP 52 GLY A 98 GLY A 99 26 0.86 CISPEP 53 ARG A 52 PRO A 53 27 0.35 CISPEP 54 GLY A 98 GLY A 99 27 0.22 CISPEP 55 ARG A 52 PRO A 53 28 0.31 CISPEP 56 GLY A 98 GLY A 99 28 0.83 CISPEP 57 ARG A 52 PRO A 53 29 0.29 CISPEP 58 GLY A 98 GLY A 99 29 0.34 CISPEP 59 ARG A 52 PRO A 53 30 -0.14 CISPEP 60 GLY A 98 GLY A 99 30 1.09 CISPEP 61 ARG A 52 PRO A 53 31 0.37 CISPEP 62 GLY A 98 GLY A 99 31 0.44 CISPEP 63 ARG A 52 PRO A 53 32 -0.08 CISPEP 64 GLY A 98 GLY A 99 32 1.02 SITE 1 AC1 18 TRP A 5 ALA A 6 ILE A 13 ARG A 43 SITE 2 AC1 18 ARG A 44 THR A 45 SER A 48 LEU A 62 SITE 3 AC1 18 THR A 63 HIS A 64 HIS A 77 VAL A 79 SITE 4 AC1 18 GLY A 98 GLY A 99 ALA A 100 GLN A 101 SITE 5 AC1 18 ILE A 102 MET A 128 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000