10 20 30 40 50 60 70 80 1IYM - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA BINDING PROTEIN 30-AUG-02 1IYM
TITLE RING-H2 FINGER DOMAIN OF EL5
COMPND MOL_ID: 1; COMPND 2 MOLECULE: EL5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RING-H2 FINGER DOMAIN; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA; SOURCE 3 ORGANISM_COMMON: RICE; SOURCE 4 ORGANISM_TAXID: 4530; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET32A
KEYWDS RING-H2 FINGER, UBIQUITIN LIGASE, DNA BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 15
AUTHOR E.KATOH,S.KATOH,E.MINAMI,T.YAMAZAKI
REVDAT 3 24-FEB-09 1IYM 1 VERSN REVDAT 2 05-AUG-03 1IYM 1 SOURCE REVDAT 1 22-JUL-03 1IYM 0
JRNL AUTH S.KATOH,C.HONG,Y.TSUNODA,K.MURATA,R.TAKAI,E.MINAMI, JRNL AUTH 2 T.YAMAZAKI,E.KATOH JRNL TITL HIGH PRECISION NMR STRUCTURE AND FUNCTION OF THE JRNL TITL 2 RING-H2 FINGER DOMAIN OF EL5, A RICE PROTEIN WHOSE JRNL TITL 3 EXPRESSION IS INCREASED UPON EXPOSURE TO JRNL TITL 4 PATHOGEN-DERIVED OLIGOSACCHARIDES JRNL REF J.BIOL.CHEM. V. 278 15341 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12588869 JRNL DOI 10.1074/JBC.M210531200
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1IYM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-SEP-02. REMARK 100 THE RCSB ID CODE IS RCSB005412.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM RING-H2 FINGER DOMAIN OF REMARK 210 EL5 U-15N, 13C; 20MM TRIS-HCL REMARK 210 BUFFER, 100MM NACL, 20UM REMARK 210 ZNSO4, 1MM DTT; 90%H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, 4D_ REMARK 210 13C/15N-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR, NMRPIPE REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 15 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 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 ASP A 129 45.64 -85.32 REMARK 500 1 VAL A 136 -66.38 -98.85 REMARK 500 1 LEU A 141 107.26 -58.68 REMARK 500 1 CYS A 153 -50.60 -120.97 REMARK 500 1 LEU A 166 -73.37 -70.84 REMARK 500 1 SER A 168 -62.61 140.96 REMARK 500 1 SER A 170 49.27 -94.95 REMARK 500 1 ARG A 176 35.46 102.28 REMARK 500 1 THR A 178 154.92 -41.98 REMARK 500 2 LEU A 138 42.07 73.50 REMARK 500 2 LEU A 141 106.59 -58.39 REMARK 500 2 CYS A 153 -51.78 -120.51 REMARK 500 2 SER A 168 -53.71 92.64 REMARK 500 2 SER A 170 52.70 -102.12 REMARK 500 2 ARG A 176 35.72 101.92 REMARK 500 2 THR A 178 154.73 -41.89 REMARK 500 3 VAL A 136 -66.37 -98.97 REMARK 500 3 GLU A 146 73.44 -114.56 REMARK 500 3 CYS A 153 -52.86 -120.40 REMARK 500 3 LEU A 166 -71.15 -64.60 REMARK 500 3 SER A 168 -63.41 127.08 REMARK 500 3 SER A 170 51.15 -95.82 REMARK 500 3 ARG A 176 37.07 101.31 REMARK 500 3 THR A 178 155.13 -41.99 REMARK 500 4 MET A 128 78.92 -178.65 REMARK 500 4 VAL A 136 -66.34 -98.68 REMARK 500 4 LEU A 141 98.20 -58.63 REMARK 500 4 GLU A 146 79.87 -118.19 REMARK 500 4 CYS A 153 -51.23 -120.51 REMARK 500 4 LEU A 166 -72.47 -68.76 REMARK 500 4 SER A 168 -64.81 136.23 REMARK 500 4 SER A 170 50.59 -95.23 REMARK 500 4 ARG A 176 35.29 102.68 REMARK 500 4 THR A 178 155.22 -41.82 REMARK 500 5 MET A 128 82.77 71.76 REMARK 500 5 VAL A 136 -66.28 -98.59 REMARK 500 5 LEU A 141 97.42 -60.30 REMARK 500 5 LEU A 166 -74.09 -77.11 REMARK 500 5 SER A 168 -61.45 144.67 REMARK 500 5 SER A 170 44.71 -94.58 REMARK 500 5 ARG A 176 31.90 99.25 REMARK 500 6 VAL A 136 -66.13 -98.57 REMARK 500 6 LEU A 141 95.82 -58.32 REMARK 500 6 CYS A 153 -50.63 -120.88 REMARK 500 6 PHE A 157 -169.55 -120.38 REMARK 500 6 SER A 168 -52.66 91.27 REMARK 500 6 SER A 170 43.74 -101.85 REMARK 500 6 ARG A 176 42.12 101.76 REMARK 500 6 THR A 178 153.79 -41.48 REMARK 500 7 MET A 128 -173.22 56.56 REMARK 500 7 VAL A 136 -66.18 -98.73 REMARK 500 7 LEU A 141 95.74 -58.53 REMARK 500 7 CYS A 153 -51.13 -120.68 REMARK 500 7 LEU A 166 -72.84 -73.55 REMARK 500 7 SER A 168 -64.45 137.72 REMARK 500 7 SER A 170 50.49 -96.43 REMARK 500 7 ARG A 176 38.03 102.07 REMARK 500 7 THR A 178 154.96 -41.60 REMARK 500 8 VAL A 136 -66.33 -98.73 REMARK 500 8 CYS A 153 -50.23 -120.91 REMARK 500 8 HIS A 158 154.68 -49.17 REMARK 500 8 SER A 168 -53.03 90.96 REMARK 500 8 SER A 170 48.36 -101.34 REMARK 500 8 ARG A 176 41.14 101.49 REMARK 500 8 THR A 178 150.52 -41.65 REMARK 500 9 ASP A 130 65.33 -104.43 REMARK 500 9 VAL A 136 -66.11 -98.76 REMARK 500 9 LEU A 141 95.63 -58.16 REMARK 500 9 CYS A 153 -51.34 -120.99 REMARK 500 9 PHE A 157 -168.99 -123.58 REMARK 500 9 LEU A 166 -73.98 -75.96 REMARK 500 9 SER A 168 -60.48 143.71 REMARK 500 9 SER A 170 48.35 -94.61 REMARK 500 9 ARG A 176 37.67 101.82 REMARK 500 9 THR A 178 154.80 -42.17 REMARK 500 10 CYS A 134 109.67 -50.85 REMARK 500 10 VAL A 136 -66.31 -98.59 REMARK 500 10 CYS A 153 -51.26 -120.47 REMARK 500 10 LEU A 166 -72.22 -68.51 REMARK 500 10 SER A 168 -63.39 134.12 REMARK 500 10 SER A 170 48.91 -94.87 REMARK 500 10 ARG A 176 35.46 102.12 REMARK 500 10 THR A 178 155.16 -42.04 REMARK 500 11 MET A 128 -174.23 52.28 REMARK 500 11 VAL A 136 -66.37 -98.66 REMARK 500 11 CYS A 153 -52.09 -120.73 REMARK 500 11 SER A 168 -52.02 88.88 REMARK 500 11 SER A 170 53.58 -99.56 REMARK 500 11 ARG A 176 36.37 102.00 REMARK 500 11 THR A 178 154.95 -42.05 REMARK 500 12 MET A 128 64.73 -160.35 REMARK 500 12 VAL A 136 -66.34 -98.69 REMARK 500 12 CYS A 153 -51.66 -120.48 REMARK 500 12 SER A 168 -53.21 91.33 REMARK 500 12 SER A 170 52.11 -99.29 REMARK 500 12 ARG A 176 36.20 101.41 REMARK 500 12 THR A 178 155.17 -42.14 REMARK 500 13 MET A 128 69.19 -156.42 REMARK 500 13 LEU A 138 41.55 78.10 REMARK 500 13 LEU A 166 -74.17 -77.66 REMARK 500 13 SER A 168 -58.74 144.02 REMARK 500 13 SER A 170 42.52 -96.37 REMARK 500 13 ARG A 176 32.96 100.29 REMARK 500 14 MET A 128 95.74 47.44 REMARK 500 14 ASP A 130 40.53 -98.52 REMARK 500 14 VAL A 136 -66.47 -98.69 REMARK 500 14 LEU A 141 101.26 -58.26 REMARK 500 14 CYS A 153 -51.85 -120.99 REMARK 500 14 HIS A 158 157.25 -49.00 REMARK 500 14 LEU A 166 -73.39 -74.06 REMARK 500 14 SER A 168 -62.51 139.54 REMARK 500 14 SER A 170 36.15 -95.03 REMARK 500 14 ARG A 176 29.82 100.24 REMARK 500 15 MET A 128 123.50 67.84 REMARK 500 15 VAL A 136 -66.25 -98.85 REMARK 500 15 LEU A 141 96.99 -58.28 REMARK 500 15 CYS A 153 -51.94 -120.79 REMARK 500 15 LEU A 166 -73.62 -74.63 REMARK 500 15 SER A 168 -60.74 143.00 REMARK 500 15 SER A 170 48.91 -94.46 REMARK 500 15 ARG A 176 36.17 101.88 REMARK 500 15 THR A 178 154.68 -41.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 148 0.27 SIDE_CHAIN REMARK 500 1 ARG A 152 0.12 SIDE_CHAIN REMARK 500 1 ARG A 176 0.27 SIDE_CHAIN REMARK 500 2 ARG A 148 0.08 SIDE_CHAIN REMARK 500 2 ARG A 152 0.25 SIDE_CHAIN REMARK 500 2 ARG A 176 0.18 SIDE_CHAIN REMARK 500 3 ARG A 152 0.22 SIDE_CHAIN REMARK 500 3 ARG A 176 0.32 SIDE_CHAIN REMARK 500 4 ARG A 148 0.21 SIDE_CHAIN REMARK 500 4 ARG A 152 0.26 SIDE_CHAIN REMARK 500 4 ARG A 176 0.30 SIDE_CHAIN REMARK 500 5 ARG A 148 0.23 SIDE_CHAIN REMARK 500 5 ARG A 152 0.21 SIDE_CHAIN REMARK 500 5 ARG A 176 0.25 SIDE_CHAIN REMARK 500 6 ARG A 148 0.18 SIDE_CHAIN REMARK 500 6 ARG A 152 0.25 SIDE_CHAIN REMARK 500 6 ARG A 176 0.31 SIDE_CHAIN REMARK 500 7 ARG A 148 0.26 SIDE_CHAIN REMARK 500 7 ARG A 152 0.32 SIDE_CHAIN REMARK 500 7 ARG A 176 0.32 SIDE_CHAIN REMARK 500 8 ARG A 148 0.22 SIDE_CHAIN REMARK 500 8 ARG A 152 0.17 SIDE_CHAIN REMARK 500 8 ARG A 176 0.20 SIDE_CHAIN REMARK 500 9 ARG A 148 0.29 SIDE_CHAIN REMARK 500 9 ARG A 176 0.31 SIDE_CHAIN REMARK 500 10 ARG A 148 0.30 SIDE_CHAIN REMARK 500 10 ARG A 152 0.31 SIDE_CHAIN REMARK 500 10 ARG A 176 0.26 SIDE_CHAIN REMARK 500 11 ARG A 148 0.30 SIDE_CHAIN REMARK 500 11 ARG A 152 0.24 SIDE_CHAIN REMARK 500 11 ARG A 176 0.25 SIDE_CHAIN REMARK 500 12 ARG A 148 0.30 SIDE_CHAIN REMARK 500 12 ARG A 152 0.32 SIDE_CHAIN REMARK 500 12 ARG A 176 0.31 SIDE_CHAIN REMARK 500 13 ARG A 148 0.27 SIDE_CHAIN REMARK 500 13 ARG A 152 0.29 SIDE_CHAIN REMARK 500 13 ARG A 176 0.28 SIDE_CHAIN REMARK 500 14 ARG A 148 0.31 SIDE_CHAIN REMARK 500 14 ARG A 152 0.26 SIDE_CHAIN REMARK 500 14 ARG A 176 0.28 SIDE_CHAIN REMARK 500 15 ARG A 148 0.17 SIDE_CHAIN REMARK 500 15 ARG A 152 0.32 SIDE_CHAIN REMARK 500 15 ARG A 176 0.32 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 182 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 158 ND1 REMARK 620 2 CYS A 161 SG 108.9 REMARK 620 3 CYS A 134 SG 108.5 112.1 REMARK 620 4 CYS A 137 SG 111.0 108.2 108.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 183 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 155 ND1 REMARK 620 2 CYS A 153 SG 107.5 REMARK 620 3 CYS A 172 SG 109.9 109.9 REMARK 620 4 CYS A 175 SG 113.6 107.5 108.5 REMARK 620 N 1 2 3
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 182 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 183
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5459 RELATED DB: BMRB REMARK 900 5459 CONTAINS THE CHEMICAL SHIFTS
DBREF 1IYM A 129 181 UNP Q9LRB7 EL5_ORYSA 129 181
SEQADV 1IYM ALA A 127 UNP Q9LRB7 CLONING ARTIFACT SEQADV 1IYM MET A 128 UNP Q9LRB7 CLONING ARTIFACT
SEQRES 1 A 55 ALA MET ASP ASP GLY VAL GLU CYS ALA VAL CYS LEU ALA SEQRES 2 A 55 GLU LEU GLU ASP GLY GLU GLU ALA ARG PHE LEU PRO ARG SEQRES 3 A 55 CYS GLY HIS GLY PHE HIS ALA GLU CYS VAL ASP MET TRP SEQRES 4 A 55 LEU GLY SER HIS SER THR CYS PRO LEU CYS ARG LEU THR SEQRES 5 A 55 VAL VAL VAL
HET ZN A 182 1 HET ZN A 183 1
HETNAM ZN ZINC ION
FORMUL 2 ZN 2(ZN 2+)
HELIX 1 1 GLU A 160 TRP A 165 1 6
SHEET 1 A 2 ARG A 148 PHE A 149 0 SHEET 2 A 2 GLY A 156 PHE A 157 -1 O PHE A 157 N ARG A 148
LINK ZN ZN A 182 ND1 HIS A 158 1555 1555 2.08 LINK ZN ZN A 183 ND1 HIS A 155 1555 1555 2.10 LINK ZN ZN A 182 SG CYS A 161 1555 1555 2.30 LINK ZN ZN A 182 SG CYS A 134 1555 1555 2.29 LINK ZN ZN A 182 SG CYS A 137 1555 1555 2.28 LINK ZN ZN A 183 SG CYS A 153 1555 1555 2.28 LINK ZN ZN A 183 SG CYS A 172 1555 1555 2.30 LINK ZN ZN A 183 SG CYS A 175 1555 1555 2.31
SITE 1 AC1 4 CYS A 134 CYS A 137 HIS A 158 CYS A 161 SITE 1 AC2 4 CYS A 153 HIS A 155 CYS A 172 CYS A 175
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