HEADER PROTEIN BINDING 19-DEC-00 1GHH TITLE SOLUTION STRUCTURE OF DINI COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-DAMAGE-INDUCIBLE PROTEIN I; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DINI; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS BICELLE, DINI, DIPOLAR COUPLING, LIQUID CRYSTAL, NMR, PF1, KEYWDS 2 RECA, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.E.RAMIREZ,O.N.VOLOSHIN,R.D.CAMERINI-OTERO,A.BAX REVDAT 2 24-FEB-09 1GHH 1 VERSN REVDAT 1 10-JAN-01 1GHH 0 SPRSDE 10-JAN-01 1GHH 1F0A JRNL AUTH B.E.RAMIREZ,O.N.VOLOSHIN,R.D.CAMERINI-OTERO,A.BAX JRNL TITL SOLUTION STRUCTURE OF DINI PROVIDES INSIGHT INTO JRNL TITL 2 ITS MODE OF RECA INACTIVATION. JRNL REF PROTEIN SCI. V. 9 2161 2000 JRNL REFN ISSN 0961-8368 JRNL PMID 11152126 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES WERE CALCULATED IN A REMARK 3 THREE STAGE PROCESS. IN THE FIRST STAGE, FOLDS WERE CALCULATED REMARK 3 FROM A FULLY-EXTENDED CHAIN BASED ONLY ON TORSION AND NOE REMARK 3 RESTRAINTS. IN THE SECOND STAGE, THE TEN BEST STRUCTURES OF REMARK 3 STAGE 1 WERE USED AS STARTING STRUCTURES IN A SIMULATED REMARK 3 ANNEALING CALCULATION THAT INCLUDED DIPOLAR RESTRAINTS REMARK 3 MEASURED IN BICELLES. IN THE LAST STAGE, THE TEN LOWEST ENERGY REMARK 3 STRUCTURES OF STAGE 2 WERE USED AS STARTING STRUCTURES IN A REMARK 3 SIMULATED ANNEALING CALCULATION THAT ALSO INCLUDED DIPOLAR REMARK 3 RESTRAINTS MEASURED IN A PHAGE LIQUID CRYSTAL. REMARK 4 REMARK 4 1GHH COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-DEC-00. REMARK 100 THE RCSB ID CODE IS RCSB001518. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0; 298.0; 302.0 REMARK 210 PH : 6.6; 6.6; 6.6 REMARK 210 IONIC STRENGTH : NULL; NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.6 MM DINI U-13C,15N, 20 MM REMARK 210 PHOSPHATE BUFFER, 100 MM NACL; REMARK 210 PH 6.6; 95% H2O, 5% D2O; 0.6 REMARK 210 MM DINI U-13C,15N, 20 MM REMARK 210 PHOSPHATE BUFFER, 100 MM NACL; REMARK 210 PH 6.6; 99% D2O, 1% H2O; 0.6 REMARK 210 MM DINI U-13C,15N, 20 MM REMARK 210 PHOSPHATE BUFFER, 100 MM NACL; REMARK 210 PH 6.6; BICELLE OR PHAGE REMARK 210 LIQUID CRYSTAL, 95% H2O, 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, 3D_ REMARK 210 13C-SEPARATED_NOESY, 2D NOESY, REMARK 210 HNCG, HN(CO)CG, IPAP_15N_HSQC, REMARK 210 HNCO, (HA)CA(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ, 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX, DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, PIPP, X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING MOLECULAR REMARK 210 DYNAMICS IN CARTESIAN SPACE REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING TWO SETS OF DIPOLAR REMARK 210 COUPLING RESTRAINTS. ONE SET WAS RECORDED IN A BICELLE LIQUID REMARK 210 CRYSTAL SOLUTION; THE OTHER SET WAS RECORDED IN A PHAGE LIQUID REMARK 210 CRYSTAL SOLUTION. SEE CITATION 1 FOR DETAILS ON SOLUTION REMARK 210 CONDITIONS. A TOTAL OF 127 N-H, 135 CA-HA, 138 CA-CO, 61 N-CO, REMARK 210 AND 64 CO-HN DIPOLAR RESTRAINTS WERE USED IN THE STRUCTURE REMARK 210 CALCULATION. ADDITIONAL RESTRAINTS INCLUDED 592 INTRARESIDUE, REMARK 210 278 SHORT RANGE, 104 MEDIUM RANGE, AND 140 LONG RANGE NOE REMARK 210 RESTRAINTS AS WELL AS 76 PHI, 51 PSI, AND 21 CHI1 DIHEDRAL REMARK 210 RESTRAINTS. A CONFORMATIONAL DATABASE WAS EMPLOYED IN THE REMARK 210 SIMULATED ANNEALING CALCULATION. NO RADIUS OF GYRATION TERM REMARK 210 WAS EMPLOYED IN THE SIMULATED ANNEALING CALCULATION. 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 PRO A 14 150.31 -48.17 REMARK 500 1 ALA A 15 48.76 -56.86 REMARK 500 2 PRO A 14 151.31 -46.80 REMARK 500 2 ALA A 15 51.48 -58.29 REMARK 500 3 PRO A 14 150.36 -47.39 REMARK 500 3 ALA A 15 50.87 -57.15 REMARK 500 4 ALA A 15 50.39 -56.72 REMARK 500 5 ALA A 15 51.04 -56.79 REMARK 500 6 PRO A 14 150.63 -47.77 REMARK 500 6 ALA A 15 50.40 -57.73 REMARK 500 7 ALA A 15 47.54 -57.09 REMARK 500 8 PRO A 14 152.90 -49.01 REMARK 500 8 ALA A 15 50.56 -58.11 REMARK 500 9 ALA A 15 52.10 -57.18 REMARK 500 10 PRO A 14 150.85 -48.02 REMARK 500 10 ALA A 15 51.79 -56.91 REMARK 500 11 ALA A 15 52.53 -56.69 REMARK 500 12 ALA A 15 48.56 -56.63 REMARK 500 13 ALA A 15 49.28 -56.98 REMARK 500 14 ALA A 15 50.91 -56.58 REMARK 500 15 ALA A 15 49.56 -56.39 REMARK 500 16 PRO A 14 151.63 -49.02 REMARK 500 16 ALA A 15 53.46 -58.44 REMARK 500 17 ALA A 15 49.09 -55.82 REMARK 500 18 PRO A 14 150.81 -49.85 REMARK 500 18 ALA A 15 49.08 -57.95 REMARK 500 19 ALA A 15 48.55 -57.09 REMARK 500 20 PRO A 14 150.06 -47.31 REMARK 500 20 ALA A 15 48.33 -56.29 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 2 0.31 SIDE_CHAIN REMARK 500 1 ARG A 27 0.29 SIDE_CHAIN REMARK 500 1 ARG A 28 0.27 SIDE_CHAIN REMARK 500 1 ARG A 43 0.19 SIDE_CHAIN REMARK 500 1 ARG A 62 0.27 SIDE_CHAIN REMARK 500 2 ARG A 2 0.10 SIDE_CHAIN REMARK 500 2 ARG A 27 0.19 SIDE_CHAIN REMARK 500 2 ARG A 28 0.30 SIDE_CHAIN REMARK 500 2 ARG A 62 0.28 SIDE_CHAIN REMARK 500 3 ARG A 28 0.30 SIDE_CHAIN REMARK 500 3 ARG A 62 0.19 SIDE_CHAIN REMARK 500 4 ARG A 43 0.25 SIDE_CHAIN REMARK 500 4 ARG A 62 0.23 SIDE_CHAIN REMARK 500 5 ARG A 2 0.30 SIDE_CHAIN REMARK 500 5 ARG A 27 0.19 SIDE_CHAIN REMARK 500 5 ARG A 28 0.30 SIDE_CHAIN REMARK 500 5 ARG A 43 0.25 SIDE_CHAIN REMARK 500 5 ARG A 62 0.10 SIDE_CHAIN REMARK 500 6 ARG A 27 0.30 SIDE_CHAIN REMARK 500 6 ARG A 28 0.31 SIDE_CHAIN REMARK 500 6 ARG A 62 0.31 SIDE_CHAIN REMARK 500 7 ARG A 2 0.24 SIDE_CHAIN REMARK 500 7 ARG A 27 0.25 SIDE_CHAIN REMARK 500 7 ARG A 28 0.08 SIDE_CHAIN REMARK 500 7 ARG A 43 0.20 SIDE_CHAIN REMARK 500 7 ARG A 62 0.29 SIDE_CHAIN REMARK 500 8 ARG A 2 0.30 SIDE_CHAIN REMARK 500 8 ARG A 27 0.21 SIDE_CHAIN REMARK 500 8 ARG A 62 0.29 SIDE_CHAIN REMARK 500 9 ARG A 2 0.20 SIDE_CHAIN REMARK 500 9 ARG A 27 0.31 SIDE_CHAIN REMARK 500 9 ARG A 28 0.25 SIDE_CHAIN REMARK 500 9 ARG A 43 0.28 SIDE_CHAIN REMARK 500 9 ARG A 62 0.12 SIDE_CHAIN REMARK 500 10 ARG A 2 0.30 SIDE_CHAIN REMARK 500 10 ARG A 27 0.25 SIDE_CHAIN REMARK 500 10 ARG A 28 0.27 SIDE_CHAIN REMARK 500 10 ARG A 62 0.08 SIDE_CHAIN REMARK 500 11 ARG A 2 0.19 SIDE_CHAIN REMARK 500 11 ARG A 27 0.15 SIDE_CHAIN REMARK 500 11 ARG A 28 0.21 SIDE_CHAIN REMARK 500 11 ARG A 43 0.24 SIDE_CHAIN REMARK 500 11 ARG A 62 0.25 SIDE_CHAIN REMARK 500 12 ARG A 2 0.30 SIDE_CHAIN REMARK 500 12 ARG A 28 0.09 SIDE_CHAIN REMARK 500 13 ARG A 2 0.24 SIDE_CHAIN REMARK 500 13 ARG A 27 0.12 SIDE_CHAIN REMARK 500 13 ARG A 28 0.27 SIDE_CHAIN REMARK 500 13 ARG A 43 0.29 SIDE_CHAIN REMARK 500 13 ARG A 62 0.25 SIDE_CHAIN REMARK 500 14 ARG A 2 0.30 SIDE_CHAIN REMARK 500 14 ARG A 27 0.28 SIDE_CHAIN REMARK 500 14 ARG A 28 0.11 SIDE_CHAIN REMARK 500 14 ARG A 43 0.28 SIDE_CHAIN REMARK 500 14 ARG A 62 0.27 SIDE_CHAIN REMARK 500 15 ARG A 2 0.29 SIDE_CHAIN REMARK 500 15 ARG A 27 0.12 SIDE_CHAIN REMARK 500 15 ARG A 28 0.29 SIDE_CHAIN REMARK 500 15 ARG A 43 0.22 SIDE_CHAIN REMARK 500 15 ARG A 62 0.31 SIDE_CHAIN REMARK 500 16 ARG A 2 0.22 SIDE_CHAIN REMARK 500 16 ARG A 27 0.17 SIDE_CHAIN REMARK 500 16 ARG A 43 0.31 SIDE_CHAIN REMARK 500 16 ARG A 62 0.22 SIDE_CHAIN REMARK 500 17 ARG A 2 0.30 SIDE_CHAIN REMARK 500 17 ARG A 27 0.30 SIDE_CHAIN REMARK 500 17 ARG A 28 0.27 SIDE_CHAIN REMARK 500 17 ARG A 43 0.16 SIDE_CHAIN REMARK 500 17 ARG A 62 0.08 SIDE_CHAIN REMARK 500 18 ARG A 27 0.15 SIDE_CHAIN REMARK 500 18 ARG A 28 0.10 SIDE_CHAIN REMARK 500 18 ARG A 43 0.14 SIDE_CHAIN REMARK 500 18 ARG A 62 0.18 SIDE_CHAIN REMARK 500 19 ARG A 2 0.28 SIDE_CHAIN REMARK 500 19 ARG A 27 0.28 SIDE_CHAIN REMARK 500 19 ARG A 43 0.17 SIDE_CHAIN REMARK 500 20 ARG A 2 0.31 SIDE_CHAIN REMARK 500 20 ARG A 27 0.16 SIDE_CHAIN REMARK 500 20 ARG A 28 0.31 SIDE_CHAIN REMARK 500 20 ARG A 43 0.16 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1GHH A 1 81 UNP P0ABR1 DINI_ECOLI 1 81 SEQRES 1 A 81 MET ARG ILE GLU VAL THR ILE ALA LYS THR SER PRO LEU SEQRES 2 A 81 PRO ALA GLY ALA ILE ASP ALA LEU ALA GLY GLU LEU SER SEQRES 3 A 81 ARG ARG ILE GLN TYR ALA PHE PRO ASP ASN GLU GLY HIS SEQRES 4 A 81 VAL SER VAL ARG TYR ALA ALA ALA ASN ASN LEU SER VAL SEQRES 5 A 81 ILE GLY ALA THR LYS GLU ASP LYS GLN ARG ILE SER GLU SEQRES 6 A 81 ILE LEU GLN GLU THR TRP GLU SER ALA ASP ASP TRP PHE SEQRES 7 A 81 VAL SER GLU HELIX 1 1 GLY A 16 PHE A 33 1 18 HELIX 2 2 THR A 56 SER A 73 1 18 HELIX 3 3 SER A 73 PHE A 78 1 6 SHEET 1 A 3 HIS A 39 ALA A 45 0 SHEET 2 A 3 ARG A 2 ALA A 8 1 N ILE A 3 O HIS A 39 SHEET 3 A 3 ASN A 49 ILE A 53 -1 O ASN A 49 N THR A 6 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 220 0 0 3 3 0 0 6 0 0 0 7 END