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, PF1, RECA, PROTEIN KEYWDS 2 BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.E.RAMIREZ,O.N.VOLOSHIN,R.D.CAMERINI-OTERO,A.BAX REVDAT 4 27-DEC-23 1GHH 1 REMARK REVDAT 3 23-FEB-22 1GHH 1 REMARK 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 ITS MODE OF JRNL TITL 2 RECA INACTIVATION. JRNL REF PROTEIN SCI. V. 9 2161 2000 JRNL REFN ISSN 0961-8368 JRNL PMID 11152126 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, X-PLOR REMARK 3 AUTHORS : DELAGLIO (NMRPIPE), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES WERE CALCULATED IN A THREE REMARK 3 STAGE PROCESS. IN THE FIRST STAGE, FOLDS WERE CALCULATED FROM A REMARK 3 FULLY-EXTENDED CHAIN BASED ONLY ON TORSION AND NOE RESTRAINTS. REMARK 3 IN THE SECOND STAGE, THE TEN BEST STRUCTURES OF STAGE 1 WERE REMARK 3 USED AS STARTING STRUCTURES IN A SIMULATED ANNEALING CALCULATION REMARK 3 THAT INCLUDED DIPOLAR RESTRAINTS MEASURED IN BICELLES. IN THE REMARK 3 LAST STAGE, THE TEN LOWEST ENERGY STRUCTURES OF STAGE 2 WERE REMARK 3 USED AS STARTING STRUCTURES IN A SIMULATED ANNEALING CALCULATION REMARK 3 THAT ALSO INCLUDED DIPOLAR RESTRAINTS MEASURED IN A PHAGE LIQUID REMARK 3 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 DEPOSITION ID IS D_1000001518. 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 MM REMARK 210 DINI U-13C,15N, 20 MM PHOSPHATE REMARK 210 BUFFER, 100 MM NACL; PH 6.6; 99% REMARK 210 D2O, 1% H2O; 0.6 MM DINI U-13C, REMARK 210 15N, 20 MM PHOSPHATE BUFFER, 100 REMARK 210 MM NACL; PH 6.6; BICELLE OR REMARK 210 PHAGE LIQUID CRYSTAL, 95% H2O, 5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 2D NOESY; HNCG; REMARK 210 HN(CO)CG; IPAP_15N_HSQC; HNCO; REMARK 210 (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 : 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 WAS REMARK 210 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 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 O PRO A 14 H GLY A 16 1.46 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 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 REMARK 500 THIS ENTRY HAS 80 PLANE DEVIATIONS. 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 MODEL 1