HEADER STRUCTURAL GENOMICS 20-SEP-99 1D1R TITLE NMR SOLUTION STRUCTURE OF THE PRODUCT OF THE E. COLI YCIH GENE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL 11.4 KD PROTEIN YCIH IN PYRF-OSMB INTERGENIC COMPND 3 REGION; COMPND 4 CHAIN: A; 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: PET-29B KEYWDS ALPHA-BETA PLAIT, OPEN-FACED BETA SANDWICH, FERREDOXIN-LIKE FOLD, KEYWDS 2 STRUCTURAL GENOMICS EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.R.CORT,E.V.KOONIN,P.A.BASH,M.A.KENNEDY REVDAT 4 21-DEC-22 1D1R 1 SEQADV REVDAT 3 16-FEB-22 1D1R 1 REMARK REVDAT 2 24-FEB-09 1D1R 1 VERSN REVDAT 1 06-OCT-99 1D1R 0 JRNL AUTH J.R.CORT,E.V.KOONIN,P.A.BASH,M.A.KENNEDY JRNL TITL A PHYLOGENETIC APPROACH TO TARGET SELECTION FOR STRUCTURAL JRNL TITL 2 GENOMICS: SOLUTION STRUCTURE OF YCIH. JRNL REF NUCLEIC ACIDS RES. V. 27 4018 1999 JRNL REFN ISSN 0305-1048 JRNL PMID 10497266 JRNL DOI 10.1093/NAR/27.20.4018 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: REMARK 3 OF 358 TOTAL RESTRAINTS, 311 ARE DISTANCE RESTRAINTS AND 47 ARE REMARK 3 DIHEDRAL ANGLE REMARK 3 RESTRAINTS. OF THE DISTANCE RESTRAINTS, 32 ARE HYDROGEN BOND REMARK 3 RESTRAINTS (TWO REMARK 3 PER H-BOND), 93 ARE SEQUENTIAL, 50 ARE MEDIUM RANGE, AND 136 ARE REMARK 3 LONG RANGE. REMARK 3 NO INTRARESIDUE DISTANCE RESTRAINTS WERE USED. REMARK 4 REMARK 4 1D1R COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-SEP-99. REMARK 100 THE DEPOSITION ID IS D_1000009716. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 200 MM NACL, 50 MM SODIUM REMARK 210 PHOSPHATE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2-3 MM YCIH U-15N,13C; 50MM REMARK 210 SODIUM PHOSPHATE PH 7.4; 200MM REMARK 210 NACL; 10MM DITHIOTHREITOL; 90% REMARK 210 H2O, 10% D2O; 2-3 MM YCIH U-15N; REMARK 210 50MM SODIUM PHOSPHATE PH 7.4; REMARK 210 200MM NACL; 10MM DITHIOTHREITOL; REMARK 210 90% H2O, 10% D2O; 2-3 MM YCIH U- REMARK 210 15N,13C; 50MM SODIUM PHOSPHATE REMARK 210 PH 7.4; 200MM NACL; 10MM REMARK 210 DITHIOTHREITOL; 99% D2O; 2-3 MM REMARK 210 YCIH U-15N; 50MM SODIUM REMARK 210 PHOSPHATE PH 7.4; 200MM NACL; REMARK 210 10MM DITHIOTHREITOL; 99% D2O; 2- REMARK 210 3 MM YCIH; 50MM SODIUM PHOSPHATE REMARK 210 PH 7.4; 200MM NACL; 10MM REMARK 210 DITHIOTHREITOL; 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 4D_13C-SEPARATED_NOESY; 2D REMARK 210 NOESY; 3D_15N-SEPARATED_NOESY; REMARK 210 HMQC-J; 3D SIMULTANEOUS 15N, 13C- REMARK 210 SEPARATED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 97, VNMR 6.1A REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 25 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 : 4 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 2 REMARK 465 SER A 3 REMARK 465 ASP A 4 REMARK 465 SER A 5 REMARK 465 ASN A 6 REMARK 465 SER A 7 REMARK 465 ARG A 8 REMARK 465 LEU A 9 REMARK 465 VAL A 10 REMARK 465 TYR A 11 REMARK 465 SER A 12 REMARK 465 THR A 13 REMARK 465 GLU A 14 REMARK 465 THR A 15 REMARK 465 GLY A 16 REMARK 465 ARG A 17 REMARK 465 ILE A 18 REMARK 465 ASP A 19 REMARK 465 GLU A 20 REMARK 465 PRO A 21 REMARK 465 LYS A 22 REMARK 465 ALA A 23 REMARK 465 ALA A 24 REMARK 465 PRO A 25 REMARK 465 VAL A 26 REMARK 465 ARG A 27 REMARK 465 PRO A 28 REMARK 465 HIS A 112 REMARK 465 HIS A 113 REMARK 465 HIS A 114 REMARK 465 HIS A 115 REMARK 465 HIS A 116 REMARK 465 HIS A 117 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 31 73.29 65.84 REMARK 500 1 ARG A 43 -74.08 -71.24 REMARK 500 1 LYS A 46 110.48 -168.37 REMARK 500 1 VAL A 54 94.17 -49.02 REMARK 500 1 ASP A 57 150.47 -45.47 REMARK 500 1 CYS A 74 110.62 112.02 REMARK 500 1 LEU A 106 98.49 -44.90 REMARK 500 2 ASP A 58 -63.13 174.12 REMARK 500 2 CYS A 74 125.33 177.66 REMARK 500 2 ALA A 77 124.42 176.78 REMARK 500 2 ASP A 80 109.72 -58.63 REMARK 500 2 LYS A 89 31.39 -158.73 REMARK 500 2 LEU A 106 -157.82 44.24 REMARK 500 3 LYS A 44 31.66 -174.09 REMARK 500 3 THR A 52 13.28 -141.60 REMARK 500 3 LEU A 56 -169.23 -129.15 REMARK 500 3 ASP A 58 -50.34 179.76 REMARK 500 3 CYS A 74 90.95 -174.92 REMARK 500 3 LYS A 89 65.98 -152.15 REMARK 500 3 ALA A 107 83.60 68.10 REMARK 500 4 ASP A 31 110.50 -178.68 REMARK 500 4 ARG A 43 160.02 70.32 REMARK 500 4 ASP A 55 78.73 -113.55 REMARK 500 4 LYS A 71 43.48 -151.52 REMARK 500 4 CYS A 74 97.42 165.36 REMARK 500 4 ASP A 80 91.49 -60.71 REMARK 500 4 ASP A 88 70.38 -177.79 REMARK 500 4 LYS A 89 49.44 -143.51 REMARK 500 4 LEU A 106 101.33 -50.52 REMARK 500 5 SER A 41 37.55 -148.92 REMARK 500 5 ARG A 43 49.00 -105.73 REMARK 500 5 THR A 52 25.89 -154.82 REMARK 500 5 CYS A 74 112.07 179.15 REMARK 500 5 LYS A 89 48.37 -141.30 REMARK 500 5 MET A 102 -158.88 -99.09 REMARK 500 5 LYS A 105 68.47 -119.61 REMARK 500 5 LEU A 106 96.61 -50.39 REMARK 500 6 THR A 40 76.79 -115.46 REMARK 500 6 THR A 52 14.01 -141.84 REMARK 500 6 VAL A 54 98.90 -44.93 REMARK 500 6 CYS A 74 134.97 172.08 REMARK 500 6 LYS A 89 52.22 -148.21 REMARK 500 6 LEU A 110 86.42 59.48 REMARK 500 7 ASP A 31 50.82 -152.23 REMARK 500 7 SER A 41 -51.00 -177.63 REMARK 500 7 LYS A 44 30.31 -161.11 REMARK 500 7 LYS A 46 -153.36 -132.98 REMARK 500 7 ASP A 57 170.71 -47.75 REMARK 500 7 CYS A 74 126.73 166.46 REMARK 500 7 LYS A 89 51.68 -142.88 REMARK 500 REMARK 500 THIS ENTRY HAS 184 RAMACHANDRAN OUTLIERS. 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 35 0.30 SIDE CHAIN REMARK 500 1 ARG A 38 0.10 SIDE CHAIN REMARK 500 1 ARG A 43 0.18 SIDE CHAIN REMARK 500 1 ARG A 90 0.27 SIDE CHAIN REMARK 500 2 ARG A 35 0.23 SIDE CHAIN REMARK 500 2 ARG A 38 0.30 SIDE CHAIN REMARK 500 2 ARG A 90 0.10 SIDE CHAIN REMARK 500 3 ARG A 35 0.32 SIDE CHAIN REMARK 500 3 ARG A 38 0.26 SIDE CHAIN REMARK 500 3 ARG A 43 0.13 SIDE CHAIN REMARK 500 3 ARG A 90 0.19 SIDE CHAIN REMARK 500 4 ARG A 35 0.22 SIDE CHAIN REMARK 500 4 ARG A 38 0.23 SIDE CHAIN REMARK 500 4 ARG A 43 0.12 SIDE CHAIN REMARK 500 4 ARG A 90 0.21 SIDE CHAIN REMARK 500 5 ARG A 35 0.26 SIDE CHAIN REMARK 500 5 ARG A 38 0.26 SIDE CHAIN REMARK 500 5 ARG A 43 0.08 SIDE CHAIN REMARK 500 5 ARG A 90 0.21 SIDE CHAIN REMARK 500 6 ARG A 35 0.32 SIDE CHAIN REMARK 500 6 ARG A 38 0.31 SIDE CHAIN REMARK 500 6 ARG A 43 0.09 SIDE CHAIN REMARK 500 6 ARG A 90 0.27 SIDE CHAIN REMARK 500 7 ARG A 35 0.20 SIDE CHAIN REMARK 500 7 ARG A 38 0.22 SIDE CHAIN REMARK 500 7 ARG A 43 0.24 SIDE CHAIN REMARK 500 7 ARG A 90 0.16 SIDE CHAIN REMARK 500 8 ARG A 35 0.32 SIDE CHAIN REMARK 500 8 ARG A 38 0.32 SIDE CHAIN REMARK 500 8 ARG A 43 0.23 SIDE CHAIN REMARK 500 8 ARG A 90 0.22 SIDE CHAIN REMARK 500 9 ARG A 35 0.22 SIDE CHAIN REMARK 500 9 ARG A 38 0.23 SIDE CHAIN REMARK 500 9 ARG A 43 0.10 SIDE CHAIN REMARK 500 9 ARG A 90 0.18 SIDE CHAIN REMARK 500 10 ARG A 35 0.22 SIDE CHAIN REMARK 500 10 ARG A 38 0.14 SIDE CHAIN REMARK 500 10 ARG A 43 0.09 SIDE CHAIN REMARK 500 10 ARG A 90 0.32 SIDE CHAIN REMARK 500 11 ARG A 35 0.21 SIDE CHAIN REMARK 500 11 ARG A 38 0.18 SIDE CHAIN REMARK 500 11 ARG A 43 0.09 SIDE CHAIN REMARK 500 11 ARG A 90 0.16 SIDE CHAIN REMARK 500 12 ARG A 35 0.27 SIDE CHAIN REMARK 500 12 ARG A 38 0.31 SIDE CHAIN REMARK 500 12 ARG A 43 0.11 SIDE CHAIN REMARK 500 12 ARG A 90 0.29 SIDE CHAIN REMARK 500 13 ARG A 35 0.29 SIDE CHAIN REMARK 500 13 ARG A 38 0.32 SIDE CHAIN REMARK 500 13 ARG A 43 0.27 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 79 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1D1R A 2 109 UNP P08245 YCIH_ECOLI 1 108 SEQADV 1D1R LEU A 110 UNP P08245 EXPRESSION TAG SEQADV 1D1R GLU A 111 UNP P08245 EXPRESSION TAG SEQADV 1D1R HIS A 112 UNP P08245 EXPRESSION TAG SEQADV 1D1R HIS A 113 UNP P08245 EXPRESSION TAG SEQADV 1D1R HIS A 114 UNP P08245 EXPRESSION TAG SEQADV 1D1R HIS A 115 UNP P08245 EXPRESSION TAG SEQADV 1D1R HIS A 116 UNP P08245 EXPRESSION TAG SEQADV 1D1R HIS A 117 UNP P08245 EXPRESSION TAG SEQRES 1 A 116 MET SER ASP SER ASN SER ARG LEU VAL TYR SER THR GLU SEQRES 2 A 116 THR GLY ARG ILE ASP GLU PRO LYS ALA ALA PRO VAL ARG SEQRES 3 A 116 PRO LYS GLY ASP GLY VAL VAL ARG ILE GLN ARG GLN THR SEQRES 4 A 116 SER GLY ARG LYS GLY LYS GLY VAL CYS LEU ILE THR GLY SEQRES 5 A 116 VAL ASP LEU ASP ASP ALA GLU LEU THR LYS LEU ALA ALA SEQRES 6 A 116 GLU LEU LYS LYS LYS CYS GLY CYS GLY GLY ALA VAL LYS SEQRES 7 A 116 ASP GLY VAL ILE GLU ILE GLN GLY ASP LYS ARG ASP LEU SEQRES 8 A 116 LEU LYS SER LEU LEU GLU ALA LYS GLY MET LYS VAL LYS SEQRES 9 A 116 LEU ALA GLY GLY LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 1 ASP A 57 LYS A 69 1 13 HELIX 2 2 LYS A 89 GLY A 101 1 13 SHEET 1 A 4 ILE A 83 ILE A 85 0 SHEET 2 A 4 CYS A 49 THR A 52 -1 O CYS A 49 N ILE A 85 SHEET 3 A 4 VAL A 33 ARG A 38 -1 O ARG A 35 N THR A 52 SHEET 4 A 4 LYS A 103 VAL A 104 1 O LYS A 103 N VAL A 34 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