HEADER RNA BINDING PROTEIN 04-DEC-02 1J1H TITLE SOLUTION STRUCTURE OF A TMRNA-BINDING PROTEIN, SMPB, FROM THERMUS TITLE 2 THERMOPHILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SMALL PROTEIN B; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; 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-11B KEYWDS SMPB, SSRA ASSOCIATED PROTEIN, OB FOLD, RIKEN STRUCTURAL KEYWDS 2 GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL GENOMICS, RNA KEYWDS 3 BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 11 MDLTYP MINIMIZED AVERAGE AUTHOR T.SOMEYA,N.NAMEKI,H.HOSOI,S.SUZUKI,H.HATANAKA,M.FUJII,T.TERADA, AUTHOR 2 M.SHIROUZU,Y.INOUE,T.SHIBATA,S.KURAMITSU,S.YOKOYAMA,G.KAWAI,RIKEN AUTHOR 3 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 27-DEC-23 1J1H 1 REMARK REVDAT 3 23-FEB-22 1J1H 1 REMARK REVDAT 2 24-FEB-09 1J1H 1 VERSN REVDAT 1 11-FEB-03 1J1H 0 JRNL AUTH T.SOMEYA,N.NAMEKI,H.HOSOI,S.SUZUKI,H.HATANAKA,M.FUJII, JRNL AUTH 2 T.TERADA,M.SHIROUZU,Y.INOUE,T.SHIBATA,S.KURAMITSU, JRNL AUTH 3 S.YOKOYAMA,G.KAWAI JRNL TITL SOLUTION STRUCTURE OF A TMRNA-BINDING PROTEIN, SMPB, FROM JRNL TITL 2 THERMUS THERMOPHILUS JRNL REF FEBS LETT. V. 535 94 2003 JRNL REFN ISSN 0014-5793 JRNL PMID 12560085 JRNL DOI 10.1016/S0014-5793(02)03880-2 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1, X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1J1H COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-DEC-02. REMARK 100 THE DEPOSITION ID IS D_1000005511. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 318 REMARK 210 PH : 3.6 REMARK 210 IONIC STRENGTH : 100 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM SMPB U-15N; 1MM HCL AND REMARK 210 100MM NACL; 0.6MM SMPB U-15N,13C; REMARK 210 1MM HCL AND 100MM NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : ON THE BASIS OF AGREEMENT WITH REMARK 210 THE EXPERIMENTAL DATA AND VAN REMARK 210 DER WAALS ENERGY 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 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 1-11 REMARK 465 RES C SSSEQI REMARK 465 LYS A 124 REMARK 465 ALA A 125 REMARK 465 TYR A 126 REMARK 465 GLU A 127 REMARK 465 LYS A 128 REMARK 465 ARG A 129 REMARK 465 ARG A 130 REMARK 465 GLU A 131 REMARK 465 ASP A 132 REMARK 465 LYS A 133 REMARK 465 LYS A 134 REMARK 465 GLU A 135 REMARK 465 ALA A 136 REMARK 465 VAL A 137 REMARK 465 ARG A 138 REMARK 465 ARG A 139 REMARK 465 ALA A 140 REMARK 465 LEU A 141 REMARK 465 GLU A 142 REMARK 465 GLU A 143 REMARK 465 LEU A 144 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 3 TYR A 20 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 4 TYR A 20 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 5 TYR A 20 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 7 TYR A 20 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 8 TYR A 20 CB - CG - CD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 8 TYR A 20 CB - CG - CD1 ANGL. DEV. = 4.2 DEGREES REMARK 500 10 TYR A 20 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES 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 VAL A 4 107.93 -49.59 REMARK 500 1 LEU A 5 158.32 57.56 REMARK 500 1 LEU A 17 -71.71 -68.67 REMARK 500 1 THR A 42 154.76 137.68 REMARK 500 1 GLU A 49 30.08 -98.60 REMARK 500 1 GLU A 56 -50.11 -129.14 REMARK 500 1 TYR A 63 39.68 178.29 REMARK 500 1 GLU A 64 47.69 -90.78 REMARK 500 1 TYR A 68 -148.35 -123.29 REMARK 500 1 ASN A 70 92.54 -172.85 REMARK 500 1 PRO A 73 -89.84 -76.18 REMARK 500 1 ARG A 74 -37.84 -175.45 REMARK 500 1 LYS A 76 -44.18 82.09 REMARK 500 1 ARG A 77 176.98 101.34 REMARK 500 1 LYS A 78 52.59 90.22 REMARK 500 1 GLN A 95 -84.02 -47.30 REMARK 500 1 LYS A 96 111.34 178.11 REMARK 500 1 LEU A 103 -46.19 -20.42 REMARK 500 2 ALA A 2 176.11 176.32 REMARK 500 2 LEU A 5 142.29 60.53 REMARK 500 2 LEU A 17 -73.31 -71.21 REMARK 500 2 THR A 42 154.20 128.80 REMARK 500 2 GLU A 56 -63.80 -128.01 REMARK 500 2 TYR A 63 54.18 -146.41 REMARK 500 2 LYS A 65 17.53 -141.39 REMARK 500 2 TYR A 68 -156.33 -120.60 REMARK 500 2 ALA A 69 87.79 44.19 REMARK 500 2 ASN A 70 -168.77 -162.69 REMARK 500 2 ARG A 74 -7.19 144.03 REMARK 500 2 ARG A 75 77.77 63.03 REMARK 500 2 LYS A 76 123.65 66.23 REMARK 500 2 ARG A 77 -139.51 -111.93 REMARK 500 2 GLN A 95 -95.18 -51.70 REMARK 500 2 LYS A 96 110.22 -172.79 REMARK 500 3 ALA A 2 147.12 175.70 REMARK 500 3 LEU A 5 150.07 57.21 REMARK 500 3 THR A 42 154.29 130.92 REMARK 500 3 PRO A 62 -159.46 -74.76 REMARK 500 3 LYS A 65 83.84 -166.58 REMARK 500 3 ALA A 69 -45.62 -146.71 REMARK 500 3 ASN A 70 32.45 -177.75 REMARK 500 3 PRO A 73 -163.62 -71.11 REMARK 500 3 LYS A 76 -95.72 53.69 REMARK 500 3 ARG A 77 114.46 -178.36 REMARK 500 3 LYS A 78 50.84 171.09 REMARK 500 3 GLN A 95 -76.66 -46.04 REMARK 500 3 LYS A 96 102.96 167.06 REMARK 500 3 PRO A 102 91.35 -69.79 REMARK 500 4 LEU A 5 148.96 53.76 REMARK 500 4 LEU A 17 -71.64 -73.51 REMARK 500 REMARK 500 THIS ENTRY HAS 149 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 8 0.25 SIDE CHAIN REMARK 500 1 ARG A 9 0.28 SIDE CHAIN REMARK 500 1 ARG A 35 0.32 SIDE CHAIN REMARK 500 1 ARG A 47 0.19 SIDE CHAIN REMARK 500 1 ARG A 74 0.30 SIDE CHAIN REMARK 500 1 ARG A 75 0.19 SIDE CHAIN REMARK 500 1 ARG A 77 0.13 SIDE CHAIN REMARK 500 1 ARG A 87 0.08 SIDE CHAIN REMARK 500 1 ARG A 110 0.20 SIDE CHAIN REMARK 500 1 ARG A 121 0.18 SIDE CHAIN REMARK 500 2 ARG A 8 0.32 SIDE CHAIN REMARK 500 2 ARG A 9 0.31 SIDE CHAIN REMARK 500 2 ARG A 11 0.22 SIDE CHAIN REMARK 500 2 ARG A 35 0.32 SIDE CHAIN REMARK 500 2 ARG A 47 0.10 SIDE CHAIN REMARK 500 2 ARG A 75 0.32 SIDE CHAIN REMARK 500 2 ARG A 77 0.20 SIDE CHAIN REMARK 500 2 ARG A 87 0.26 SIDE CHAIN REMARK 500 2 ARG A 88 0.31 SIDE CHAIN REMARK 500 2 ARG A 110 0.28 SIDE CHAIN REMARK 500 2 ARG A 121 0.18 SIDE CHAIN REMARK 500 3 ARG A 8 0.25 SIDE CHAIN REMARK 500 3 ARG A 9 0.10 SIDE CHAIN REMARK 500 3 ARG A 11 0.23 SIDE CHAIN REMARK 500 3 ARG A 35 0.26 SIDE CHAIN REMARK 500 3 ARG A 47 0.32 SIDE CHAIN REMARK 500 3 ARG A 74 0.32 SIDE CHAIN REMARK 500 3 ARG A 75 0.22 SIDE CHAIN REMARK 500 3 ARG A 77 0.09 SIDE CHAIN REMARK 500 3 ARG A 87 0.28 SIDE CHAIN REMARK 500 3 ARG A 88 0.28 SIDE CHAIN REMARK 500 3 ARG A 110 0.28 SIDE CHAIN REMARK 500 3 ARG A 121 0.32 SIDE CHAIN REMARK 500 4 ARG A 8 0.20 SIDE CHAIN REMARK 500 4 ARG A 11 0.29 SIDE CHAIN REMARK 500 4 ARG A 35 0.27 SIDE CHAIN REMARK 500 4 ARG A 47 0.30 SIDE CHAIN REMARK 500 4 ARG A 74 0.32 SIDE CHAIN REMARK 500 4 ARG A 75 0.32 SIDE CHAIN REMARK 500 4 ARG A 77 0.27 SIDE CHAIN REMARK 500 4 ARG A 87 0.26 SIDE CHAIN REMARK 500 4 ARG A 110 0.31 SIDE CHAIN REMARK 500 4 ARG A 121 0.24 SIDE CHAIN REMARK 500 5 ARG A 8 0.16 SIDE CHAIN REMARK 500 5 ARG A 9 0.12 SIDE CHAIN REMARK 500 5 ARG A 11 0.32 SIDE CHAIN REMARK 500 5 ARG A 35 0.13 SIDE CHAIN REMARK 500 5 ARG A 74 0.16 SIDE CHAIN REMARK 500 5 ARG A 75 0.29 SIDE CHAIN REMARK 500 5 ARG A 77 0.28 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 123 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TTK003000801.1 RELATED DB: TARGETDB DBREF 1J1H A 1 144 UNP Q8RR57 SSRP_THET8 1 144 SEQRES 1 A 144 MET ALA PRO VAL LEU GLU ASN ARG ARG ALA ARG HIS ASP SEQRES 2 A 144 TYR GLU ILE LEU GLU THR TYR GLU ALA GLY ILE ALA LEU SEQRES 3 A 144 LYS GLY THR GLU VAL LYS SER LEU ARG ALA GLY LYS VAL SEQRES 4 A 144 ASP PHE THR GLY SER PHE ALA ARG PHE GLU ASP GLY GLU SEQRES 5 A 144 LEU TYR LEU GLU ASN LEU TYR ILE ALA PRO TYR GLU LYS SEQRES 6 A 144 GLY SER TYR ALA ASN VAL ASP PRO ARG ARG LYS ARG LYS SEQRES 7 A 144 LEU LEU LEU HIS LYS HIS GLU LEU ARG ARG LEU LEU GLY SEQRES 8 A 144 LYS VAL GLU GLN LYS GLY LEU THR LEU VAL PRO LEU LYS SEQRES 9 A 144 ILE TYR PHE ASN GLU ARG GLY TYR ALA LYS VAL LEU LEU SEQRES 10 A 144 GLY LEU ALA ARG GLY LYS LYS ALA TYR GLU LYS ARG ARG SEQRES 11 A 144 GLU ASP LYS LYS GLU ALA VAL ARG ARG ALA LEU GLU GLU SEQRES 12 A 144 LEU HELIX 1 1 ASN A 7 ASP A 13 1 7 HELIX 2 2 THR A 29 ALA A 36 1 8 HELIX 3 3 HIS A 82 GLU A 94 1 13 SHEET 1 A 3 GLU A 21 GLY A 23 0 SHEET 2 A 3 LYS A 114 LEU A 116 -1 O VAL A 115 N ALA A 22 SHEET 3 A 3 LYS A 104 TYR A 106 -1 N TYR A 106 O LYS A 114 SHEET 1 B 2 LYS A 38 VAL A 39 0 SHEET 2 B 2 ILE A 60 ALA A 61 -1 O ALA A 61 N LYS A 38 SHEET 1 C 2 ALA A 46 PHE A 48 0 SHEET 2 C 2 LEU A 53 LEU A 55 -1 O TYR A 54 N ARG A 47 SHEET 1 D 2 LEU A 98 THR A 99 0 SHEET 2 D 2 ALA A 120 ARG A 121 -1 O ALA A 120 N THR A 99 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