PDB Short entry for 1QKH HEADER RIBOSOMAL PROTEIN 20-JUL-99 1QKH TITLE SOLUTION STRUCTURE OF THE RIBOSOMAL PROTEIN S19 FROM THERMUS TITLE 2 THERMOPHILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 30S RIBOSOMAL PROTEIN S19; 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_STRAIN: B834(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PACA; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTTHS19 KEYWDS RIBOSOME, RIBOSOMAL PROTEIN, THERMUS THERMOPHILUS, S19 EXPDTA SOLUTION NMR NUMMDL 21 AUTHOR M.HELGSTRAND,A.V.RAK,P.ALLARD,N.DAVYDOVA,M.B.GARBER,T.HARD REVDAT 6 17-JAN-18 1QKH 1 JRNL REMARK REVDAT 5 24-FEB-09 1QKH 1 VERSN REVDAT 4 08-OCT-99 1QKH 1 JRNL REVDAT 3 14-SEP-99 1QKH 1 REMARK REVDAT 2 02-AUG-99 1QKH 1 HELIX REVDAT 1 21-JUL-99 1QKH 0 JRNL AUTH M.HELGSTRAND,A.V.RAK,P.ALLARD,N.DAVYDOVA,M.B.GARBER,T.HARD JRNL TITL SOLUTION STRUCTURE OF THE RIBOSOMAL PROTEIN S19 FROM THERMUS JRNL TITL 2 THERMOPHILUS. JRNL REF J. MOL. BIOL. V. 292 1071 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10512703 JRNL DOI 10.1006/JMBI.1999.3122 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER STRUCTURAL STATISTICS: 21 SA STRUCTURES REMARK 3 SAAVEMIN[A] RMS DEVIATIONS FROM EXP. RESTRAINTS REMARK 3 NOE DISTANCE RESTRAINTS (1104) 0.036 A 0.032 A REMARK 3 DIHEDRAL ANGLE RESTRAINTS (42) 0.380 DEG 0.380 DEG REMARK 3 DEVIATIONS FROM IDEAL GEOMETRY BONDS 0.0045 A REMARK 3 0.0041 A ANGLES 0.71 DEG 0.66 DEG IMPROPERS 0.54 REMARK 3 DEG 0.49 DEG REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS DETERMINED USING 1104 REMARK 3 DISTANCE RESTRAINTS, 42 DIHEDRAL ANGLE RESTRAINTS AND 14 REMARK 3 HYDROGEN BOND RESTRAINTS. 50 STRUCTURES WERE CALCULATED AND REMARK 3 REFINED USING AN AB INITIO SIMULATED ANNEALING PROTOCOL FOR X- REMARK 3 PLOR AND THEN REFINED IN TWO STEPS. AN R-6 AVERAGING PROTOCOL REMARK 3 WAS USED FOR NON-STEREOSPECIFICALLY ASSIGNED PROTONS [1]. DURING REMARK 3 THE SIMULATED ANNEALING STEP AND THE FIRST REFINEMENT STEP ONLY REMARK 3 THE REPULSIVE PART OF THE VAN DER WAALS INTERACTION WAS REMARK 3 INCLUDED. IN THE SECOND REFINEMENT STEP THE VAN DER WAALS REMARK 3 INTERACTION WAS PARAMETERIZED USING A LENNARD-JONES POTENTIAL REMARK 3 INCLUDING THE ATTRACTIVE PART. 21 STRUCTURES WERE SELECTED ON REMARK 3 THE BASIS OF CUMULATIVE RMSD VALUES OF STRUCTURES, ORDERED AFTER REMARK 3 OVERALL ENERGY, AND RAMACHANDRAN BEHAVIOR FOR REGIONS WITH LOW REMARK 3 RESTRAINT DENSITIES. [1] BRUNGER, A. T., CLORE, G. M., REMARK 3 GRONENBORN, A. M. & KARPLUS, M. (1986). THREE-DIMENSIONAL REMARK 3 STRUCTURE OF PROTEINS DETERMINED BY MOLECULAR DYNAMICS WITH REMARK 3 INTERPROTON DISTANCE RESTRAINTS: APPLICATION TO CRAMBIN. PROC REMARK 3 NATL ACAD SCI USA 83, 3801-3805. OTHER DETAILS OF STRUCTURE REMARK 3 REFINEMENT CAN BE FOUND IN THE JRNL CITATION. REMARK 4 REMARK 4 1QKH COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1290002955. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.250 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 90% WATER/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCA; HN(CO)CA; CBCANH; REMARK 210 CBCA(CO)NH; C(CO)NH-TOCSY; HCCH- REMARK 210 TOCSY; (HB)CB(CGCD)HD; (HB) REMARK 210 CB(CGCDCE)HE; 15N-EDITED NOESY- REMARK 210 HSQC; 15N-EDITED TOCSY-HSQC; 3D REMARK 210 HNHA; 2D NOESY; 2D TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 5.3, PRONTO (VERSION REMARK 210 970523) 970523), X-PLOR (VERSION REMARK 210 3.851) 3.851), MOLMOL (VERSION REMARK 210 2.6) 2.6), PROCHECK-NMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : CUMULATIVE RMSD OF STRUCTURES REMARK 210 SORTED AFTER TOTAL ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 1-21 REMARK 465 RES C SSSEQI REMARK 465 PRO A 2 REMARK 465 ARG A 3 REMARK 465 SER A 4 REMARK 465 LEU A 5 REMARK 465 LYS A 6 REMARK 465 LYS A 7 REMARK 465 ARG A 81 REMARK 465 GLY A 82 REMARK 465 HIS A 83 REMARK 465 GLY A 84 REMARK 465 LYS A 85 REMARK 465 GLU A 86 REMARK 465 ALA A 87 REMARK 465 LYS A 88 REMARK 465 ALA A 89 REMARK 465 THR A 90 REMARK 465 LYS A 91 REMARK 465 LYS A 92 REMARK 465 LYS A 93 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 LYS A 28 59.68 -107.30 REMARK 500 1 ARG A 29 -154.34 -102.88 REMARK 500 1 TRP A 34 35.01 -144.49 REMARK 500 1 SER A 35 -96.03 -84.63 REMARK 500 1 ARG A 36 -61.91 -171.81 REMARK 500 1 VAL A 45 -1.19 -57.50 REMARK 500 1 LYS A 55 -24.90 -140.65 REMARK 500 1 PRO A 59 87.37 -66.08 REMARK 500 1 THR A 63 -155.47 -101.03 REMARK 500 1 ASN A 65 24.15 -146.92 REMARK 500 1 HIS A 69 -85.04 -122.03 REMARK 500 1 LYS A 70 -30.64 178.68 REMARK 500 1 LEU A 71 -16.00 174.46 REMARK 500 2 ASP A 12 108.70 -47.93 REMARK 500 2 LYS A 28 77.40 -113.10 REMARK 500 2 ARG A 29 -154.85 -116.93 REMARK 500 2 TRP A 34 75.71 -152.46 REMARK 500 2 SER A 35 -82.20 -123.28 REMARK 500 2 ARG A 36 -64.17 -167.97 REMARK 500 2 SER A 38 124.92 -37.90 REMARK 500 2 VAL A 45 0.63 -61.24 REMARK 500 2 LYS A 55 -26.27 -140.87 REMARK 500 2 PRO A 59 90.32 -65.77 REMARK 500 2 THR A 63 -157.20 -94.92 REMARK 500 2 ASN A 65 19.72 -148.79 REMARK 500 2 HIS A 69 -81.42 -128.13 REMARK 500 2 LYS A 70 -31.46 177.76 REMARK 500 2 LEU A 71 -16.45 173.73 REMARK 500 3 ARG A 29 -154.34 -113.44 REMARK 500 3 TRP A 34 30.72 -145.54 REMARK 500 3 SER A 35 -96.91 -86.33 REMARK 500 3 ARG A 36 -66.34 -170.27 REMARK 500 3 ARG A 37 45.24 -99.73 REMARK 500 3 VAL A 45 5.03 -62.14 REMARK 500 3 LYS A 55 -27.82 -140.48 REMARK 500 3 PRO A 59 87.51 -65.09 REMARK 500 3 THR A 63 -153.98 -104.99 REMARK 500 3 HIS A 69 -84.99 -121.72 REMARK 500 3 LYS A 70 -30.54 178.36 REMARK 500 3 LEU A 71 -15.31 173.30 REMARK 500 3 PRO A 76 48.88 -86.66 REMARK 500 3 THR A 77 -56.43 -139.46 REMARK 500 4 ASP A 12 102.88 -48.93 REMARK 500 4 ARG A 29 -157.19 -115.84 REMARK 500 4 TRP A 34 37.01 -145.74 REMARK 500 4 SER A 35 -155.45 -100.21 REMARK 500 4 ARG A 37 35.26 -99.38 REMARK 500 4 VAL A 45 7.34 -66.68 REMARK 500 4 LYS A 55 -24.97 -140.71 REMARK 500 4 PRO A 59 88.75 -66.65 REMARK 500 REMARK 500 THIS ENTRY HAS 304 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 29 0.30 SIDE CHAIN REMARK 500 1 ARG A 36 0.30 SIDE CHAIN REMARK 500 1 ARG A 37 0.31 SIDE CHAIN REMARK 500 1 ARG A 78 0.32 SIDE CHAIN REMARK 500 2 ARG A 29 0.31 SIDE CHAIN REMARK 500 2 ARG A 36 0.30 SIDE CHAIN REMARK 500 2 ARG A 37 0.29 SIDE CHAIN REMARK 500 2 ARG A 78 0.32 SIDE CHAIN REMARK 500 3 ARG A 29 0.31 SIDE CHAIN REMARK 500 3 ARG A 36 0.32 SIDE CHAIN REMARK 500 3 ARG A 37 0.29 SIDE CHAIN REMARK 500 3 ARG A 78 0.32 SIDE CHAIN REMARK 500 4 ARG A 29 0.31 SIDE CHAIN REMARK 500 4 ARG A 36 0.32 SIDE CHAIN REMARK 500 4 ARG A 37 0.32 SIDE CHAIN REMARK 500 4 ARG A 78 0.31 SIDE CHAIN REMARK 500 5 ARG A 29 0.32 SIDE CHAIN REMARK 500 5 ARG A 36 0.32 SIDE CHAIN REMARK 500 5 ARG A 37 0.31 SIDE CHAIN REMARK 500 5 ARG A 78 0.32 SIDE CHAIN REMARK 500 6 ARG A 29 0.32 SIDE CHAIN REMARK 500 6 ARG A 36 0.26 SIDE CHAIN REMARK 500 6 ARG A 37 0.30 SIDE CHAIN REMARK 500 6 ARG A 78 0.32 SIDE CHAIN REMARK 500 7 ARG A 29 0.29 SIDE CHAIN REMARK 500 7 ARG A 36 0.32 SIDE CHAIN REMARK 500 7 ARG A 37 0.28 SIDE CHAIN REMARK 500 7 ARG A 78 0.32 SIDE CHAIN REMARK 500 8 ARG A 29 0.32 SIDE CHAIN REMARK 500 8 ARG A 36 0.32 SIDE CHAIN REMARK 500 8 ARG A 37 0.32 SIDE CHAIN REMARK 500 8 ARG A 78 0.30 SIDE CHAIN REMARK 500 9 ARG A 29 0.30 SIDE CHAIN REMARK 500 9 ARG A 36 0.28 SIDE CHAIN REMARK 500 9 ARG A 37 0.31 SIDE CHAIN REMARK 500 9 ARG A 78 0.31 SIDE CHAIN REMARK 500 10 ARG A 29 0.32 SIDE CHAIN REMARK 500 10 ARG A 36 0.29 SIDE CHAIN REMARK 500 10 ARG A 37 0.32 SIDE CHAIN REMARK 500 10 ARG A 78 0.32 SIDE CHAIN REMARK 500 11 ARG A 29 0.32 SIDE CHAIN REMARK 500 11 ARG A 36 0.31 SIDE CHAIN REMARK 500 11 ARG A 37 0.32 SIDE CHAIN REMARK 500 11 ARG A 78 0.29 SIDE CHAIN REMARK 500 12 ARG A 29 0.31 SIDE CHAIN REMARK 500 12 ARG A 36 0.32 SIDE CHAIN REMARK 500 12 ARG A 37 0.31 SIDE CHAIN REMARK 500 12 ARG A 78 0.32 SIDE CHAIN REMARK 500 13 ARG A 29 0.31 SIDE CHAIN REMARK 500 13 ARG A 36 0.32 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 84 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: KABSCH AND SANDER REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: KABSCH AND SANDER REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QKF RELATED DB: PDB REMARK 900 THE MINIMIZED AVERAGE SOLUTION STRUCTURE THE EXPERIMENTAL REMARK 900 RESTRAINTS ARE PRESENTED IN PDB ENTRY 1QKH MR. DBREF 1QKH A 2 93 UNP P80381 RS19_THETH 2 93 SEQRES 1 A 92 PRO ARG SER LEU LYS LYS GLY VAL PHE VAL ASP ASP HIS SEQRES 2 A 92 LEU LEU GLU LYS VAL LEU GLU LEU ASN ALA LYS GLY GLU SEQRES 3 A 92 LYS ARG LEU ILE LYS THR TRP SER ARG ARG SER THR ILE SEQRES 4 A 92 VAL PRO GLU MET VAL GLY HIS THR ILE ALA VAL TYR ASN SEQRES 5 A 92 GLY LYS GLN HIS VAL PRO VAL TYR ILE THR GLU ASN MET SEQRES 6 A 92 VAL GLY HIS LYS LEU GLY GLU PHE ALA PRO THR ARG THR SEQRES 7 A 92 TYR ARG GLY HIS GLY LYS GLU ALA LYS ALA THR LYS LYS SEQRES 8 A 92 LYS HELIX 1 H1 ASP A 13 LYS A 25 1 13 HELIX 2 H2 PRO A 42 MET A 44 5 3 SHEET 1 S1 3 LEU A 30 LYS A 32 0 SHEET 2 S1 3 HIS A 47 TYR A 52 1 N ALA A 50 O ILE A 31 SHEET 3 S1 3 HIS A 57 ILE A 62 -1 N VAL A 58 O VAL A 51 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