HEADER RIBOSOMAL PROTEIN 06-MAY-08 2K3F TITLE RIBOSOMAL PROTEIN L11 FROM THERMOTOGA MARITIMA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L11; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: RPLK; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET11A KEYWDS L11, RIBOSOMAL PROTEIN, METHYLATION, RIBONUCLEOPROTEIN, RNA-BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.R.A.JONKER,S.ILIN,H.SCHWALBE,J.WOEHNERT REVDAT 4 01-MAY-24 2K3F 1 REMARK REVDAT 3 04-SEP-13 2K3F 1 JRNL VERSN REVDAT 2 24-FEB-09 2K3F 1 VERSN REVDAT 1 17-JUN-08 2K3F 0 JRNL AUTH S.ILIN,A.HOSKINS,O.OHLENSCHLAGER,H.R.A.JONKER,H.SCHWALBE, JRNL AUTH 2 J.WOEHNERT JRNL TITL DOMAIN REORIENTATION AND INDUCED FIT UPON RNA BINDING: JRNL TITL 2 SOLUTION STRUCTURE AND DYNAMICS OF RIBOSOMAL PROTEIN L11 JRNL TITL 3 FROM THERMOTOGA MARITIMA JRNL REF CHEMBIOCHEM V. 6 1611 2005 JRNL REFN ISSN 1439-4227 JRNL PMID 16094695 JRNL DOI 10.1002/CBIC.200500091 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.R.A.JONKER,S.ILIN,S.K.GRIMM,J.WOEHNERT,H.SCHWALBE REMARK 1 TITL L11 DOMAIN REARRANGEMENT UPON BINDING TO RNA AND REMARK 1 TITL 2 THIOSTREPTON STUDIED BY NMR SPECTROSCOPY REMARK 1 REF NUCLEIC ACIDS RES. V. 35 441 2007 REMARK 1 REFN ISSN 0305-1048 REMARK 1 PMID 17169991 REMARK 1 DOI 10.1093/NAR/GKL1066 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.0, CNS, ARIA1.2 REMARK 3 AUTHORS : BRUKER BIOSPIN (XWINNMR), BRUNGER, ADAMS, CLORE, REMARK 3 GROS, NILGES AND READ (CNS), NILGES (ARIA1.2) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: INITIAL COORDINATES ARE CALCULATED BY REMARK 3 CNS AND FURTHER REFINEMENT IN WATER HAS BEEN PERFORMED USING REMARK 3 ARIA PROTOCOLS WITH ADDITIONAL DIFFUSION ANISOTROPY DATA REMARK 4 REMARK 4 2K3F COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000100626. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.1 REMARK 210 IONIC STRENGTH : 70 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2 MM [U-100% 15N] L11, 20 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 10 % [U-100% REMARK 210 2H] D2O, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; IPAP(1H,15N)HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DRX; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.0, VNMR, XEASY, CNS, REMARK 210 ARIA1.2 REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 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 : 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 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 HG13 VAL A 24 HD11 ILE A 35 1.13 REMARK 500 HZ2 LYS A 103 OE2 GLU A 107 1.55 REMARK 500 HG1 THR A 72 OD2 ASP A 115 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 2 TYR A 61 CE1 TYR A 61 CZ -0.095 REMARK 500 2 TYR A 61 CZ TYR A 61 CE2 0.127 REMARK 500 5 PHE A 66 CE1 PHE A 66 CZ 0.147 REMARK 500 5 PHE A 66 CZ PHE A 66 CE2 -0.150 REMARK 500 6 TYR A 61 CE1 TYR A 61 CZ -0.086 REMARK 500 6 TYR A 61 CZ TYR A 61 CE2 0.102 REMARK 500 7 TYR A 61 CE1 TYR A 61 CZ -0.090 REMARK 500 7 TYR A 61 CZ TYR A 61 CE2 0.098 REMARK 500 8 TYR A 61 CZ TYR A 61 CE2 0.101 REMARK 500 8 PHE A 66 CE1 PHE A 66 CZ 0.203 REMARK 500 8 PHE A 66 CZ PHE A 66 CE2 -0.202 REMARK 500 9 PHE A 66 CE1 PHE A 66 CZ 0.214 REMARK 500 9 PHE A 66 CZ PHE A 66 CE2 -0.185 REMARK 500 10 TYR A 61 CE1 TYR A 61 CZ -0.083 REMARK 500 10 TYR A 61 CZ TYR A 61 CE2 0.109 REMARK 500 10 PHE A 66 CE1 PHE A 66 CZ 0.168 REMARK 500 10 PHE A 66 CZ PHE A 66 CE2 -0.161 REMARK 500 11 PHE A 66 CE1 PHE A 66 CZ 0.213 REMARK 500 11 PHE A 66 CZ PHE A 66 CE2 -0.208 REMARK 500 13 PHE A 66 CE1 PHE A 66 CZ 0.180 REMARK 500 13 PHE A 66 CZ PHE A 66 CE2 -0.165 REMARK 500 13 PHE A 77 CE1 PHE A 77 CZ 0.160 REMARK 500 13 PHE A 77 CZ PHE A 77 CE2 -0.117 REMARK 500 14 PHE A 66 CE1 PHE A 66 CZ 0.235 REMARK 500 14 PHE A 66 CZ PHE A 66 CE2 -0.231 REMARK 500 16 PHE A 66 CE1 PHE A 66 CZ 0.167 REMARK 500 16 PHE A 66 CZ PHE A 66 CE2 -0.160 REMARK 500 17 TYR A 61 CE1 TYR A 61 CZ -0.113 REMARK 500 17 TYR A 61 CZ TYR A 61 CE2 0.120 REMARK 500 20 TYR A 61 CE1 TYR A 61 CZ -0.088 REMARK 500 20 TYR A 61 CZ TYR A 61 CE2 0.089 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 1 PRO A 20 C - N - CA ANGL. DEV. = 10.2 DEGREES REMARK 500 8 PRO A 20 C - N - CA ANGL. DEV. = 11.4 DEGREES REMARK 500 9 PRO A 20 C - N - CA ANGL. DEV. = 10.4 DEGREES REMARK 500 9 PRO A 20 N - CA - CB ANGL. DEV. = -8.0 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 ALA A 7 -168.28 -168.02 REMARK 500 1 LYS A 17 29.52 -147.32 REMARK 500 1 THR A 19 140.30 -177.69 REMARK 500 1 PRO A 20 23.68 -42.17 REMARK 500 1 ALA A 21 174.22 -57.88 REMARK 500 1 PRO A 23 -71.83 -38.11 REMARK 500 1 ALA A 27 -78.09 -53.28 REMARK 500 1 ILE A 53 91.00 -67.09 REMARK 500 1 LYS A 64 4.94 84.10 REMARK 500 1 THR A 72 99.04 -49.17 REMARK 500 1 PRO A 74 -60.69 -26.21 REMARK 500 1 ALA A 75 -23.95 -171.43 REMARK 500 1 LYS A 81 33.05 -67.76 REMARK 500 1 ALA A 82 -60.35 -170.48 REMARK 500 1 ILE A 85 32.66 -153.18 REMARK 500 1 GLU A 86 7.00 -69.80 REMARK 500 1 LYS A 87 -46.42 -169.22 REMARK 500 1 GLU A 91 -46.35 -175.50 REMARK 500 1 PRO A 92 109.79 -39.67 REMARK 500 1 LYS A 93 74.95 -155.48 REMARK 500 1 ARG A 94 41.09 -78.94 REMARK 500 1 LYS A 95 -37.81 84.31 REMARK 500 1 VAL A 100 -143.71 -150.73 REMARK 500 2 ALA A 18 129.66 -170.33 REMARK 500 2 THR A 19 -44.87 -176.87 REMARK 500 2 ALA A 21 -87.15 9.63 REMARK 500 2 PRO A 22 -55.99 -26.07 REMARK 500 2 PRO A 23 -73.96 -80.48 REMARK 500 2 ALA A 27 -98.51 -46.37 REMARK 500 2 ILE A 53 91.78 -66.55 REMARK 500 2 LYS A 64 1.20 83.33 REMARK 500 2 PHE A 66 -176.79 -171.09 REMARK 500 2 ALA A 75 -25.59 72.51 REMARK 500 2 GLU A 86 40.27 -171.41 REMARK 500 2 LYS A 87 16.11 -162.77 REMARK 500 2 GLU A 91 96.35 -174.82 REMARK 500 2 ARG A 94 -37.12 -166.36 REMARK 500 2 LYS A 95 8.98 -160.34 REMARK 500 2 VAL A 100 -165.22 -163.76 REMARK 500 2 LEU A 116 2.05 -64.18 REMARK 500 3 ALA A 18 139.39 -171.20 REMARK 500 3 THR A 19 -66.88 -170.74 REMARK 500 3 ALA A 21 -83.87 20.44 REMARK 500 3 VAL A 24 -42.09 111.10 REMARK 500 3 ALA A 27 -98.08 -51.72 REMARK 500 3 ILE A 53 91.87 -65.68 REMARK 500 3 LYS A 64 6.60 81.30 REMARK 500 3 PRO A 74 -29.70 -37.44 REMARK 500 3 ALA A 75 -45.73 75.59 REMARK 500 3 LYS A 81 33.58 -61.98 REMARK 500 REMARK 500 THIS ENTRY HAS 382 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 140 ASP A 141 1 141.09 REMARK 500 THR A 19 PRO A 20 3 -148.40 REMARK 500 VAL A 140 ASP A 141 5 141.61 REMARK 500 VAL A 140 ASP A 141 7 145.23 REMARK 500 VAL A 140 ASP A 141 9 138.93 REMARK 500 LYS A 49 ALA A 50 12 146.96 REMARK 500 VAL A 140 ASP A 141 12 138.79 REMARK 500 VAL A 140 ASP A 141 14 145.45 REMARK 500 VAL A 140 ASP A 141 17 140.79 REMARK 500 VAL A 140 ASP A 141 18 140.89 REMARK 500 VAL A 140 ASP A 141 20 143.19 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 2 TYR A 61 0.08 SIDE CHAIN REMARK 500 6 TYR A 61 0.06 SIDE CHAIN REMARK 500 8 TYR A 61 0.08 SIDE CHAIN REMARK 500 9 PHE A 38 0.07 SIDE CHAIN REMARK 500 10 TYR A 61 0.07 SIDE CHAIN REMARK 500 12 PHE A 66 0.08 SIDE CHAIN REMARK 500 17 TYR A 61 0.05 SIDE CHAIN REMARK 500 18 ARG A 41 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5513 RELATED DB: BMRB REMARK 900 NMR ASSIGNMENT AND SECONDARY STRUCTURE IDENTIFICATION OF THE REMARK 900 RIBOSOMAL PROTEIN L11 FROM THERMOTOGA MARITIMA DBREF 2K3F A 1 141 UNP P29395 RL11_THEMA 1 141 SEQRES 1 A 141 MET ALA LYS LYS VAL ALA ALA GLN ILE LYS LEU GLN LEU SEQRES 2 A 141 PRO ALA GLY LYS ALA THR PRO ALA PRO PRO VAL GLY PRO SEQRES 3 A 141 ALA LEU GLY GLN HIS GLY VAL ASN ILE MET GLU PHE CYS SEQRES 4 A 141 LYS ARG PHE ASN ALA GLU THR ALA ASP LYS ALA GLY MET SEQRES 5 A 141 ILE LEU PRO VAL VAL ILE THR VAL TYR GLU ASP LYS SER SEQRES 6 A 141 PHE THR PHE ILE ILE LYS THR PRO PRO ALA SER PHE LEU SEQRES 7 A 141 LEU LYS LYS ALA ALA GLY ILE GLU LYS GLY SER SER GLU SEQRES 8 A 141 PRO LYS ARG LYS ILE VAL GLY LYS VAL THR ARG LYS GLN SEQRES 9 A 141 ILE GLU GLU ILE ALA LYS THR LYS MET PRO ASP LEU ASN SEQRES 10 A 141 ALA ASN SER LEU GLU ALA ALA MET LYS ILE ILE GLU GLY SEQRES 11 A 141 THR ALA LYS SER MET GLY ILE GLU VAL VAL ASP HELIX 1 1 PRO A 23 GLN A 30 1 8 HELIX 2 2 ASN A 34 ALA A 47 1 14 HELIX 3 3 ASP A 48 ALA A 50 5 3 HELIX 4 4 LEU A 78 GLY A 84 1 7 HELIX 5 5 THR A 101 LYS A 112 1 12 HELIX 6 6 SER A 120 GLY A 136 1 17 SHEET 1 A 3 VAL A 5 GLN A 8 0 SHEET 2 A 3 LEU A 54 TYR A 61 -1 O VAL A 60 N ALA A 6 SHEET 3 A 3 LEU A 11 LEU A 13 -1 N LEU A 11 O VAL A 56 SHEET 1 B 3 VAL A 5 GLN A 8 0 SHEET 2 B 3 LEU A 54 TYR A 61 -1 O VAL A 60 N ALA A 6 SHEET 3 B 3 PHE A 68 ILE A 70 -1 O ILE A 69 N VAL A 57 SHEET 1 C 2 LYS A 99 VAL A 100 0 SHEET 2 C 2 GLU A 138 VAL A 139 1 O GLU A 138 N VAL A 100 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