PDB Short entry for 1GYZ HEADER RIBOSOMAL PROTEIN 02-MAY-02 1GYZ TITLE BACTERIAL RIBOSOMAL PROTEIN L20 FROM AQUIFEX AEOLICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L20; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 59-118; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 224324; SOURCE 4 STRAIN: VF5; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PUBS520; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11C KEYWDS RIBOSOMAL PROTEIN, RIBOSOME, PROTEIN SYNTHESIS, KEYWDS 2 TRANSLATIONAL CONTROL, RRNA-BINDING, COMPLETE PROTEOME EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.RAIBAUD,I.LEBARS,F.BONTEMS,F.DARDEL REVDAT 3 24-FEB-09 1GYZ 1 VERSN REVDAT 2 10-OCT-02 1GYZ 1 JRNL REMARK REVDAT 1 10-MAY-02 1GYZ 0 JRNL AUTH S.RAIBAUD,I.LEBARS,M.GUILLIER,C.CHIARUTTINI, JRNL AUTH 2 F.BONTEMS,A.RAK,M.GARBER,F.ALLEMAND,M.SPRINGER, JRNL AUTH 3 F.DARDEL JRNL TITL NMR STRUCTURE OF BACTERIAL RIBOSOMAL PROTEIN L20: JRNL TITL 2 IMPLICATIONS FOR RIBOSOME ASSEMBLY AND JRNL TITL 3 TRANSLATIONAL CONTROL JRNL REF J.MOL.BIOL. V. 323 143 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12368106 JRNL DOI 10.1016/S0022-2836(02)00921-X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.89 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESTRAINED SIMUATED ANNEALING REMARK 3 FOLLOWED BY A FINAL MINIMIZATION USING THE CHARMM22 FORCEFIELD REMARK 4 REMARK 4 1GYZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-MAY-02. REMARK 100 THE PDBE ID CODE IS EBI-9812. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 318 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.5 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCA,NOESY-HMQC, REMARK 210 TOCSY-HMQC, REMARK 210 HCCH-TOCSY, REMARK 210 NOESY, REMARK 210 DQF-COSY, REMARK 210 HNHA, REMARK 210 HNHB REMARK 210 REMARK 210 SPECTROMETER FIELD STRENGTH : 600 REMARK 210 SPECTROMETER MODEL : DRX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DIANA,XPLOR REMARK 210 METHOD USED : HYBRID : DIANA FOLLOWED REMARK 210 BY RESTRAINED SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST DIANA TARGET REMARK 210 FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 7 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE REMARK 210 NMR SPECTROSCOPY ON 13C, 15N-LABELED L20. THE FIRST 58 REMARK 210 RESIDUES ARE PRESENT IN THE SAMPLE BUT ARE DISORDERED IN REMARK 210 SOLUTION 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 HD11 LEU A 72 - HG1 THR A 76 1.54 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 TYR A 74 CB - CG - CD1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 TYR A 74 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 3 TYR A 74 CB - CG - CD1 ANGL. DEV. = 5.2 DEGREES REMARK 500 3 TYR A 74 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 3 LEU A 93 CB - CA - C ANGL. DEV. = -12.4 DEGREES REMARK 500 5 PHE A 77 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES REMARK 500 9 TRP A 59 CA - CB - CG ANGL. DEV. = 20.2 DEGREES REMARK 500 9 LYS A 91 C - N - CA ANGL. DEV. = 16.1 DEGREES REMARK 500 9 LEU A 93 CB - CA - C ANGL. DEV. = -11.5 DEGREES REMARK 500 10 ALA A 94 CB - CA - C ANGL. DEV. = -9.1 DEGREES REMARK 500 13 TRP A 59 CA - CB - CG ANGL. DEV. = 12.7 DEGREES REMARK 500 13 TRP A 59 CB - CG - CD2 ANGL. DEV. = -9.2 DEGREES REMARK 500 13 ALA A 94 N - CA - CB ANGL. DEV. = -10.8 DEGREES REMARK 500 15 TYR A 74 CB - CG - CD1 ANGL. DEV. = 4.2 DEGREES REMARK 500 15 TYR A 74 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 16 ALA A 94 CB - CA - C ANGL. DEV. = -10.5 DEGREES REMARK 500 17 LEU A 93 CB - CA - C ANGL. DEV. = -11.6 DEGREES REMARK 500 19 LEU A 81 CB - CA - C ANGL. DEV. = -11.7 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 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 ILE A 60 -61.03 -147.50 REMARK 500 1 TYR A 74 -24.22 84.80 REMARK 500 1 LEU A 88 -166.98 -127.94 REMARK 500 1 LYS A 91 126.35 136.23 REMARK 500 1 ILE A 92 22.12 82.30 REMARK 500 1 LEU A 115 -72.11 -100.30 REMARK 500 2 ILE A 60 -60.91 -154.49 REMARK 500 2 ALA A 69 -45.86 172.32 REMARK 500 2 TYR A 74 -36.97 91.00 REMARK 500 2 ARG A 90 -33.51 120.25 REMARK 500 2 LYS A 91 127.99 -178.01 REMARK 500 2 ILE A 92 76.08 79.79 REMARK 500 2 LEU A 93 -35.04 177.35 REMARK 500 2 LEU A 115 -77.24 -71.61 REMARK 500 2 VAL A 117 40.74 81.07 REMARK 500 3 ALA A 61 -13.70 71.46 REMARK 500 3 TYR A 74 -27.13 85.09 REMARK 500 3 ILE A 86 -64.86 -99.42 REMARK 500 3 ASP A 89 -141.91 -139.94 REMARK 500 3 ARG A 90 -179.20 76.79 REMARK 500 4 ILE A 60 -63.18 -152.39 REMARK 500 4 TYR A 74 -28.66 84.00 REMARK 500 4 ILE A 86 -62.85 -100.50 REMARK 500 4 GLU A 87 71.67 32.04 REMARK 500 4 ARG A 90 -24.03 101.69 REMARK 500 4 LYS A 91 118.87 -175.52 REMARK 500 4 ILE A 92 81.81 78.46 REMARK 500 4 LEU A 93 -36.08 176.13 REMARK 500 4 VAL A 98 -63.73 -91.07 REMARK 500 4 GLN A 116 51.51 71.00 REMARK 500 5 ILE A 60 44.89 -148.49 REMARK 500 5 TYR A 74 -39.51 96.16 REMARK 500 5 ILE A 86 -65.41 -106.10 REMARK 500 5 ARG A 90 -38.26 171.81 REMARK 500 5 LYS A 91 131.92 169.08 REMARK 500 5 ILE A 92 78.04 70.18 REMARK 500 5 LEU A 93 -34.07 169.54 REMARK 500 5 LEU A 115 -76.94 -103.80 REMARK 500 6 ILE A 60 -63.85 -160.05 REMARK 500 6 TYR A 74 -21.48 87.07 REMARK 500 6 ILE A 86 -70.88 -105.85 REMARK 500 6 ARG A 90 -27.51 89.96 REMARK 500 6 LYS A 91 118.67 -178.57 REMARK 500 6 ILE A 92 82.41 79.50 REMARK 500 6 LEU A 93 -32.92 167.80 REMARK 500 6 GLN A 116 50.71 71.16 REMARK 500 7 ILE A 60 -64.19 -147.57 REMARK 500 7 TYR A 74 -25.57 83.43 REMARK 500 7 ASP A 89 2.57 174.33 REMARK 500 7 ARG A 90 39.34 -95.74 REMARK 500 7 LYS A 91 131.89 112.57 REMARK 500 7 ILE A 92 12.96 86.88 REMARK 500 7 LEU A 115 -75.85 -102.76 REMARK 500 8 ILE A 60 -60.38 -141.50 REMARK 500 8 ARG A 68 31.71 -86.88 REMARK 500 8 TYR A 74 -22.20 82.12 REMARK 500 8 ILE A 86 -71.48 -98.09 REMARK 500 8 ARG A 90 -26.77 107.89 REMARK 500 8 LYS A 91 132.07 177.52 REMARK 500 8 ILE A 92 14.92 85.53 REMARK 500 9 ILE A 60 -58.90 -137.52 REMARK 500 9 ALA A 69 -49.61 175.91 REMARK 500 9 TYR A 74 -26.63 84.76 REMARK 500 9 LEU A 88 -166.70 -124.13 REMARK 500 9 ASP A 89 164.56 48.99 REMARK 500 9 ARG A 90 66.76 95.44 REMARK 500 9 LYS A 91 73.61 43.73 REMARK 500 9 ILE A 92 -48.14 -149.60 REMARK 500 9 VAL A 111 33.79 -93.55 REMARK 500 9 LEU A 115 -81.53 -71.60 REMARK 500 10 ILE A 60 -64.99 -131.07 REMARK 500 10 TYR A 74 -26.69 84.66 REMARK 500 10 ILE A 86 -72.88 -88.79 REMARK 500 10 ASP A 89 -51.22 -149.46 REMARK 500 10 LEU A 93 -36.99 -156.70 REMARK 500 11 ILE A 60 -62.08 -161.39 REMARK 500 11 TYR A 74 -29.44 81.15 REMARK 500 11 GLU A 87 80.01 58.22 REMARK 500 11 LEU A 88 -153.33 -121.05 REMARK 500 11 ASP A 89 90.88 25.25 REMARK 500 11 LYS A 91 132.48 171.78 REMARK 500 11 ILE A 92 24.38 85.22 REMARK 500 11 GLN A 116 49.85 70.59 REMARK 500 12 ILE A 60 -62.09 -148.51 REMARK 500 12 TYR A 74 -28.81 79.44 REMARK 500 12 LYS A 91 126.21 126.65 REMARK 500 12 ILE A 92 82.45 81.18 REMARK 500 12 LEU A 93 -35.84 179.08 REMARK 500 13 ILE A 60 -69.27 -138.26 REMARK 500 13 TYR A 74 -19.04 83.08 REMARK 500 13 ASP A 89 131.51 161.99 REMARK 500 13 ARG A 90 80.52 179.38 REMARK 500 13 LYS A 91 61.35 76.11 REMARK 500 13 ILE A 92 -33.75 -152.63 REMARK 500 13 ALA A 94 -47.12 -25.98 REMARK 500 14 ILE A 60 -77.44 -141.56 REMARK 500 14 TYR A 74 -28.96 83.10 REMARK 500 14 ARG A 90 53.81 94.70 REMARK 500 14 LYS A 91 64.55 68.75 REMARK 500 14 ILE A 92 -47.09 -158.70 REMARK 500 14 GLN A 116 -69.64 -157.86 REMARK 500 14 VAL A 117 -26.73 -162.33 REMARK 500 15 ILE A 60 -57.39 -147.47 REMARK 500 15 ALA A 69 -47.98 -179.57 REMARK 500 15 TYR A 74 -22.87 92.36 REMARK 500 15 LEU A 88 -161.26 -126.94 REMARK 500 15 LYS A 91 137.99 165.74 REMARK 500 15 ILE A 92 4.89 86.97 REMARK 500 15 VAL A 98 -62.73 -97.51 REMARK 500 15 ASP A 100 75.44 -119.44 REMARK 500 15 GLN A 116 42.14 70.86 REMARK 500 16 ILE A 60 -74.40 -149.10 REMARK 500 16 TYR A 74 -26.83 82.16 REMARK 500 16 ILE A 86 -66.91 -98.23 REMARK 500 16 LEU A 88 -127.72 -121.08 REMARK 500 16 ASP A 89 -173.96 73.41 REMARK 500 16 ARG A 90 50.35 87.11 REMARK 500 16 LYS A 91 65.68 70.16 REMARK 500 16 ILE A 92 -46.55 -159.38 REMARK 500 17 ILE A 60 -86.63 -141.03 REMARK 500 17 TYR A 74 -15.01 83.31 REMARK 500 17 ARG A 90 -168.88 -125.77 REMARK 500 17 GLN A 116 36.87 71.48 REMARK 500 18 ILE A 60 -65.02 -160.04 REMARK 500 18 TYR A 74 -31.67 82.54 REMARK 500 18 ILE A 86 -71.37 -111.44 REMARK 500 18 ARG A 90 -33.36 -148.19 REMARK 500 18 LYS A 91 135.81 177.16 REMARK 500 18 ILE A 92 -3.19 91.54 REMARK 500 19 ILE A 60 -56.28 -150.22 REMARK 500 19 TYR A 74 -30.42 85.56 REMARK 500 19 ILE A 86 -69.43 -103.18 REMARK 500 19 GLU A 87 62.76 37.93 REMARK 500 19 ARG A 90 -29.65 163.55 REMARK 500 19 LYS A 91 123.67 -178.41 REMARK 500 19 ILE A 92 82.89 76.18 REMARK 500 19 LEU A 93 -33.64 168.33 REMARK 500 20 ILE A 60 -76.21 -159.17 REMARK 500 20 ARG A 68 35.40 -90.19 REMARK 500 20 TYR A 74 -28.03 81.38 REMARK 500 20 GLU A 87 76.65 22.46 REMARK 500 20 LEU A 88 -135.42 -126.70 REMARK 500 20 ASP A 89 96.44 70.10 REMARK 500 20 ARG A 90 58.69 -160.62 REMARK 500 20 LYS A 91 65.80 66.33 REMARK 500 20 ILE A 92 -53.18 -151.07 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 LEU A 115 GLN A 116 1 -144.04 REMARK 500 LEU A 115 GLN A 116 5 -145.47 REMARK 500 LEU A 115 GLN A 116 7 -144.31 REMARK 500 VAL A 111 LYS A 112 9 149.93 REMARK 500 ASP A 89 ARG A 90 10 -145.01 REMARK 500 ASP A 89 ARG A 90 13 111.56 REMARK 500 LEU A 115 GLN A 116 18 -146.91 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 13 TRP A 59 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 9 ARG A 90 24.9 L L OUTSIDE RANGE REMARK 500 9 LYS A 91 19.0 L L OUTSIDE RANGE REMARK 500 10 ILE A 60 24.6 L L OUTSIDE RANGE REMARK 500 20 ILE A 60 24.9 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL DBREF 1GYZ A 59 118 UNP O67086 RL20_AQUAE 59 118 SEQRES 1 A 60 TRP ILE ALA ARG ILE ASN ALA ALA VAL ARG ALA TYR GLY SEQRES 2 A 60 LEU ASN TYR SER THR PHE ILE ASN GLY LEU LYS LYS ALA SEQRES 3 A 60 GLY ILE GLU LEU ASP ARG LYS ILE LEU ALA ASP MET ALA SEQRES 4 A 60 VAL ARG ASP PRO GLN ALA PHE GLU GLN VAL VAL ASN LYS SEQRES 5 A 60 VAL LYS GLU ALA LEU GLN VAL GLN HELIX 1 1 ILE A 60 ARG A 68 1 9 HELIX 2 2 TYR A 74 GLY A 85 1 12 HELIX 3 3 LEU A 93 ASP A 100 1 8 HELIX 4 4 ASP A 100 LEU A 115 1 16 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