10 20 30 40 50 60 70 80 2GKY - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA/RNA BINDING PROTEIN 03-APR-06 2GKY
TITLE DYNAMIC STRUCTURES OF THE L11-RRNA COMPLEX (MDI)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L11; COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: RNA (58-MER); COMPND 6 CHAIN: B; COMPND 7 OTHER_DETAILS: L11 RIBOSOMAL RNA
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_COMMON: BACTERIA; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 6 ORGANISM_COMMON: BACTERIA
KEYWDS L11-RRNA COMPLEX
EXPDTA THEORETICAL MODEL
AUTHOR W.LI,J.SENGUPTA,B.RATH,J.FRANK
REVDAT 1 09-MAY-06 2GKY 0
JRNL AUTH W.LI,J.SENGUPTA,B.RATH,J.FRANK JRNL TITL DYNAMIC STRUCTURES OF THE L11-RRNA COMPLEX (MDI) JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.VALLE,A.ZAVIALOV,W.LI,S.M.STAGG,J.SENGUPTA, REMARK 1 AUTH 2 R.C.NIELSEN,P.NISSEN,S.C.HARVEY,M.EHRENBERG,J.FRANK REMARK 1 TITL INCORPORATION OF AMINOACYL-TRNA INTO THE RIBOSOME REMARK 1 TITL 2 AS SEEN BY CRYO-ELECTRON MICROSCOPY. REMARK 1 REF NAT.STRUCT.MOL.BIOL. V. 10 899 2003 REMARK 1 REFN US ISSN 1545-9993 REMARK 1 REFERENCE 2 REMARK 1 AUTH B.T.WIMBERLY,R.GUYMON,J.P.MCCUTCHEON,S.W.WHITE, REMARK 1 AUTH 2 V.RAMAKRISHNAN REMARK 1 TITL A DETAILED VIEW OF A RIBOSOMAL ACTIVE SITE: THE REMARK 1 TITL 2 STRUCTURE OF THE L11-RNA COMPLEX REMARK 1 REF CELL (CAMBRIDGE,MASS.) V. 97 491 1999 REMARK 1 REFN ASTM CELLB5 US ISSN 0092-8674
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, D.A. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MOLECULAR DYNAMICS SIMULATION
REMARK 4 REMARK 4 2GKY COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-2006. REMARK 100 THE RCSB ID CODE IS RCSB037247.
REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*.
REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL
REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS.
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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLN A 1 CD GLN A 1 OE1 -0.770 REMARK 500 LYS A 10 CB LYS A 10 CG -0.940 REMARK 500 LYS A 10 CD LYS A 10 CE -1.027 REMARK 500 LYS A 10 CE LYS A 10 NZ -0.847 REMARK 500 GLN A 23 CD GLN A 23 OE1 -1.009 REMARK 500 ASP A 41 CG ASP A 41 OD1 -0.725 REMARK 500 GLU A 55 CD GLU A 55 OE1 -0.773 REMARK 500 LYS A 57 CE LYS A 57 NZ -0.788 REMARK 500 ARG A 95 CZ ARG A 95 NH1 -0.745 REMARK 500 LYS A 96 CE LYS A 96 NZ -0.813 REMARK 500 GLU A 100 CD GLU A 100 OE1 -0.798 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLN A 1 CG - CD - NE2 ANGL. DEV. = 36.5 DEGREES REMARK 500 LEU A 4 CD1 - CG - CD2 ANGL. DEV. =-46.3 DEGREES REMARK 500 LYS A 10 CG - CD - CE ANGL. DEV. = 55.3 DEGREES REMARK 500 LYS A 10 CD - CE - NZ ANGL. DEV. = 36.7 DEGREES REMARK 500 LEU A 21 CD1 - CG - CD2 ANGL. DEV. =-39.4 DEGREES REMARK 500 GLN A 23 OE1 - CD - NE2 ANGL. DEV. =-54.1 DEGREES REMARK 500 GLN A 23 CG - CD - NE2 ANGL. DEV. = 49.6 DEGREES REMARK 500 GLU A 30 OE1 - CD - OE2 ANGL. DEV. =-38.9 DEGREES REMARK 500 GLU A 55 OE1 - CD - OE2 ANGL. DEV. =-93.8 DEGREES REMARK 500 GLU A 55 CG - CD - OE1 ANGL. DEV. = 42.2 DEGREES REMARK 500 GLU A 55 CG - CD - OE2 ANGL. DEV. = 51.9 DEGREES REMARK 500 LYS A 57 CD - CE - NZ ANGL. DEV. = 59.3 DEGREES REMARK 500 LYS A 73 CB - CG - CD ANGL. DEV. = 35.7 DEGREES REMARK 500 GLU A 79 OE1 - CD - OE2 ANGL. DEV. =-38.6 DEGREES REMARK 500 GLU A 84 OE1 - CD - OE2 ANGL. DEV. =-43.9 DEGREES REMARK 500 LYS A 88 CD - CE - NZ ANGL. DEV. = 54.7 DEGREES REMARK 500 LYS A 92 CD - CE - NZ ANGL. DEV. = 36.7 DEGREES REMARK 500 LYS A 96 CG - CD - CE ANGL. DEV. = 35.0 DEGREES REMARK 500 LYS A 96 CD - CE - NZ ANGL. DEV. = 43.8 DEGREES
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GKZ RELATED DB: PDB REMARK 900 DYNAMIC STRUCTURE OF L11-RRNA COMPLEX (MDII)
DBREF 2GKY A 1 133 UNP P29395 RL11_THEMA 7 139 DBREF 2GKY B 134 191 GB 12057205 AE000512 19188 19194
SEQRES 1 A 133 GLN ILE LYS LEU GLN LEU PRO ALA GLY LYS ALA THR PRO SEQRES 2 A 133 ALA PRO PRO VAL GLY PRO ALA LEU GLY GLN HIS GLY VAL SEQRES 3 A 133 ASN ILE MET GLU PHE CYS LYS ARG PHE ASN ALA GLU THR SEQRES 4 A 133 ALA ASP LYS ALA GLY MET ILE LEU PRO VAL VAL ILE THR SEQRES 5 A 133 VAL TYR GLU ASP LYS SER PHE THR PHE ILE ILE LYS THR SEQRES 6 A 133 PRO PRO ALA SER PHE LEU LEU LYS LYS ALA ALA GLY ILE SEQRES 7 A 133 GLU LYS GLY SER SER GLU PRO LYS ARG LYS ILE VAL GLY SEQRES 8 A 133 LYS VAL THR ARG LYS GLN ILE GLU GLU ILE ALA LYS THR SEQRES 9 A 133 LYS MET PRO ASP LEU ASN ALA ASN SER LEU GLU ALA ALA SEQRES 10 A 133 MET LYS ILE ILE GLU GLY THR ALA LYS SER MET GLY ILE SEQRES 11 A 133 GLU VAL VAL SEQRES 1 B 58 G C U G G G A U G U U G G SEQRES 2 B 58 C U U A G A A G C A G C C SEQRES 3 B 58 A U C A U U U A A A G A G SEQRES 4 B 58 U G C G U A A C A G C U C SEQRES 5 B 58 A C C A G C
HELIX 1 1 VAL A 17 GLY A 22 1 6 HELIX 2 2 GLN A 23 GLY A 25 5 3 HELIX 3 3 ASN A 27 GLU A 38 1 12 HELIX 4 4 THR A 39 ALA A 43 5 5 HELIX 5 5 PRO A 67 GLY A 77 1 11 HELIX 6 6 THR A 94 MET A 106 1 13 HELIX 7 7 PRO A 107 LEU A 109 5 3 HELIX 8 8 SER A 113 SER A 127 1 15
SHEET 1 A 3 ILE A 2 PRO A 7 0 SHEET 2 A 3 ILE A 46 VAL A 53 -1 O LEU A 47 N LEU A 6 SHEET 3 A 3 PHE A 59 ILE A 63 -1 O THR A 60 N THR A 52
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