Header list of 1byj.pdb file
Complete list - l 29 2 Bytes
HEADER RNA 16-OCT-98 1BYJ TITLE GENTAMICIN C1A A-SITE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (16S RNA); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DECODING REGION; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: 16S RIBOSOMAL RNA (NTS 1404-1412/1488-1497) COMPLEXED COMPND 7 WITH GENTAMICIN C1A SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: 16S RNA WAS CHEMICALLY SYNTHESIZED. KEYWDS COMPLEX (AMINOGLYCOSIDE-RIBOSOMAL RNA), RNA EXPDTA SOLUTION NMR NUMMDL 38 AUTHOR S.YOSHIZAWA,D.FOURMY,J.D.PUGLISI REVDAT 3 29-JUL-20 1BYJ 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 24-FEB-09 1BYJ 1 VERSN REVDAT 1 29-OCT-99 1BYJ 0 JRNL AUTH S.YOSHIZAWA,D.FOURMY,J.D.PUGLISI JRNL TITL STRUCTURAL ORIGINS OF GENTAMICIN ANTIBIOTIC ACTION. JRNL REF EMBO J. V. 17 6437 1998 JRNL REFN ISSN 0261-4189 JRNL PMID 9822590 JRNL DOI 10.1093/EMBOJ/17.22.6437 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER REMARK 3 AUTHORS : BIOSYM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BYJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-AUG-99. REMARK 100 THE DEPOSITION ID IS D_1000007034. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.4 REMARK 210 IONIC STRENGTH : 10 MM SODIUM PHOSPHATE REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D; 3D; 4D-NOESY; COSY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : UNITY+ 500; DMX750 REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMR ARCHITECT, DISCOVER REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 38 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 38 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 2 REMARK 210 REMARK 210 REMARK: REMARK 210 A TOTAL OF 326 RNA, 7 GENTAMICIN AND 46 GENTAMICIN-RNA RESTRAINTS REMARK 210 WERE USED. REMARK 210 111 EXPERIMENTAL DIHEDRAL RESTRAINTS WERE USED. FOR 38 THE FINAL REMARK 210 STRUCTURES REMARK 210 DEVIATIONS FROM EXPERIMENTAL RESTRAINTS ARE: RMSD NMR DISTANCE REMARK 210 RESTRAINTS (379) REMARK 210 (A): 0.0249 (0.0002) RMSD NMR DIHEDRAL RESTRAINTS (111) (DEG): REMARK 210 0.0127 (0.0016) REMARK 210 DEVIATIONS FROM DEALIZED GEOMETRY (CVFF FORCEFIELD) RMSD BONDS (A) REMARK 210 : 0.0260 ( REMARK 210 0.0000) RMSD ANGLES (DEG): 0.0621 (0.0001) RMSD IMPROPERS (DEG): REMARK 210 0.0485 ( REMARK 210 0.0025) HEAVY ATOM RMS DEVIATIONS OF AVERAGE, MINIMIZED STRUCTURE REMARK 210 FROM BEST- REMARK 210 FIT SUPERPOSITION OF THE 38 FINAL STRUCTURES RMSD ALL RNA + REMARK 210 GENTAMICIN (A): 0.89 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: 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 1 G A 1 N1 G A 1 C2 0.106 REMARK 500 1 G A 1 N3 G A 1 C4 0.097 REMARK 500 1 G A 1 C4 G A 1 C5 0.059 REMARK 500 1 G A 1 C5 G A 1 C6 0.130 REMARK 500 1 G A 1 N7 G A 1 C8 0.069 REMARK 500 1 G A 1 C2 G A 1 N2 0.070 REMARK 500 1 G A 2 N1 G A 2 C2 0.105 REMARK 500 1 G A 2 N3 G A 2 C4 0.097 REMARK 500 1 G A 2 C4 G A 2 C5 0.058 REMARK 500 1 G A 2 C5 G A 2 C6 0.130 REMARK 500 1 G A 2 N7 G A 2 C8 0.071 REMARK 500 1 G A 2 C2 G A 2 N2 0.070 REMARK 500 1 C A 3 C4 C A 3 N4 0.080 REMARK 500 1 C A 3 N1 C A 3 C6 0.131 REMARK 500 1 C A 3 C2 C A 3 N3 0.121 REMARK 500 1 C A 3 C4 C A 3 C5 -0.055 REMARK 500 1 G A 4 N1 G A 4 C2 0.103 REMARK 500 1 G A 4 N3 G A 4 C4 0.100 REMARK 500 1 G A 4 C4 G A 4 C5 0.056 REMARK 500 1 G A 4 C5 G A 4 C6 0.123 REMARK 500 1 G A 4 N7 G A 4 C8 0.065 REMARK 500 1 G A 4 C2 G A 4 N2 0.068 REMARK 500 1 U A 5 N1 U A 5 C6 0.118 REMARK 500 1 U A 5 C4 U A 5 C5 0.118 REMARK 500 1 C A 6 C4 C A 6 N4 0.075 REMARK 500 1 C A 6 N1 C A 6 C6 0.132 REMARK 500 1 C A 6 C2 C A 6 N3 0.120 REMARK 500 1 C A 6 C4 C A 6 C5 -0.056 REMARK 500 1 A A 7 N3 A A 7 C4 0.122 REMARK 500 1 A A 7 C4 A A 7 C5 0.078 REMARK 500 1 A A 7 N7 A A 7 C8 0.065 REMARK 500 1 C A 8 C4 C A 8 N4 0.083 REMARK 500 1 C A 8 N1 C A 8 C6 0.133 REMARK 500 1 C A 8 C2 C A 8 N3 0.117 REMARK 500 1 C A 8 C4 C A 8 C5 -0.055 REMARK 500 1 A A 9 N3 A A 9 C4 0.122 REMARK 500 1 A A 9 C4 A A 9 C5 0.076 REMARK 500 1 A A 9 N7 A A 9 C8 0.068 REMARK 500 1 C A 10 C4 C A 10 N4 0.079 REMARK 500 1 C A 10 N1 C A 10 C6 0.133 REMARK 500 1 C A 10 C2 C A 10 N3 0.118 REMARK 500 1 C A 10 C4 C A 10 C5 -0.054 REMARK 500 1 C A 11 C4 C A 11 N4 0.079 REMARK 500 1 C A 11 N1 C A 11 C6 0.130 REMARK 500 1 C A 11 C2 C A 11 N3 0.115 REMARK 500 1 C A 11 C4 C A 11 C5 -0.053 REMARK 500 1 U A 12 N1 U A 12 C6 0.093 REMARK 500 1 U A 12 C4 U A 12 C5 0.120 REMARK 500 1 U A 13 N1 U A 13 C6 0.097 REMARK 500 1 U A 13 C4 U A 13 C5 0.121 REMARK 500 REMARK 500 THIS ENTRY HAS 4256 BOND DEVIATIONS. 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 G A 1 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 1 G A 1 C2 - N3 - C4 ANGL. DEV. = 11.4 DEGREES REMARK 500 1 G A 1 N3 - C4 - C5 ANGL. DEV. = -11.1 DEGREES REMARK 500 1 G A 1 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 G A 1 C4 - C5 - N7 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 G A 1 C5 - N7 - C8 ANGL. DEV. = -7.2 DEGREES REMARK 500 1 G A 1 N7 - C8 - N9 ANGL. DEV. = 9.1 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -7.2 DEGREES REMARK 500 1 G A 1 N9 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 G A 1 N3 - C4 - N9 ANGL. DEV. = 8.5 DEGREES REMARK 500 1 G A 1 C6 - C5 - N7 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 G A 1 C5 - C6 - O6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 G A 2 OP1 - P - OP2 ANGL. DEV. = -10.5 DEGREES REMARK 500 1 G A 2 C2 - N3 - C4 ANGL. DEV. = 11.4 DEGREES REMARK 500 1 G A 2 N3 - C4 - C5 ANGL. DEV. = -11.0 DEGREES REMARK 500 1 G A 2 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 G A 2 C4 - C5 - N7 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 G A 2 C5 - N7 - C8 ANGL. DEV. = -7.1 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 8.8 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -7.0 DEGREES REMARK 500 1 G A 2 N9 - C4 - C5 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 G A 2 N3 - C4 - N9 ANGL. DEV. = 8.2 DEGREES REMARK 500 1 G A 2 C6 - C5 - N7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 G A 2 C5 - C6 - O6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 C A 3 OP1 - P - OP2 ANGL. DEV. = -10.5 DEGREES REMARK 500 1 C A 3 C6 - N1 - C2 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 C A 3 C4 - C5 - C6 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 4 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 1 G A 4 C2 - N3 - C4 ANGL. DEV. = 11.2 DEGREES REMARK 500 1 G A 4 N3 - C4 - C5 ANGL. DEV. = -11.0 DEGREES REMARK 500 1 G A 4 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 G A 4 C4 - C5 - N7 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 G A 4 C5 - N7 - C8 ANGL. DEV. = -6.9 DEGREES REMARK 500 1 G A 4 N7 - C8 - N9 ANGL. DEV. = 8.6 DEGREES REMARK 500 1 G A 4 C8 - N9 - C4 ANGL. DEV. = -6.9 DEGREES REMARK 500 1 G A 4 N9 - C4 - C5 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 G A 4 N3 - C4 - N9 ANGL. DEV. = 8.5 DEGREES REMARK 500 1 G A 4 C6 - C5 - N7 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 G A 4 C5 - C6 - O6 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 U A 5 OP1 - P - OP2 ANGL. DEV. = -10.5 DEGREES REMARK 500 1 U A 5 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 U A 5 N1 - C2 - N3 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 U A 5 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 U A 5 C5 - C4 - O4 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 C A 6 OP1 - P - OP2 ANGL. DEV. = -10.6 DEGREES REMARK 500 1 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 C A 6 C6 - N1 - C2 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 C A 6 C4 - C5 - C6 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 7 OP1 - P - OP2 ANGL. DEV. = -10.6 DEGREES REMARK 500 1 A A 7 C2 - N3 - C4 ANGL. DEV. = 5.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 7070 ANGLE DEVIATIONS. 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 A A 9 0.05 SIDE CHAIN REMARK 500 1 G A 22 0.09 SIDE CHAIN REMARK 500 2 G A 22 0.12 SIDE CHAIN REMARK 500 2 U A 23 0.06 SIDE CHAIN REMARK 500 3 G A 22 0.11 SIDE CHAIN REMARK 500 3 U A 23 0.06 SIDE CHAIN REMARK 500 4 A A 20 0.08 SIDE CHAIN REMARK 500 4 G A 22 0.09 SIDE CHAIN REMARK 500 4 U A 23 0.06 SIDE CHAIN REMARK 500 5 G A 22 0.12 SIDE CHAIN REMARK 500 6 G A 22 0.11 SIDE CHAIN REMARK 500 6 U A 23 0.07 SIDE CHAIN REMARK 500 7 A A 21 0.08 SIDE CHAIN REMARK 500 7 G A 22 0.11 SIDE CHAIN REMARK 500 8 G A 22 0.11 SIDE CHAIN REMARK 500 8 U A 23 0.06 SIDE CHAIN REMARK 500 9 A A 21 0.08 SIDE CHAIN REMARK 500 9 G A 22 0.11 SIDE CHAIN REMARK 500 10 G A 22 0.11 SIDE CHAIN REMARK 500 11 G A 22 0.11 SIDE CHAIN REMARK 500 11 U A 23 0.06 SIDE CHAIN REMARK 500 12 G A 22 0.11 SIDE CHAIN REMARK 500 12 U A 23 0.06 SIDE CHAIN REMARK 500 13 A A 21 0.07 SIDE CHAIN REMARK 500 13 G A 22 0.10 SIDE CHAIN REMARK 500 14 A A 21 0.06 SIDE CHAIN REMARK 500 14 G A 22 0.11 SIDE CHAIN REMARK 500 15 A A 21 0.08 SIDE CHAIN REMARK 500 15 G A 22 0.11 SIDE CHAIN REMARK 500 16 G A 22 0.07 SIDE CHAIN REMARK 500 16 U A 23 0.07 SIDE CHAIN REMARK 500 17 G A 22 0.09 SIDE CHAIN REMARK 500 17 U A 23 0.06 SIDE CHAIN REMARK 500 18 G A 22 0.11 SIDE CHAIN REMARK 500 19 G A 22 0.12 SIDE CHAIN REMARK 500 19 U A 23 0.06 SIDE CHAIN REMARK 500 20 G A 22 0.11 SIDE CHAIN REMARK 500 20 U A 23 0.06 SIDE CHAIN REMARK 500 21 A A 21 0.08 SIDE CHAIN REMARK 500 21 G A 22 0.11 SIDE CHAIN REMARK 500 22 A A 21 0.07 SIDE CHAIN REMARK 500 22 G A 22 0.11 SIDE CHAIN REMARK 500 23 G A 22 0.08 SIDE CHAIN REMARK 500 23 U A 23 0.07 SIDE CHAIN REMARK 500 24 G A 22 0.12 SIDE CHAIN REMARK 500 24 U A 23 0.06 SIDE CHAIN REMARK 500 25 A A 21 0.08 SIDE CHAIN REMARK 500 25 G A 22 0.11 SIDE CHAIN REMARK 500 26 A A 21 0.08 SIDE CHAIN REMARK 500 26 G A 22 0.11 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 78 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1BYJ A 1 27 PDB 1BYJ 1BYJ 1 27 SEQRES 1 A 27 G G C G U C A C A C C U U SEQRES 2 A 27 C G G G U G A A G U C G C SEQRES 3 A 27 C HET GE1 A 28 23 HET GE2 A 29 21 HET GE3 A 30 26 HETNAM GE1 2,6-DIAMINO-2,3,4,6-TETRADEOXY-ALPHA-D-ERYTHRO- HETNAM 2 GE1 HEXOPYRANOSE HETNAM GE2 3,5-DIAMINO-CYCLOHEXANOL HETNAM GE3 3-DEOXY-4-C-METHYL-3-(METHYLAMINO)-BETA-L- HETNAM 2 GE3 ARABINOPYRANOSE FORMUL 2 GE1 C6 H14 N2 O2 FORMUL 3 GE2 C6 H14 N2 O FORMUL 4 GE3 C7 H15 N O4 LINK O1 GE1 A 28 C4 GE2 A 29 1555 1555 1.45 LINK C2 GE2 A 29 O1 GE3 A 30 1555 1555 1.45 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
Complete list - l 29 2 Bytes