PDB Short entry for 1NEM HEADER RNA 15-MAR-99 1NEM TITLE SACCHARIDE-RNA RECOGNITION IN THE NEOMYCIN B / RNA APTAMER COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*AP*CP*UP*GP*GP*GP*CP*GP*AP*GP*AP*AP*GP*UP*UP*UP COMPND 3 *AP*GP*UP*CP*C)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: COMPLEXED WITH NEOMYCIN B; HETERO GROUPS BDG (RING A), COMPND 7 NEB (RING B), RIB (RING C), AND NED (RING D) SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS RNA APTAMER, AMINOGLYCOSIDE, ANTIBIOTIC, RNA EXPDTA SOLUTION NMR NUMMDL 9 AUTHOR L.JIANG,A.MAJUMDAR,W.HU,T.J.JAISHREE,W.XU,D.J.PATEL REVDAT 4 29-JUL-20 1NEM 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 24-FEB-09 1NEM 1 VERSN REVDAT 2 19-SEP-06 1NEM 2 CONECT COMPND JRNL TITLE REVDAT 2 2 2 REMARK REVDAT 1 31-AUG-99 1NEM 0 JRNL AUTH L.JIANG,A.MAJUMDAR,W.HU,T.J.JAISHREE,W.XU,D.J.PATEL JRNL TITL SACCHARIDE-RNA RECOGNITION IN A COMPLEX FORMED BETWEEN JRNL TITL 2 NEOMYCIN B AND AN RNA APTAMER JRNL REF STRUCTURE FOLD.DES. V. 7 817 1999 JRNL REFN ISSN 0969-2126 JRNL PMID 10425683 JRNL DOI 10.1016/S0969-2126(99)80105-1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NEM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAR-99. REMARK 100 THE DEPOSITION ID IS D_1000000653. 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 : 10MM NA3PO4 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : DISTANCE RESTRAINED MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: REMARK 210 EXPERIMENTS CONDUCTED IN D2O: 2D NOESY (50MS,120MS,200MS,300MS) REMARK 210 PHASE-SENSITIVE REMARK 210 COSY, TOCSY, (1H)- (13)C HSQC 3D (1H)-(13)C NOESY-HMQC (120MS, REMARK 210 300MS) 3D HCCH- REMARK 210 COSY 3D HCCH-TOCSY 2D (1H)-(13)C HCCH-TOCSY (65MS) 2D (1H)-(31)P REMARK 210 CORRELATION REMARK 210 3D (1H)-(13)C-(31)P CORRELATION 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, B 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 A A 6 N9 A A 6 C4 0.044 REMARK 500 1 A A 14 N9 A A 14 C4 0.042 REMARK 500 1 A A 17 N9 A A 17 C4 0.041 REMARK 500 1 U A 19 N1 U A 19 C2 0.055 REMARK 500 1 U A 20 N1 U A 20 C2 0.055 REMARK 500 1 U A 24 N1 U A 24 C2 0.061 REMARK 500 2 A A 6 N9 A A 6 C4 0.048 REMARK 500 2 A A 14 N9 A A 14 C4 0.040 REMARK 500 2 A A 17 N9 A A 17 C4 0.043 REMARK 500 2 U A 19 N1 U A 19 C2 0.056 REMARK 500 2 U A 20 N1 U A 20 C2 0.055 REMARK 500 2 U A 24 N1 U A 24 C2 0.063 REMARK 500 3 A A 6 N9 A A 6 C4 0.040 REMARK 500 3 U A 8 N1 U A 8 C2 0.055 REMARK 500 3 A A 14 N9 A A 14 C4 0.037 REMARK 500 3 A A 17 N9 A A 17 C4 0.038 REMARK 500 3 U A 24 N1 U A 24 C2 0.058 REMARK 500 4 C A 12 N1 C A 12 C2 0.064 REMARK 500 4 A A 14 N9 A A 14 C4 0.038 REMARK 500 4 A A 17 N9 A A 17 C4 0.040 REMARK 500 4 U A 19 N1 U A 19 C2 0.057 REMARK 500 4 U A 20 N1 U A 20 C2 0.055 REMARK 500 4 U A 21 N1 U A 21 C2 0.059 REMARK 500 4 U A 24 N1 U A 24 C2 0.060 REMARK 500 5 A A 6 N9 A A 6 C4 0.046 REMARK 500 5 C A 12 N1 C A 12 C2 0.062 REMARK 500 5 A A 14 N9 A A 14 C4 0.040 REMARK 500 5 A A 16 N9 A A 16 C4 0.038 REMARK 500 5 A A 17 N9 A A 17 C4 0.038 REMARK 500 5 U A 19 N1 U A 19 C2 0.056 REMARK 500 5 U A 24 N1 U A 24 C2 0.064 REMARK 500 6 C A 12 N1 C A 12 C2 0.062 REMARK 500 6 A A 14 N9 A A 14 C4 0.038 REMARK 500 6 A A 17 N9 A A 17 C4 0.046 REMARK 500 6 U A 19 N1 U A 19 C2 0.058 REMARK 500 6 U A 20 N1 U A 20 C2 0.062 REMARK 500 6 U A 21 N1 U A 21 C2 0.055 REMARK 500 6 U A 24 N1 U A 24 C2 0.061 REMARK 500 7 A A 6 N9 A A 6 C4 0.044 REMARK 500 7 A A 14 N9 A A 14 C4 0.038 REMARK 500 7 A A 17 N9 A A 17 C4 0.042 REMARK 500 7 U A 20 N1 U A 20 C2 0.057 REMARK 500 7 U A 21 N1 U A 21 C2 0.055 REMARK 500 7 U A 24 N1 U A 24 C2 0.057 REMARK 500 8 A A 6 N9 A A 6 C4 0.044 REMARK 500 8 U A 8 N1 U A 8 C2 0.054 REMARK 500 8 A A 14 N9 A A 14 C4 0.040 REMARK 500 8 A A 17 N9 A A 17 C4 0.042 REMARK 500 8 U A 19 N1 U A 19 C2 0.061 REMARK 500 8 U A 20 N1 U A 20 C2 0.056 REMARK 500 REMARK 500 THIS ENTRY HAS 56 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 4 N3 - C2 - N2 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 G A 5 N3 - C2 - N2 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 A A 6 N1 - C6 - N6 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 C A 7 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 C A 7 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 G A 9 N3 - C2 - N2 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 G A 10 C2 - N3 - C4 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 G A 10 N3 - C2 - N2 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 G A 11 N3 - C2 - N2 ANGL. DEV. = 6.6 DEGREES REMARK 500 1 C A 12 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 C A 12 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 G A 13 N3 - C2 - N2 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 A A 14 N1 - C6 - N6 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 15 N3 - C2 - N2 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 A A 16 N1 - C6 - N6 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 17 N1 - C6 - N6 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 18 N3 - C2 - N2 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 G A 18 N1 - C6 - O6 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 U A 21 C3' - O3' - P ANGL. DEV. = 12.9 DEGREES REMARK 500 1 A A 22 N1 - C6 - N6 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 G A 23 N3 - C2 - N2 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 C A 25 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 C A 26 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 G A 4 N3 - C2 - N2 ANGL. DEV. = 5.6 DEGREES REMARK 500 2 G A 5 N3 - C2 - N2 ANGL. DEV. = 6.1 DEGREES REMARK 500 2 A A 6 N1 - C6 - N6 ANGL. DEV. = 6.2 DEGREES REMARK 500 2 C A 7 C6 - N1 - C2 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 C A 7 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 9 N3 - C2 - N2 ANGL. DEV. = 6.5 DEGREES REMARK 500 2 G A 9 C5 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 G A 10 N3 - C2 - N2 ANGL. DEV. = 6.7 DEGREES REMARK 500 2 G A 10 C5 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 G A 11 P - O5' - C5' ANGL. DEV. = 10.0 DEGREES REMARK 500 2 G A 11 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 G A 11 N3 - C2 - N2 ANGL. DEV. = 6.2 DEGREES REMARK 500 2 G A 11 C3' - O3' - P ANGL. DEV. = 16.8 DEGREES REMARK 500 2 C A 12 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 C A 12 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 C A 12 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 G A 13 N3 - C2 - N2 ANGL. DEV. = 6.9 DEGREES REMARK 500 2 A A 14 N1 - C6 - N6 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 G A 15 N3 - C2 - N2 ANGL. DEV. = 5.6 DEGREES REMARK 500 2 A A 16 N1 - C6 - N6 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 A A 17 N1 - C6 - N6 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 18 N3 - C2 - N2 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 G A 18 N1 - C6 - O6 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 G A 18 C5 - C6 - O6 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 A A 22 N1 - C6 - N6 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 G A 23 N3 - C2 - N2 ANGL. DEV. = 7.0 DEGREES REMARK 500 2 C A 25 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 213 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1NEM A 4 26 PDB 1NEM 1NEM 4 26 SEQRES 1 A 23 G G A C U G G G C G A G A SEQRES 2 A 23 A G U U U A G U C C HET BDR B 1 17 HET IDG B 2 26 HET BDG A 27 26 HET NEB A 28 24 HETNAM BDR BETA-D-RIBOFURANOSE HETNAM IDG 2,6-DIAMINO-2,6-DIDEOXY-BETA-L-IDOPYRANOSE HETNAM BDG 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSE HETNAM NEB 2-DEOXY-D-STREPTAMINE FORMUL 2 BDR C5 H10 O5 FORMUL 2 IDG C6 H14 N2 O4 FORMUL 3 BDG C6 H14 N2 O4 FORMUL 4 NEB C6 H15 N2 O3 1+ LINK C1 BDG A 27 O4 NEB A 28 1555 1555 1.40 LINK O5 NEB A 28 C1 BDR B 1 1555 1555 1.43 LINK O3 BDR B 1 C1 IDG B 2 1555 1555 1.40 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