HEADER RNA 29-JAN-03 1NTB TITLE 2.9 A CRYSTAL STRUCTURE OF STREPTOMYCIN RNA-APTAMER COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*AP*UP*CP*GP*CP*AP*UP*UP*UP*GP*GP*AP*CP*UP*UP*CP COMPND 3 *UP*GP*CP*C)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-R(*CP*GP*GP*CP*AP*CP*CP*AP*CP*GP*GP*UP*CP*GP*GP*AP*UP*C) COMPND 8 -3'; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS STREPTOMYCIN RNA-APTAMER, MAGNESIUM FORM, RNA EXPDTA X-RAY DIFFRACTION AUTHOR V.TERESHKO,E.SKRIPKIN,D.J.PATEL REVDAT 4 03-APR-24 1NTB 1 REMARK REVDAT 3 14-FEB-24 1NTB 1 REMARK LINK REVDAT 2 24-FEB-09 1NTB 1 VERSN REVDAT 1 13-MAY-03 1NTB 0 JRNL AUTH V.TERESHKO,E.SKRIPKIN,D.J.PATEL JRNL TITL ENCAPSULATING STREPTOMYCIN WITHIN A SMALL 40-MER RNA JRNL REF CHEM.BIOL. V. 10 175 2003 JRNL REFN ISSN 1074-5521 JRNL PMID 12618190 JRNL DOI 10.1016/S1074-5521(03)00024-3 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.13 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 3394 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.300 REMARK 3 FREE R VALUE TEST SET COUNT : 349 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 234 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE SET COUNT : 22 REMARK 3 BIN FREE R VALUE : 0.3590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 842 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.51000 REMARK 3 B22 (A**2) : 0.51000 REMARK 3 B33 (A**2) : -1.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.396 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.299 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.131 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 988 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 327 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1525 ; 1.746 ; 2.121 REMARK 3 BOND ANGLES OTHERS (DEGREES): 854 ; 1.710 ; 2.049 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 175 ; 0.412 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 418 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 4 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 177 ; 0.179 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 407 ; 0.227 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 198 ; 0.110 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 30 ; 0.178 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 18 ; 0.123 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 10 ; 0.225 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 1 ; 0.149 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 988 ; 0.853 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1525 ; 1.372 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 22 REMARK 3 ORIGIN FOR THE GROUP (A): 13.0915 30.3084 0.7858 REMARK 3 T TENSOR REMARK 3 T11: 0.2346 T22: 0.2111 REMARK 3 T33: 0.3656 T12: 0.2198 REMARK 3 T13: 0.0239 T23: 0.0065 REMARK 3 L TENSOR REMARK 3 L11: 4.4955 L22: 5.6035 REMARK 3 L33: 9.3740 L12: 0.2268 REMARK 3 L13: -0.5570 L23: -3.8731 REMARK 3 S TENSOR REMARK 3 S11: -0.4998 S12: 0.3799 S13: -0.2448 REMARK 3 S21: 0.1511 S22: 0.5065 S23: -0.3314 REMARK 3 S31: 0.0325 S32: -0.0659 S33: -0.0066 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1NTB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018183. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3942 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: BARIUM FORM OF STREPTOMYCIN RNA-APTAMER REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES BUFFER, MAGNESIUM CLORIDE, SODIUM REMARK 280 CLORIDE, MPD, PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 41.31700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.31700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 24.57650 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.31700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.31700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 24.57650 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 41.31700 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 41.31700 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 24.57650 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 41.31700 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 41.31700 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 24.57650 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC 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 A A 8 O5' A A 8 C5' -0.070 REMARK 500 U A 11 C1' U A 11 N1 0.107 REMARK 500 U A 11 C4 U A 11 O4 0.075 REMARK 500 C B 106 O5' C B 106 C5' 0.185 REMARK 500 U B 112 P U B 112 OP2 0.217 REMARK 500 U B 117 P U B 117 OP2 0.215 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 G A 6 C3' - O3' - P ANGL. DEV. = 9.5 DEGREES REMARK 500 A A 8 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 C B 106 O5' - C5' - C4' ANGL. DEV. = -19.7 DEGREES REMARK 500 C B 106 P - O5' - C5' ANGL. DEV. = -10.9 DEGREES REMARK 500 C B 107 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 U B 112 C1' - O4' - C4' ANGL. DEV. = -7.7 DEGREES REMARK 500 U B 112 C3' - C2' - C1' ANGL. DEV. = -4.3 DEGREES REMARK 500 U B 112 O4' - C1' - C2' ANGL. DEV. = 8.2 DEGREES REMARK 500 U B 112 N1 - C1' - C2' ANGL. DEV. = 14.1 DEGREES REMARK 500 U B 112 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 U B 112 N1 - C2 - N3 ANGL. DEV. = 6.3 DEGREES REMARK 500 U B 112 C2 - N3 - C4 ANGL. DEV. = -5.8 DEGREES REMARK 500 U B 112 N3 - C4 - C5 ANGL. DEV. = 3.6 DEGREES REMARK 500 U B 112 C5 - C4 - O4 ANGL. DEV. = -7.3 DEGREES REMARK 500 U B 112 C6 - N1 - C1' ANGL. DEV. = -9.0 DEGREES REMARK 500 U B 112 C2 - N1 - C1' ANGL. DEV. = 9.7 DEGREES REMARK 500 U B 117 C4' - C3' - C2' ANGL. DEV. = 10.2 DEGREES REMARK 500 U B 117 O4' - C1' - C2' ANGL. DEV. = 9.5 DEGREES REMARK 500 U B 117 O4' - C1' - N1 ANGL. DEV. = 7.1 DEGREES REMARK 500 U B 117 N1 - C2 - N3 ANGL. DEV. = 5.4 DEGREES REMARK 500 U B 117 C2 - N3 - C4 ANGL. DEV. = -5.0 DEGREES REMARK 500 U B 117 C5 - C4 - O4 ANGL. DEV. = -4.2 DEGREES REMARK 500 U B 117 C6 - N1 - C1' ANGL. DEV. = -9.9 DEGREES REMARK 500 U B 117 C2 - N1 - C1' ANGL. DEV. = 9.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 SRY A 25 REMARK 615 HOH B 11 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 23 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 7 OP2 REMARK 620 2 A A 8 O2' 113.1 REMARK 620 3 U A 10 OP2 125.8 98.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 1 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 10 O2 REMARK 620 2 U A 11 O4 97.6 REMARK 620 3 HOH A 26 O 85.6 164.3 REMARK 620 4 HOH B 7 O 99.4 100.3 64.0 REMARK 620 5 C B 109 O5' 161.3 92.2 89.3 94.4 REMARK 620 6 C B 109 O4' 89.4 76.3 119.2 170.9 77.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 24 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 15 OP2 REMARK 620 2 U A 16 O4 71.6 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 23 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 24 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NTA RELATED DB: PDB REMARK 900 2.9 A CRYSTAL STRUCTURE OF STREPTOMYCIN RNA-APTAMER (BARIUM FORM) DBREF 1NTB A 1 22 PDB 1NTB 1NTB 1 22 DBREF 1NTB B 101 118 PDB 1NTB 1NTB 101 118 SEQRES 1 A 22 G G A U C G C A U U U G G SEQRES 2 A 22 A C U U C U G C C SEQRES 1 B 18 C G G C A C C A C G G U C SEQRES 2 B 18 G G A U C HET NA A 23 1 HET NA A 24 1 HET SRY A 25 40 HET MG B 1 1 HETNAM NA SODIUM ION HETNAM SRY STREPTOMYCIN HETNAM MG MAGNESIUM ION HETSYN SRY STREPTOMYCIN A FORMUL 3 NA 2(NA 1+) FORMUL 5 SRY C21 H39 N7 O12 FORMUL 6 MG MG 2+ FORMUL 7 HOH *6(H2 O) LINK OP2 C A 7 NA NA A 23 1555 1555 2.48 LINK O2' A A 8 NA NA A 23 1555 1555 2.50 LINK OP2 U A 10 NA NA A 23 1555 1555 2.48 LINK O2 U A 10 MG MG B 1 1555 1555 2.20 LINK O4 U A 11 MG MG B 1 1555 1555 2.25 LINK OP2 C A 15 NA NA A 24 1555 1555 2.25 LINK O4 U A 16 NA NA A 24 1555 1555 2.20 LINK O HOH A 26 MG MG B 1 1555 1555 2.09 LINK MG MG B 1 O HOH B 7 1555 1555 2.50 LINK MG MG B 1 O5' C B 109 1555 1555 2.20 LINK MG MG B 1 O4' C B 109 1555 1555 2.19 SITE 1 AC1 5 U A 10 U A 11 HOH A 26 HOH B 7 SITE 2 AC1 5 C B 109 SITE 1 AC2 3 C A 7 A A 8 U A 10 SITE 1 AC3 2 C A 15 U A 16 CRYST1 82.634 82.634 49.153 90.00 90.00 90.00 I 4 8 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 0.012102 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012102 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020345 0.00000