HEADER RNA 13-JUN-05 1ZZ5 TITLE MOLECULAR RECOGNITION OF RNA BY NEOMYCIN AND A RESTRICTED NEOMYCIN TITLE 2 DERIVATIVE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3'; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: RIBOSOMAL RNA A-SITE; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*C)-3'; COMPND 8 CHAIN: B, D; COMPND 9 FRAGMENT: RIBOSOMAL RNA A-SITE; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN ESCHERICHIA COLI SOURCE 4 (BACTERIA) EXCEPT ONE RESIDUE WAS REMOVED NEAR 3' TERMINAL; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN ESCHERICHIA COLI SOURCE 8 (BACTERIA) EXCEPT ONE RESIDUE WAS REMOVED NEAR 3' TERMINAL KEYWDS RIBOSOME, RNA, A-SITE. DOUBLE HELIX, RESTRICTED NEOMYCIN, CYCLICNEO, KEYWDS 2 NEOCYCLIC EXPDTA X-RAY DIFFRACTION AUTHOR Q.ZHAO,F.ZHAO,K.F.BLOUNT,Q.HAN,Y.TOR,T.HERMANN REVDAT 3 14-FEB-24 1ZZ5 1 REMARK LINK REVDAT 2 24-FEB-09 1ZZ5 1 VERSN REVDAT 1 20-SEP-05 1ZZ5 0 JRNL AUTH F.ZHAO,Q.ZHAO,K.F.BLOUNT,Q.HAN,Y.TOR,T.HERMANN JRNL TITL MOLECULAR RECOGNITION OF RNA BY NEOMYCIN AND A RESTRICTED JRNL TITL 2 NEOMYCIN DERIVATIVE JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 44 5329 2005 JRNL REFN ESSN 0570-0833 JRNL PMID 16037995 JRNL DOI 10.1002/ANIE.200500903 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 74.8 REMARK 3 NUMBER OF REFLECTIONS : 5581 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 SET) : 0.233 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 606 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.19 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 37.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3310 REMARK 3 BIN FREE R VALUE : 0.3620 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 64 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.045 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 1228 REMARK 3 HETEROGEN ATOMS : 166 REMARK 3 SOLVENT ATOMS : 25 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.44 REMARK 3 ESD FROM SIGMAA (A) : 0.46 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.48 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.44 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.121 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZZ5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000033291. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 103 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9195, 0.9202, 0.9068 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6704 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.2 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : 0.04600 REMARK 200 FOR THE DATA SET : 26.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.16200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, MAGNESIUM ACETATE, CACODYLATE, PH REMARK 280 5.6, EVAPORATION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 25.37000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.36000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.37500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.36000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.37000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.37500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE CHAINS A AND B, C AND D FORM TWO DOUBLE-HELIX RNA REMARK 300 BIOLOGICAL UNIT. THE TWO UNITS ARE RELATED BY NON-CRYSTALLOGRAPHIC REMARK 300 SYMMETRY IN THE ASYMMETRIC UNIT. 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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: 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 G B 24 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL 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 MG A 100 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 105 O REMARK 620 2 HOH A 106 O 85.8 REMARK 620 3 HOH A 107 O 89.2 82.7 REMARK 620 4 HOH A 108 O 176.8 91.2 89.3 REMARK 620 5 HOH A 109 O 89.6 171.5 90.2 93.3 REMARK 620 6 HOH A 110 O 94.0 98.0 176.8 87.5 89.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 200 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 47 O REMARK 620 2 HOH D 201 O 85.7 REMARK 620 3 HOH D 202 O 89.2 82.6 REMARK 620 4 HOH D 203 O 176.7 91.2 89.4 REMARK 620 5 HOH D 204 O 89.6 171.4 90.1 93.3 REMARK 620 6 HOH D 205 O 94.0 98.0 176.8 87.5 89.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CNY C 41 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CNY A 42 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CNY A 43 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CNY C 44 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZX7 RELATED DB: PDB DBREF 1ZZ5 A 2 16 PDB 1ZZ5 1ZZ5 2 16 DBREF 1ZZ5 B 21 34 PDB 1ZZ5 1ZZ5 21 34 DBREF 1ZZ5 C 2 16 PDB 1ZZ5 1ZZ5 2 16 DBREF 1ZZ5 D 21 34 PDB 1ZZ5 1ZZ5 21 34 SEQRES 1 A 15 G U G G U G A A G U C G C SEQRES 2 A 15 G G SEQRES 1 B 14 C G C G U C A C A C C A C SEQRES 2 B 14 C SEQRES 1 C 15 G U G G U G A A G U C G C SEQRES 2 C 15 G G SEQRES 1 D 14 C G C G U C A C A C C A C SEQRES 2 D 14 C HET MG A 100 1 HET CNY A 42 41 HET CNY A 43 41 HET CNY C 41 41 HET CNY C 44 41 HET MG D 200 1 HETNAM MG MAGNESIUM ION HETNAM CNY 13,15-DIAMINO-2-(AMINOMETHYL)-3,4,9,12- HETNAM 2 CNY TETRAHYDROXYHEXADECAHYDRO-2H-7,10-EPOXYPYRANO[2,3- HETNAM 3 CNY B][1,10,4]BENZODIOXAZACYCLODODECIN-8-YL 2,6-DIAMINO-2, HETNAM 4 CNY 6-DIDEOXYHEXOPYRANOSIDE HETSYN CNY CYCLIC NEOMYCIN FORMUL 5 MG 2(MG 2+) FORMUL 6 CNY 4(C23 H44 N6 O12) FORMUL 11 HOH *25(H2 O) LINK MG MG A 100 O HOH A 105 1555 1555 2.24 LINK MG MG A 100 O HOH A 106 1555 1555 2.12 LINK MG MG A 100 O HOH A 107 1555 1555 2.00 LINK MG MG A 100 O HOH A 108 1555 1555 2.00 LINK MG MG A 100 O HOH A 109 1555 1555 2.02 LINK MG MG A 100 O HOH A 110 1555 1555 2.17 LINK O HOH C 47 MG MG D 200 1555 1555 2.24 LINK MG MG D 200 O HOH D 201 1555 1555 2.12 LINK MG MG D 200 O HOH D 202 1555 1555 2.00 LINK MG MG D 200 O HOH D 203 1555 1555 2.00 LINK MG MG D 200 O HOH D 204 1555 1555 2.01 LINK MG MG D 200 O HOH D 205 1555 1555 2.17 SITE 1 AC1 6 HOH A 105 HOH A 106 HOH A 107 HOH A 108 SITE 2 AC1 6 HOH A 109 HOH A 110 SITE 1 AC2 6 HOH C 47 HOH D 201 HOH D 202 HOH D 203 SITE 2 AC2 6 HOH D 204 HOH D 205 SITE 1 AC3 9 U C 6 G C 7 A C 8 A C 9 SITE 2 AC3 9 G C 10 U C 11 HOH C 45 U D 25 SITE 3 AC3 9 A D 27 SITE 1 AC4 10 G A 7 A A 8 A A 9 G A 10 SITE 2 AC4 10 U A 11 HOH A 101 G B 24 U B 25 SITE 3 AC4 10 C B 26 A B 27 SITE 1 AC5 10 U A 11 C A 12 C A 14 G A 15 SITE 2 AC5 10 G A 16 A B 32 C B 33 C B 34 SITE 3 AC5 10 G C 2 C D 34 SITE 1 AC6 9 G A 2 C B 34 U C 11 C C 12 SITE 2 AC6 9 C C 14 G C 15 G C 16 C D 33 SITE 3 AC6 9 C D 34 CRYST1 50.740 50.750 144.720 90.00 90.00 90.00 P 21 21 21 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 0.019708 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019704 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006910 0.00000