10 20 30 40 50 60 70 80 2A04 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 15-JUN-05 2A04
TITLE MOLECULAR RECOGNITION OF RNA BY NEOMYCIN AND A RESTRICTED TITLE 2 NEOMYCIN DERIVATIVE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3'; COMPND 4 CHAIN: A, C; COMPND 5 FRAGMENT: RIBOSOMAL RNA A-SITE; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*C)- COMPND 9 3'; COMPND 10 CHAIN: B, D; COMPND 11 FRAGMENT: RIBOSOMAL RNA A-SITE; COMPND 12 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN SOURCE 4 ESCHERICHIA COLI (BACTERIA) EXCEPT ONE RESIDUE WAS REMOVED SOURCE 5 NEAR 3' TERMINAL; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN SOURCE 9 ESCHERICHIA COLI (BACTERIA) EXCEPT ONE RESIDUE WAS REMOVED SOURCE 10 NEAR 5' TERMINAL
KEYWDS RIBOSOME, RNA, A-SITE. DOUBLE HELIX, NEOMYCIN
EXPDTA X-RAY DIFFRACTION
AUTHOR Q.ZHAO,F.ZHAO,K.F.BLOUNT,Q.HAN,Y.TOR,T.HERMANN
REVDAT 2 24-FEB-09 2A04 1 VERSN REVDAT 1 20-SEP-05 2A04 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 JRNL TITL 2 RESTRICTED NEOMYCIN DERIVATIVE JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 44 5329 2005 JRNL REFN ISSN 1433-7851 JRNL PMID 16037995 JRNL DOI 10.1002/ANIE.200500903
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.95 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 2.95 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) (%) : 88.2 REMARK 3 NUMBER OF REFLECTIONS : 6650 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) : 0.254 REMARK 3 FREE R VALUE : 0.318 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 723 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) : 2.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3950 REMARK 3 BIN FREE R VALUE : 0.4120 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 79 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.046 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 : 170 REMARK 3 SOLVENT ATOMS : 20 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 75.70 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) : 0.46 REMARK 3 ESD FROM SIGMAA (A) : 0.62 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) : 0.57 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.40 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 9.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.48 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 2A04 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUN-05. REMARK 100 THE RCSB ID CODE IS RCSB033325.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-02 REMARK 200 TEMPERATURE (KELVIN) : 103 REMARK 200 PH : 6.0 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE 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 : 7103 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.950 REMARK 200 RESOLUTION RANGE LOW (A) : 28.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : 0.12700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.53500 REMARK 200 R SYM FOR SHELL (I) : 0.53500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 72.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, MAGNESIUM SULFATE, POTASSIUM REMARK 280 CHLORIDE, SODIUM CHLORIDE, CACODYLATE, PH 6.0, EVAPORATION, REMARK 280 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 24.90000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.30000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.30000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.90000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.95000 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- REMARK 300 CRYSTALLOGRAPHIC 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH D 10 O HOH D 14 1.08 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 U A 3 0.06 SIDE_CHAIN REMARK 500 U D 25 0.07 SIDE_CHAIN REMARK 500 A D 29 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 C 48 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G C 2 N7 REMARK 620 2 NMY A 18 O20 60.6 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 NMY C 1 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NMY A 17 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NMY C 17 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NMY A 18 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 41 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 48
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZX7 RELATED DB: PDB REMARK 900 RELATED ID: 1ZZ5 RELATED DB: PDB
DBREF 2A04 A 2 16 PDB 2A04 2A04 2 16 DBREF 2A04 B 21 34 PDB 2A04 2A04 21 34 DBREF 2A04 C 2 16 PDB 2A04 2A04 2 16 DBREF 2A04 D 21 34 PDB 2A04 2A04 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 NMY C 1 42 HET NMY A 17 42 HET NMY C 17 42 HET NMY A 18 42 HET MG A 41 1 HET MG C 48 1
HETNAM NMY NEOMYCIN HETNAM MG MAGNESIUM ION
HETSYN NMY MYCIFRADIN; NEOMAS; PIMAVECORT; VONAMYCIN
FORMUL 5 NMY 4(C23 H46 N6 O13) FORMUL 9 MG 2(MG 2+) FORMUL 11 HOH *20(H2 O)
LINK MG MG A 41 N7 G A 2 1555 1555 2.99 LINK MG MG C 48 N7 G C 2 1555 1555 2.71 LINK MG MG C 48 O20 NMY A 18 1555 2664 2.93
SITE 1 AC1 13 U C 6 G C 7 A C 8 A C 9 SITE 2 AC1 13 G C 10 U C 11 HOH C 50 HOH C 51 SITE 3 AC1 13 G D 24 U D 25 C D 26 A D 27 SITE 4 AC1 13 C D 28 SITE 1 AC2 11 U A 6 G A 7 A A 8 A A 9 SITE 2 AC2 11 G A 10 U A 11 G B 24 U B 25 SITE 3 AC2 11 C B 26 A B 27 C B 28 SITE 1 AC3 11 G A 2 C B 33 C B 34 U C 11 SITE 2 AC3 11 C C 12 C C 14 G C 15 G C 16 SITE 3 AC3 11 A D 32 C D 33 C D 34 SITE 1 AC4 12 U A 11 C A 12 C A 14 G A 15 SITE 2 AC4 12 G A 16 A B 32 C B 33 C B 34 SITE 3 AC4 12 G C 2 MG C 48 C D 33 C D 34 SITE 1 AC5 1 G A 2 SITE 1 AC6 2 NMY A 18 G C 2
CRYST1 49.800 49.900 144.600 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 0.020080 0.000000 0.000000 0.00000
SCALE2 0.000000 0.020040 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006916 0.00000