HEADER RNA 23-OCT-98 435D TITLE 5'-R(*UP*AP*GP*CP*CP*CP*C)-3', 5'-R(*GP*GP*GP*GP*CP*UP*A)-3' COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*UP*AP*GP*CP*CP*CP*C)-3'); COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (5'-R(*GP*GP*GP*GP*CP*UP*A)-3'); COMPND 7 CHAIN: B, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS 7 BASE-PAIR TRNA ALA ACCEPTOR STEM C70 MUTANT, DOUBLE HELIX EXPDTA X-RAY DIFFRACTION AUTHOR U.MUELLER,H.SCHUEBEL,M.SPRINZL,U.HEINEMANN REVDAT 3 24-FEB-09 435D 1 VERSN REVDAT 2 01-APR-03 435D 1 JRNL REVDAT 1 14-JUN-99 435D 0 JRNL AUTH U.MUELLER,H.SCHUBEL,M.SPRINZL,U.HEINEMANN JRNL TITL CRYSTAL STRUCTURE OF ACCEPTOR STEM OF TRNA(ALA) JRNL TITL 2 FROM ESCHERICHIA COLI SHOWS UNIQUE G.U WOBBLE BASE JRNL TITL 3 PAIR AT 1.16 A RESOLUTION. JRNL REF RNA V. 5 670 1999 JRNL REFN ISSN 1355-8382 JRNL PMID 10334337 JRNL DOI 10.1017/S1355838299982304 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.7 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : THIN SHELL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.160 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.158 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 627 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 13695 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.138 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.136 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 497 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 10683 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 586 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 133 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 721.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 6493 REMARK 3 NUMBER OF RESTRAINTS : 20551 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.028 REMARK 3 ANGLE DISTANCES (A) : 0.010 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.034 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.021 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.009 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.004 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.025 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.018 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.043 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER,J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : PARKINSON, G. ET AL. REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 435D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-97 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13834 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.7 REMARK 200 DATA REDUNDANCY : 1.600 REMARK 200 R MERGE (I) : 0.05700 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) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28800 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: AMORE REMARK 200 STARTING MODEL: CANONICAL A-FORM RNA DUPLEX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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: 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 U A 1 C3' U A 1 C2' -0.087 REMARK 500 A A 2 C3' A A 2 C2' -0.073 REMARK 500 G A 3 C3' G A 3 C2' -0.071 REMARK 500 C A 4 C3' C A 4 C2' -0.073 REMARK 500 C A 7 C3' C A 7 C2' -0.068 REMARK 500 G B 9 C3' G B 9 C2' -0.077 REMARK 500 G B 11 C3' G B 11 C2' -0.067 REMARK 500 C B 12 C3' C B 12 C2' -0.077 REMARK 500 U B 13 C3' U B 13 C2' -0.081 REMARK 500 U C 1 C3' U C 1 C2' -0.082 REMARK 500 A C 2 C3' A C 2 C2' -0.068 REMARK 500 C C 4 C3' C C 4 C2' -0.069 REMARK 500 C C 5 C3' C C 5 C2' -0.081 REMARK 500 G D 8 C3' G D 8 C2' -0.090 REMARK 500 G D 9 C3' G D 9 C2' -0.071 REMARK 500 G D 10 C3' G D 10 C2' -0.070 REMARK 500 G D 11 C3' G D 11 C2' -0.072 REMARK 500 C D 12 C3' C D 12 C2' -0.084 REMARK 500 U D 13 C3' U D 13 C2' -0.071 REMARK 500 A D 14 C3' A D 14 C2' -0.074 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 U A 1 C1' - O4' - C4' ANGL. DEV. = -4.7 DEGREES REMARK 500 A A 2 O5' - C5' - C4' ANGL. DEV. = -9.1 DEGREES REMARK 500 G A 3 C1' - O4' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 C A 4 O5' - C5' - C4' ANGL. DEV. = -5.7 DEGREES REMARK 500 C A 7 C1' - O4' - C4' ANGL. DEV. = -4.8 DEGREES REMARK 500 G B 8 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 G B 8 C3' - O3' - P ANGL. DEV. = 10.3 DEGREES REMARK 500 G B 10 C1' - O4' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 G B 10 C3' - C2' - C1' ANGL. DEV. = -4.4 DEGREES REMARK 500 G B 11 P - O5' - C5' ANGL. DEV. = 13.9 DEGREES REMARK 500 U B 13 O5' - C5' - C4' ANGL. DEV. = -4.8 DEGREES REMARK 500 A C 2 P - O5' - C5' ANGL. DEV. = -10.6 DEGREES REMARK 500 G C 3 O5' - C5' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 G C 3 C1' - O4' - C4' ANGL. DEV. = -4.4 DEGREES REMARK 500 G C 3 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 C C 6 C1' - O4' - C4' ANGL. DEV. = -4.5 DEGREES REMARK 500 G D 8 O5' - C5' - C4' ANGL. DEV. = -6.6 DEGREES REMARK 500 G D 9 O5' - C5' - C4' ANGL. DEV. = -5.9 DEGREES REMARK 500 G D 9 C1' - O4' - C4' ANGL. DEV. = -4.5 DEGREES REMARK 500 G D 9 C3' - C2' - C1' ANGL. DEV. = -4.7 DEGREES REMARK 500 G D 9 C5 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 G D 10 C1' - O4' - C4' ANGL. DEV. = -4.5 DEGREES REMARK 500 G D 10 C3' - C2' - C1' ANGL. DEV. = -4.3 DEGREES REMARK 500 G D 11 C1' - O4' - C4' ANGL. DEV. = -4.7 DEGREES REMARK 500 C D 12 C1' - O4' - C4' ANGL. DEV. = -4.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH C1063 DISTANCE = 5.17 ANGSTROMS REMARK 525 HOH A1075 DISTANCE = 9.51 ANGSTROMS REMARK 525 HOH A1096 DISTANCE = 5.16 ANGSTROMS REMARK 525 HOH C1100 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH A1103 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A1136 DISTANCE = 7.45 ANGSTROMS 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 8 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1113 O REMARK 620 2 HOH A1137 O 64.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA D 1 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH D1115 O REMARK 620 2 HOH D1053 O 79.1 REMARK 620 3 HOH D1048 O 95.3 79.5 REMARK 620 4 HOH C1076 O 145.3 73.5 100.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA D 1 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 8 DBREF 435D A 1 7 PDB 435D 435D 1 7 DBREF 435D B 8 14 PDB 435D 435D 8 14 DBREF 435D C 1 7 PDB 435D 435D 1 7 DBREF 435D D 8 14 PDB 435D 435D 8 14 SEQRES 1 A 7 U A G C C C C SEQRES 1 B 7 G G G G C U A SEQRES 1 C 7 U A G C C C C SEQRES 1 D 7 G G G G C U A HET NA D 1 1 HET NA A 8 1 HETNAM NA SODIUM ION FORMUL 5 NA 2(NA 1+) FORMUL 7 HOH *133(H2 O) LINK NA NA A 8 O HOH A1113 1555 1555 2.22 LINK NA NA A 8 O HOH A1137 1555 1555 2.11 LINK NA NA D 1 O HOH D1115 1555 1555 2.41 LINK NA NA D 1 O HOH D1053 1555 1555 2.10 LINK NA NA D 1 O HOH D1048 1555 1555 2.24 LINK NA NA D 1 O HOH C1076 1555 1555 2.41 SITE 1 AC1 4 HOH C1076 HOH D1048 HOH D1053 HOH D1115 SITE 1 AC2 2 HOH A1113 HOH A1137 CRYST1 26.680 26.697 30.459 104.29 104.22 91.66 P 1 2 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 0.037481 0.001086 0.010137 0.00000 SCALE2 0.000000 0.037473 0.010177 0.00000 SCALE3 0.000000 0.000000 0.035096 0.00000 MASTER 297 0 2 0 0 0 2 6 0 0 0 4 END