PDB Short entry for 434D HEADER RNA 23-OCT-98 434D TITLE 5'-R(*UP*AP*GP*CP*UP*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*UP*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, DOUBLE HELIX, RNA EXPDTA X-RAY DIFFRACTION AUTHOR U.MUELLER,H.SCHUEBEL,M.SPRINZL,U.HEINEMANN REVDAT 5 03-APR-24 434D 1 REMARK REVDAT 4 28-FEB-24 434D 1 REMARK LINK REVDAT 3 24-FEB-09 434D 1 VERSN REVDAT 2 01-APR-03 434D 1 JRNL REVDAT 1 14-JUN-99 434D 0 JRNL AUTH U.MUELLER,H.SCHUBEL,M.SPRINZL,U.HEINEMANN JRNL TITL CRYSTAL STRUCTURE OF ACCEPTOR STEM OF TRNA(ALA) FROM JRNL TITL 2 ESCHERICHIA COLI SHOWS UNIQUE G.U WOBBLE BASE PAIR AT 1.16 A JRNL TITL 3 RESOLUTION. JRNL REF RNA V. 5 670 1999 JRNL REFN ISSN 1355-8382 JRNL PMID 10334337 JRNL DOI 10.1017/S1355838299982304 REMARK 2 REMARK 2 RESOLUTION. 1.16 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) : 1.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.4 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) : 0.125 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.123 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2425 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 23758 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.117 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.115 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1673 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 16414 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 : 155 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 739.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 11 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 6691 REMARK 3 NUMBER OF RESTRAINTS : 20934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.019 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.039 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.032 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.010 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.007 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.033 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.098 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL 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 434D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000179229. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-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 : X11 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 : 23758 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.160 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.4 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.54000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: CANONICAL A-FORM RNA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 A A 2 C2' A A 2 C1' -0.058 REMARK 500 G A 3 C2' G A 3 C1' -0.050 REMARK 500 C A 6 C2' C A 6 C1' -0.053 REMARK 500 G B 10 C2' G B 10 C1' -0.051 REMARK 500 C B 12 C2' C B 12 C1' -0.056 REMARK 500 U B 13 C2' U B 13 C1' -0.052 REMARK 500 C C 4 C2' C C 4 C1' -0.049 REMARK 500 C C 6 C2' C C 6 C1' -0.069 REMARK 500 G D 8 C2' G D 8 C1' -0.057 REMARK 500 G D 9 C2' G D 9 C1' -0.060 REMARK 500 C D 12 C2' C D 12 C1' -0.054 REMARK 500 U D 13 C2' U D 13 C1' -0.050 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 A A 2 N1 - C6 - N6 ANGL. DEV. = -3.6 DEGREES REMARK 500 G A 3 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 C A 7 N1 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 G B 9 O5' - C5' - C4' ANGL. DEV. = -5.5 DEGREES REMARK 500 G B 9 C1' - O4' - C4' ANGL. DEV. = -4.5 DEGREES REMARK 500 G B 10 O5' - C5' - C4' ANGL. DEV. = -5.6 DEGREES REMARK 500 G B 11 O5' - C5' - C4' ANGL. DEV. = -6.0 DEGREES REMARK 500 A C 2 O5' - C5' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 A C 2 C1' - O4' - C4' ANGL. DEV. = -4.7 DEGREES REMARK 500 A C 2 O4' - C1' - N9 ANGL. DEV. = -5.6 DEGREES REMARK 500 G C 3 O5' - C5' - C4' ANGL. DEV. = -10.1 DEGREES REMARK 500 G C 3 P - O5' - C5' ANGL. DEV. = -20.4 DEGREES REMARK 500 G C 3 N9 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 G C 3 N1 - C6 - O6 ANGL. DEV. = -4.2 DEGREES REMARK 500 G C 3 C5 - C6 - O6 ANGL. DEV. = 3.9 DEGREES REMARK 500 C C 4 C2 - N3 - C4 ANGL. DEV. = 3.7 DEGREES REMARK 500 C C 4 N3 - C4 - C5 ANGL. DEV. = -3.4 DEGREES REMARK 500 C C 6 C1' - O4' - C4' ANGL. DEV. = -4.4 DEGREES REMARK 500 G D 9 C3' - C2' - C1' ANGL. DEV. = -4.3 DEGREES REMARK 500 G D 11 C1' - O4' - C4' ANGL. DEV. = -5.3 DEGREES REMARK 500 G D 11 C5 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 A D 14 N1 - C6 - N6 ANGL. DEV. = 4.8 DEGREES 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 SR B 1 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 7 O3' REMARK 620 2 C A 7 O2' 59.7 REMARK 620 3 HOH A1015 O 72.0 77.2 REMARK 620 4 HOH A1017 O 126.4 68.7 84.0 REMARK 620 5 HOH A1022 O 95.6 67.7 144.0 76.5 REMARK 620 6 A B 14 O3' 151.9 132.0 131.6 76.7 72.8 REMARK 620 7 A B 14 O2' 130.4 140.3 72.8 82.7 132.6 61.1 REMARK 620 8 HOH B1023 O 69.3 98.8 136.7 135.4 59.5 83.0 120.8 REMARK 620 9 HOH B1034 O 73.7 133.3 87.4 153.5 122.4 90.7 70.8 64.0 REMARK 620 N 1 2 3 4 5 6 7 8 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 A1026 O REMARK 620 2 HOH A1141 O 56.9 REMARK 620 3 HOH B1001 O 149.8 152.2 REMARK 620 4 HOH B1002 O 121.9 133.7 51.6 REMARK 620 5 HOH B1006 O 118.0 118.4 51.5 102.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 8 DBREF 434D A 1 7 PDB 434D 434D 1 7 DBREF 434D B 8 14 PDB 434D 434D 8 14 DBREF 434D C 1 7 PDB 434D 434D 1 7 DBREF 434D D 8 14 PDB 434D 434D 8 14 SEQRES 1 A 7 U A G C U C C SEQRES 1 B 7 G G G G C U A SEQRES 1 C 7 U A G C U C C SEQRES 1 D 7 G G G G C U A HET NA A 8 1 HET SR B 1 1 HETNAM NA SODIUM ION HETNAM SR STRONTIUM ION FORMUL 5 NA NA 1+ FORMUL 6 SR SR 2+ FORMUL 7 HOH *155(H2 O) LINK O3' C A 7 SR SR B 1 1566 1555 2.61 LINK O2' C A 7 SR SR B 1 1566 1555 2.71 LINK NA NA A 8 O HOH A1026 1555 1555 2.94 LINK NA NA A 8 O HOH A1141 1555 1555 2.23 LINK NA NA A 8 O HOH B1001 1555 1555 2.96 LINK NA NA A 8 O HOH B1002 1555 1555 2.22 LINK NA NA A 8 O HOH B1006 1555 1555 2.55 LINK O HOH A1015 SR SR B 1 1566 1555 2.60 LINK O HOH A1017 SR SR B 1 1566 1555 2.56 LINK O HOH A1022 SR SR B 1 1566 1555 2.46 LINK SR SR B 1 O3' A B 14 1555 1555 2.53 LINK SR SR B 1 O2' A B 14 1555 1555 2.59 LINK SR SR B 1 O HOH B1023 1555 1555 2.44 LINK SR SR B 1 O HOH B1034 1555 1555 2.47 SITE 1 AC1 7 C A 7 HOH A1015 HOH A1017 HOH A1022 SITE 2 AC1 7 A B 14 HOH B1023 HOH B1034 SITE 1 AC2 5 HOH A1026 HOH A1141 HOH B1001 HOH B1002 SITE 2 AC2 5 HOH B1006 CRYST1 26.300 28.900 28.900 110.50 96.90 96.90 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 0.038023 0.004601 0.006785 0.00000 SCALE2 0.000000 0.034855 0.013880 0.00000 SCALE3 0.000000 0.000000 0.037517 0.00000