PDB Short entry for 464D HEADER RNA 14-APR-99 464D TITLE DISORDER AND TWIN REFINEMENT OF RNA HEPTAMER DOUBLE HELIX 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*(IU)P*A)-3'); COMPND 7 CHAIN: B, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SEQUENCE FROM TRNA(ALA) OF ESCHERICHIA COLI; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: SEQUENCE FROM TRNA(ALA) OF ESCHERICHIA COLI KEYWDS 7 BASE-PAIR TRNA ALA ACCEPTOR STEM, DOUBLE HELIX, RIBONUCLEIC ACID, KEYWDS 2 DISORDERED MODEL, RNA EXPDTA X-RAY DIFFRACTION AUTHOR U.MUELLER,Y.A.MULLER,R.HERBST-IRMER,M.SPRINZL,U.HEINEMANN REVDAT 5 28-FEB-24 464D 1 REMARK LINK REVDAT 4 24-FEB-09 464D 1 VERSN REVDAT 3 28-JUN-02 464D 1 REMARK REVDAT 2 27-NOV-00 464D 5 REVDAT 1 16-AUG-99 464D 0 JRNL AUTH U.MUELLER,Y.A.MULLER,R.HERBST-IRMER,M.SPRINZL,U.HEINEMANN JRNL TITL DISORDER AND TWIN REFINEMENT OF RNA HEPTAMER DOUBLE HELICES. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 55 1405 1999 JRNL REFN ISSN 0907-4449 JRNL PMID 10417408 JRNL DOI 10.1107/S0907444999007441 REMARK 2 REMARK 2 RESOLUTION. 1.23 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) : 1.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : THIN RESOLUTION SHELLS REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.129 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.129 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 955 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 18337 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.127 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.125 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 927 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 17400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 588 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 155 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 6709 REMARK 3 NUMBER OF RESTRAINTS : 21012 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.029 REMARK 3 ANGLE DISTANCES (A) : 0.018 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.019 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) : 0.012 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.006 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.012 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.041 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.092 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 ET AL. REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 464D 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_1000179243. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-SEP-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9049 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 : 64180 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.230 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 (%) : 82.8 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 32.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.30800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 MM RNA DUPLEX, 12 MM SPERMINE, 40 REMARK 280 MM NA-CACODYLATE PH 6.0, 80 MM SRCL2,40 MM LICL, 10 % (V/V) MPD REMARK 280 AGAINST 0.5 ML 35 % (V/V) MPD, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 C2' U A 1 C1' -0.051 REMARK 500 G A 3 C2' G A 3 C1' -0.074 REMARK 500 C A 6 C2' C A 6 C1' -0.055 REMARK 500 C B 12 C2' C B 12 C1' -0.058 REMARK 500 A C 2 C5' A C 2 C4' -0.057 REMARK 500 C C 4 C2' C C 4 C1' -0.058 REMARK 500 C C 7 C2' C C 7 C1' -0.049 REMARK 500 G D 8 C2' G D 8 C1' -0.066 REMARK 500 G D 10 C5' G D 10 C4' -0.066 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 3 C6 - C5 - N7 ANGL. DEV. = -3.7 DEGREES REMARK 500 G A 3 N1 - C6 - O6 ANGL. DEV. = 5.6 DEGREES REMARK 500 G A 3 C5 - C6 - O6 ANGL. DEV. = -4.1 DEGREES REMARK 500 U C 1 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 C C 4 C4 - C5 - C6 ANGL. DEV. = 3.0 DEGREES REMARK 500 G D 9 C5 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 G D 10 C4' - C3' - C2' ANGL. DEV. = -6.9 DEGREES REMARK 500 G D 11 N1 - C6 - O6 ANGL. DEV. = 5.5 DEGREES REMARK 500 G D 11 C5 - C6 - O6 ANGL. DEV. = -5.2 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 101 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 7 O3' REMARK 620 2 C A 7 O2' 59.0 REMARK 620 3 A B 14 O3' 54.5 22.8 REMARK 620 4 A B 14 O2' 51.7 19.6 4.7 REMARK 620 5 HOH B1115 O 53.8 23.6 1.0 4.9 REMARK 620 6 HOH B1116 O 49.2 18.0 8.3 3.7 8.4 REMARK 620 7 HOH B1118 O 47.9 23.8 6.5 5.0 5.9 5.9 REMARK 620 8 HOH C1117 O 55.2 18.4 4.4 3.5 5.3 6.3 8.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 102 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B1014 O REMARK 620 2 HOH B1045 O 73.7 REMARK 620 3 HOH B1131 O 77.6 67.8 REMARK 620 N 1 2 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 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 102 DBREF 464D A 1 7 PDB 464D 464D 1 7 DBREF 464D B 8 14 PDB 464D 464D 8 14 DBREF 464D C 1 7 PDB 464D 464D 1 7 DBREF 464D D 8 14 PDB 464D 464D 8 14 SEQRES 1 A 7 U A G C U C C SEQRES 1 B 7 G G G G C IU A SEQRES 1 C 7 U A G C U C C SEQRES 1 D 7 G G G G C IU A MODRES 464D IU B 13 U 5-IODOURIDINE-5'-MONOPHOSPHATE MODRES 464D IU D 13 U 5-IODOURIDINE-5'-MONOPHOSPHATE HET IU B 13 21 HET IU D 13 21 HET SR B 101 1 HET NA B 102 1 HETNAM IU 5-IODOURIDINE-5'-MONOPHOSPHATE HETNAM SR STRONTIUM ION HETNAM NA SODIUM ION FORMUL 2 IU 2(C9 H12 I N2 O9 P) FORMUL 5 SR SR 2+ FORMUL 6 NA NA 1+ FORMUL 7 HOH *155(H2 O) LINK O3' C B 12 P IU B 13 1555 1555 1.58 LINK O3' IU B 13 P A B 14 1555 1555 1.59 LINK O3' C D 12 P IU D 13 1555 1555 1.59 LINK O3' IU D 13 P A D 14 1555 1555 1.60 LINK O3' C A 7 SR SR B 101 1555 1544 2.57 LINK O2' C A 7 SR SR B 101 1555 1544 2.78 LINK O3' A B 14 SR SR B 101 1555 1555 2.72 LINK O2' A B 14 SR SR B 101 1555 1555 2.63 LINK SR SR B 101 O HOH B1115 1555 1555 2.65 LINK SR SR B 101 O HOH B1116 1555 1555 2.67 LINK SR SR B 101 O HOH B1118 1555 1555 2.48 LINK SR SR B 101 O HOH C1117 1555 1555 2.66 LINK NA NA B 102 O HOH B1014 1555 1555 2.65 LINK NA NA B 102 O HOH B1045 1555 1555 2.51 LINK NA NA B 102 O HOH B1131 1555 1555 2.33 SITE 1 AC1 6 C A 7 A B 14 HOH B1115 HOH B1116 SITE 2 AC1 6 HOH B1118 HOH C1117 SITE 1 AC2 3 HOH B1014 HOH B1045 HOH B1131 CRYST1 26.375 28.995 28.995 110.37 96.62 96.62 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 0.037915 0.004402 0.006464 0.00000 SCALE2 0.000000 0.034720 0.013665 0.00000 SCALE3 0.000000 0.000000 0.037313 0.00000