PDB Short entry for 485D HEADER DNA-RNA HYBRID 13-AUG-99 485D TITLE A SULFATE POCKET FORMED BY THREE GOU PAIRS IN THE STRUCTURE OF A TITLE 2 NONAMERIC RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA/DNA(5'-R(*CP*GP*UP*GP*AP*UP*CP*GP)-D(*C)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS RNA, DNA/RNA HYBRID, SULFATE ION, DNA-RNA HYBRID COMPLEX, DNA-RNA KEYWDS 2 HYBRID EXPDTA X-RAY DIFFRACTION AUTHOR B.MASQUIDA,C.SAUTER,E.WESTHOF REVDAT 4 27-DEC-23 485D 1 KEYWDS REMARK REVDAT 3 24-FEB-09 485D 1 VERSN REVDAT 2 01-APR-03 485D 1 JRNL REVDAT 1 18-DEC-99 485D 0 JRNL AUTH B.MASQUIDA,C.SAUTER,E.WESTHOF JRNL TITL A SULFATE POCKET FORMED BY THREE GOU PAIRS IN THE 0.97 A JRNL TITL 2 RESOLUTION X-RAY STRUCTURE OF A NONAMERIC RNA. JRNL REF RNA V. 5 1384 1999 JRNL REFN ISSN 1355-8382 JRNL PMID 10573129 JRNL DOI 10.1017/S1355838299991173 REMARK 2 REMARK 2 RESOLUTION. 0.97 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) : 0.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : THIN SHELLS REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.150 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.150 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1292 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 23838 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 342 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 84 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 : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 0.018 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 485D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-AUG-99. REMARK 100 THE DEPOSITION ID IS D_1000001324. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 110 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) : 0.9343 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23838 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.970 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.910 REMARK 200 R MERGE (I) : 0.04100 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) : 0.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.63 REMARK 200 R MERGE FOR SHELL (I) : 0.44600 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2-2.6 M AMMONIUM SULFATE, 5-50 MM REMARK 280 MAGNESIUM SULFATE, 50 MM SODIUM CACODYLATE, 1MM SPERMINE, PH 6.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 310K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.97900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 11.53488 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.48167 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 19.97900 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 11.53488 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 22.48167 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 19.97900 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 11.53488 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 22.48167 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 23.06976 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 44.96333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 23.06976 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 44.96333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 23.06976 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 44.96333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 S SO4 B 19 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 101 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 123 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 133 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 153 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 102 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 104 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 107 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 DC A 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DC A 1 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC A 1 C6 REMARK 470 DC B 10 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DC B 10 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC B 10 C6 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 DC A 1 O3' G A 2 P -0.125 REMARK 500 G A 2 C2' G A 2 C1' -0.059 REMARK 500 G A 2 O4' G A 2 C1' 0.088 REMARK 500 U A 3 C2' U A 3 C1' -0.058 REMARK 500 G A 4 C2' G A 4 C1' -0.067 REMARK 500 A A 5 C2' A A 5 C1' -0.049 REMARK 500 A A 5 N1 A A 5 C2 -0.077 REMARK 500 A A 5 N3 A A 5 C4 -0.054 REMARK 500 A A 5 C6 A A 5 N1 0.048 REMARK 500 A A 5 C5 A A 5 N7 -0.045 REMARK 500 A A 5 N7 A A 5 C8 0.044 REMARK 500 U A 6 C2' U A 6 C1' -0.068 REMARK 500 U A 6 O4' U A 6 C1' 0.075 REMARK 500 G A 8 C2' G A 8 C1' -0.056 REMARK 500 DC B 10 O3' G B 11 P -0.118 REMARK 500 G B 11 C2' G B 11 C1' -0.061 REMARK 500 U B 12 C2' U B 12 C1' -0.067 REMARK 500 A B 14 N1 A B 14 C2 -0.074 REMARK 500 A B 14 N3 A B 14 C4 -0.063 REMARK 500 A B 14 C5 A B 14 N7 -0.060 REMARK 500 G B 17 C2' G B 17 C1' -0.075 REMARK 500 DC B 18 C4 DC B 18 C5 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 G A 2 N9 - C1' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 G A 2 O4' - C1' - N9 ANGL. DEV. = -6.4 DEGREES REMARK 500 U A 3 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 G A 4 N1 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 A A 5 C4 - C5 - N7 ANGL. DEV. = 3.3 DEGREES REMARK 500 A A 5 N7 - C8 - N9 ANGL. DEV. = -3.0 DEGREES REMARK 500 A A 5 N9 - C4 - C5 ANGL. DEV. = -2.5 DEGREES REMARK 500 C A 7 C1' - O4' - C4' ANGL. DEV. = -4.2 DEGREES REMARK 500 C A 7 C2 - N3 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 G A 8 P - O5' - C5' ANGL. DEV. = 17.0 DEGREES REMARK 500 G A 8 N1 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 DC A 9 O4' - C4' - C3' ANGL. DEV. = -3.9 DEGREES REMARK 500 G B 11 OP1 - P - OP2 ANGL. DEV. = -10.9 DEGREES REMARK 500 U B 12 N1 - C2 - O2 ANGL. DEV. = -5.8 DEGREES REMARK 500 U B 12 N3 - C2 - O2 ANGL. DEV. = 5.7 DEGREES REMARK 500 A B 14 C4 - C5 - N7 ANGL. DEV. = 3.0 DEGREES REMARK 500 A B 14 N9 - C4 - C5 ANGL. DEV. = -3.0 DEGREES REMARK 500 U B 15 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 19 DBREF 485D A 1 9 PDB 485D 485D 1 9 DBREF 485D B 10 18 PDB 485D 485D 10 18 SEQRES 1 A 9 DC G U G A U C G DC SEQRES 1 B 9 DC G U G A U C G DC HET SO4 B 19 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *84(H2 O) SITE 1 AC1 4 G B 17 DC B 18 HOH B 103 HOH B 145 CRYST1 39.958 39.958 67.445 90.00 90.00 120.00 H 3 18 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 0.025026 0.014449 0.000000 0.00000 SCALE2 0.000000 0.028898 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014827 0.00000