HEADER RNA 22-JUN-05 2A2E TITLE CRYSTAL STRUCTURE OF THE RNA SUBUNIT OF RIBONUCLEASE P. BACTERIAL A- TITLE 2 TYPE. CAVEAT 2A2E C A 191 HAS WRONG CHIRALITY AT ATOM C1' CHIRALITY ERROR AT CAVEAT 2 2A2E C1' CENTER OF C 191. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA SUBUNIT OF RNASE P; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN THERMOTOGA SOURCE 4 MARITIMA. THE RNA WAS PREPARED BY IN VITRO TRANSCRPTION. KEYWDS RNASE P, RIBONUCLEASE P RNA, P RNA, RIBOZYME, TRNA, PRE-TRNA, KEYWDS 2 THERMOTOGA MARITIMA, TETRALOOP-RECEPTOR, T-LOOP, COAXIAL HELICES, KEYWDS 3 RIBOSE ZIPPERS, RNA EXPDTA X-RAY DIFFRACTION AUTHOR A.TORRES-LARIOS,K.K.SWINGER,A.S.KRASILNIKOV,T.PAN,A.MONDRAGON REVDAT 7 23-AUG-23 2A2E 1 REMARK REVDAT 6 28-JUL-21 2A2E 1 REMARK REVDAT 5 22-JAN-20 2A2E 1 CAVEAT REMARK REVDAT 4 28-DEC-11 2A2E 1 CAVEAT VERSN REVDAT 3 24-FEB-09 2A2E 1 VERSN REVDAT 2 27-SEP-05 2A2E 1 JRNL REVDAT 1 06-SEP-05 2A2E 0 JRNL AUTH A.TORRES-LARIOS,K.K.SWINGER,A.S.KRASILNIKOV,T.PAN, JRNL AUTH 2 A.MONDRAGON JRNL TITL CRYSTAL STRUCTURE OF THE RNA COMPONENT OF BACTERIAL JRNL TITL 2 RIBONUCLEASE P. JRNL REF NATURE V. 437 584 2005 JRNL REFN ISSN 0028-0836 JRNL PMID 16113684 JRNL DOI 10.1038/NATURE04074 REMARK 2 REMARK 2 RESOLUTION. 3.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 12652 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) : 0.344 REMARK 3 FREE R VALUE : 0.362 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 602 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) : 3.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 4.01 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 59.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 903 REMARK 3 BIN R VALUE (WORKING SET) : 0.3770 REMARK 3 BIN FREE R VALUE : 0.4310 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 55 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.051 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 5758 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 81.17 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.870 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.140 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: NO BULK SOLVENT CORRECTION APPLIED. REMARK 3 ONLY THE PHOSPHATE BACKBONE WAS TRACED (PHOSPHATE ATOM ONLY) FOR REMARK 3 NUCLEOTIDES 39, 45-48, 52, 62-63, 68, 207, 212-214, 262-267, 288- REMARK 3 297 AND 305-314. THERE ARE LONG P-O3* DISTANCES BETWEEN THE REMARK 3 FOLLOWING NUCLEOTIDES: 67-68,206-207. THE AUTHORS STATE THAT THEY REMARK 3 ARE AWARE ABOUT SOME P-O3* DISTANCES BEING TOO FAR APART. THE LOW REMARK 3 RESOLUTION OF THE REMARK 3 STRUCTURE AND THE FACT THAT THE P ATOMS WERE REFINED AS PHOSPHATE REMARK 3 IONS WITHOUT CONSTRAINTS ON THE REMARK 3 RELATIVE DISTANCES MAY CAUSE THIS. REMARK 3 DENSITY WAS NOT FOUND FOR 29 OF THE 338 NUCLEOTIDES (30-33, 120- REMARK 3 122, 131-135, 221-223, 229, 234, 239-241, 247-248, 253-255 AND 335- REMARK 3 338). REMARK 4 REMARK 4 2A2E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1000033406. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-04; 11-NOV-04; 11-NOV-04; REMARK 200 11-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : 100; 100; 100; 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 4 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y; Y; Y REMARK 200 RADIATION SOURCE : APS; APS; APS; APS REMARK 200 BEAMLINE : 5ID-B; 5ID-B; 5ID-B; 5ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL; NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M; M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.13974; 1.14079; 1.105; 1.13974 REMARK 200 MONOCHROMATOR : SI MIRRORS; SI MIRRORS; SI REMARK 200 MIRRORS; SI MIRRORS REMARK 200 OPTICS : MIRRORS; MIRRORS; MIRRORS; REMARK 200 MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD; CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; MARRESEARCH; REMARK 200 MARRESEARCH; MARCCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13927 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.850 REMARK 200 RESOLUTION RANGE LOW (A) : 21.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.23100 REMARK 200 R SYM FOR SHELL (I) : 0.23100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH; SINGLE REMARK 200 WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER, SHARP, SOLOMON REMARK 200 STARTING MODEL: PDB ENTRY 1U9S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% MPD, 200 MM KCL, 5 MM SRCL2, 50 MM REMARK 280 MES PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 303K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 89.63850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.61550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 89.63850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 42.61550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 300 THE AUTHORS STATE THEY HAVE NOT ASSESSED YET THE REMARK 300 BIOLOGICAL SIGNIFICANCE OF THE DIMER GENERATED IN REMARK 300 REMARK 350. 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 G A 19 REMARK 465 A A 29 REMARK 465 C A 30 REMARK 465 A A 31 REMARK 465 C A 32 REMARK 465 C A 33 REMARK 465 U A 34 REMARK 465 G A 120 REMARK 465 A A 121 REMARK 465 A A 122 REMARK 465 C A 130 REMARK 465 G A 131 REMARK 465 U A 132 REMARK 465 U A 133 REMARK 465 G A 134 REMARK 465 A A 135 REMARK 465 G A 136 REMARK 465 G A 221 REMARK 465 C A 222 REMARK 465 A A 223 REMARK 465 U A 229 REMARK 465 U A 234 REMARK 465 C A 239 REMARK 465 C A 240 REMARK 465 C A 241 REMARK 465 U A 246 REMARK 465 U A 247 REMARK 465 G A 253 REMARK 465 G A 254 REMARK 465 G A 255 REMARK 465 C A 335 REMARK 465 G A 336 REMARK 465 U A 337 REMARK 465 G A 338 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 U A 39 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 U A 39 O3' C2' O2' C1' N1 C2 O2 REMARK 470 U A 39 N3 C4 O4 C5 C6 REMARK 470 A A 45 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 A A 45 O3' C2' O2' C1' N9 C8 N7 REMARK 470 A A 45 C5 C6 N6 N1 C2 N3 C4 REMARK 470 G A 46 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 G A 46 O3' C2' O2' C1' N9 C8 N7 REMARK 470 G A 46 C5 C6 O6 N1 C2 N2 N3 REMARK 470 G A 46 C4 REMARK 470 G A 47 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 G A 47 O3' C2' O2' C1' N9 C8 N7 REMARK 470 G A 47 C5 C6 O6 N1 C2 N2 N3 REMARK 470 G A 47 C4 REMARK 470 A A 48 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 A A 48 O3' C2' O2' C1' N9 C8 N7 REMARK 470 A A 48 C5 C6 N6 N1 C2 N3 C4 REMARK 470 U A 52 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 U A 52 O3' C2' O2' C1' N1 C2 O2 REMARK 470 U A 52 N3 C4 O4 C5 C6 REMARK 470 G A 62 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 G A 62 O3' C2' O2' C1' N9 C8 N7 REMARK 470 G A 62 C5 C6 O6 N1 C2 N2 N3 REMARK 470 G A 62 C4 REMARK 470 G A 68 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 G A 68 O3' C2' O2' C1' N9 C8 N7 REMARK 470 G A 68 C5 C6 O6 N1 C2 N2 N3 REMARK 470 G A 68 C4 REMARK 470 U A 207 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 U A 207 O3' C2' O2' C1' N1 C2 O2 REMARK 470 U A 207 N3 C4 O4 C5 C6 REMARK 470 C A 212 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 C A 212 O3' C2' O2' C1' N1 C2 O2 REMARK 470 C A 212 N3 C4 N4 C5 C6 REMARK 470 A A 213 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 A A 213 O3' C2' O2' C1' N9 C8 N7 REMARK 470 A A 213 C5 C6 N6 N1 C2 N3 C4 REMARK 470 A A 214 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 A A 214 O3' C2' O2' C1' N9 C8 N7 REMARK 470 A A 214 C5 C6 N6 N1 C2 N3 C4 REMARK 470 G A 262 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 G A 262 O3' C2' O2' C1' N9 C8 N7 REMARK 470 G A 262 C5 C6 O6 N1 C2 N2 N3 REMARK 470 G A 262 C4 REMARK 470 C A 263 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 C A 263 O3' C2' O2' C1' N1 C2 O2 REMARK 470 C A 263 N3 C4 N4 C5 C6 REMARK 470 U A 264 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 U A 264 O3' C2' O2' C1' N1 C2 O2 REMARK 470 U A 264 N3 C4 O4 C5 C6 REMARK 470 U A 265 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 U A 265 O3' C2' O2' C1' N1 C2 O2 REMARK 470 U A 265 N3 C4 O4 C5 C6 REMARK 470 G A 266 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 G A 266 O3' C2' O2' C1' N9 C8 N7 REMARK 470 G A 266 C5 C6 O6 N1 C2 N2 N3 REMARK 470 G A 266 C4 REMARK 470 A A 267 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 A A 267 O3' C2' O2' C1' N9 C8 N7 REMARK 470 A A 267 C5 C6 N6 N1 C2 N3 C4 REMARK 470 C A 288 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 C A 288 O3' C2' O2' C1' N1 C2 O2 REMARK 470 C A 288 N3 C4 N4 C5 C6 REMARK 470 C A 289 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 C A 289 O3' C2' O2' C1' N1 C2 O2 REMARK 470 C A 289 N3 C4 N4 C5 C6 REMARK 470 A A 290 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 A A 290 O3' C2' O2' C1' N9 C8 N7 REMARK 470 A A 290 C5 C6 N6 N1 C2 N3 C4 REMARK 470 G A 291 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 G A 291 O3' C2' O2' C1' N9 C8 N7 REMARK 470 G A 291 C5 C6 O6 N1 C2 N2 N3 REMARK 470 G A 291 C4 REMARK 470 A A 292 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 A A 292 O3' C2' O2' C1' N9 C8 N7 REMARK 470 A A 292 C5 C6 N6 N1 C2 N3 C4 REMARK 470 U A 293 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 U A 293 O3' C2' O2' C1' N1 C2 O2 REMARK 470 U A 293 N3 C4 O4 C5 C6 REMARK 470 U A 294 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 U A 294 O3' C2' O2' C1' N1 C2 O2 REMARK 470 U A 294 N3 C4 O4 C5 C6 REMARK 470 G A 295 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 G A 295 O3' C2' O2' C1' N9 C8 N7 REMARK 470 G A 295 C5 C6 O6 N1 C2 N2 N3 REMARK 470 G A 295 C4 REMARK 470 A A 296 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 A A 296 O3' C2' O2' C1' N9 C8 N7 REMARK 470 A A 296 C5 C6 N6 N1 C2 N3 C4 REMARK 470 U A 297 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 U A 297 O3' C2' O2' C1' N1 C2 O2 REMARK 470 U A 297 N3 C4 O4 C5 C6 REMARK 470 C A 305 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 C A 305 O3' C2' O2' C1' N1 C2 O2 REMARK 470 C A 305 N3 C4 N4 C5 C6 REMARK 470 A A 306 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 A A 306 O3' C2' O2' C1' N9 C8 N7 REMARK 470 A A 306 C5 C6 N6 N1 C2 N3 C4 REMARK 470 C A 307 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 C A 307 O3' C2' O2' C1' N1 C2 O2 REMARK 470 C A 307 N3 C4 N4 C5 C6 REMARK 470 G A 308 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 G A 308 O3' C2' O2' C1' N9 C8 N7 REMARK 470 G A 308 C5 C6 O6 N1 C2 N2 N3 REMARK 470 G A 308 C4 REMARK 470 A A 309 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 A A 309 O3' C2' O2' C1' N9 C8 N7 REMARK 470 A A 309 C5 C6 N6 N1 C2 N3 C4 REMARK 470 C A 310 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 C A 310 O3' C2' O2' C1' N1 C2 O2 REMARK 470 C A 310 N3 C4 N4 C5 C6 REMARK 470 A A 311 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 A A 311 O3' C2' O2' C1' N9 C8 N7 REMARK 470 A A 311 C5 C6 N6 N1 C2 N3 C4 REMARK 470 G A 312 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 G A 312 O3' C2' O2' C1' N9 C8 N7 REMARK 470 G A 312 C5 C6 O6 N1 C2 N2 N3 REMARK 470 G A 312 C4 REMARK 470 A A 313 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 A A 313 O3' C2' O2' C1' N9 C8 N7 REMARK 470 A A 313 C5 C6 N6 N1 C2 N3 C4 REMARK 470 A A 314 OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 A A 314 O3' C2' O2' C1' N9 C8 N7 REMARK 470 A A 314 C5 C6 N6 N1 C2 N3 C4 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 O6 G A 152 N1 G A 163 1.85 REMARK 500 REMARK 500 REMARK: NULL 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 G A 25 N9 G A 25 C4 0.064 REMARK 500 G A 44 O3' A A 45 P 0.197 REMARK 500 G A 163 O3' C A 164 P 0.081 REMARK 500 G A 211 O3' C A 212 P 0.082 REMARK 500 C A 261 O3' G A 262 P -0.078 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 12 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 U A 17 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 C A 38 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 C A 38 C3' - O3' - P ANGL. DEV. = -16.5 DEGREES REMARK 500 G A 44 C3' - O3' - P ANGL. DEV. = 14.0 DEGREES REMARK 500 G A 51 C2' - C3' - O3' ANGL. DEV. = 12.3 DEGREES REMARK 500 G A 51 C3' - O3' - P ANGL. DEV. = -9.7 DEGREES REMARK 500 C A 53 OP1 - P - OP2 ANGL. DEV. = -12.8 DEGREES REMARK 500 C A 53 O5' - P - OP1 ANGL. DEV. = -8.2 DEGREES REMARK 500 G A 56 C4' - C3' - O3' ANGL. DEV. = -13.7 DEGREES REMARK 500 G A 56 N9 - C1' - C2' ANGL. DEV. = 9.1 DEGREES REMARK 500 U A 61 C3' - O3' - P ANGL. DEV. = -9.6 DEGREES REMARK 500 A A 79 N9 - C1' - C2' ANGL. DEV. = 10.4 DEGREES REMARK 500 C A 81 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 G A 82 N9 - C1' - C2' ANGL. DEV. = 11.8 DEGREES REMARK 500 C A 101 N1 - C1' - C2' ANGL. DEV. = 13.5 DEGREES REMARK 500 A A 104 N9 - C1' - C2' ANGL. DEV. = 8.5 DEGREES REMARK 500 C A 105 N1 - C1' - C2' ANGL. DEV. = 16.0 DEGREES REMARK 500 A A 118 N9 - C1' - C2' ANGL. DEV. = 11.7 DEGREES REMARK 500 A A 124 N9 - C1' - C2' ANGL. DEV. = 12.1 DEGREES REMARK 500 G A 137 O5' - P - OP1 ANGL. DEV. = -6.2 DEGREES REMARK 500 G A 137 O4' - C1' - N9 ANGL. DEV. = -4.8 DEGREES REMARK 500 A A 140 N9 - C1' - C2' ANGL. DEV. = 8.7 DEGREES REMARK 500 A A 149 C4' - C3' - O3' ANGL. DEV. = -14.0 DEGREES REMARK 500 A A 149 N9 - C1' - C2' ANGL. DEV. = 16.8 DEGREES REMARK 500 C A 150 C2' - C3' - O3' ANGL. DEV. = -16.0 DEGREES REMARK 500 C A 150 N1 - C1' - C2' ANGL. DEV. = 12.7 DEGREES REMARK 500 A A 159 N9 - C1' - C2' ANGL. DEV. = 8.7 DEGREES REMARK 500 G A 163 O3' - P - O5' ANGL. DEV. = 23.7 DEGREES REMARK 500 G A 163 C2' - C3' - O3' ANGL. DEV. = 18.0 DEGREES REMARK 500 G A 163 N9 - C1' - C2' ANGL. DEV. = 9.1 DEGREES REMARK 500 G A 163 C3' - O3' - P ANGL. DEV. = 43.3 DEGREES REMARK 500 C A 164 O3' - P - O5' ANGL. DEV. = -29.5 DEGREES REMARK 500 C A 164 O3' - P - OP2 ANGL. DEV. = -21.5 DEGREES REMARK 500 C A 164 O3' - P - OP1 ANGL. DEV. = 44.4 DEGREES REMARK 500 C A 166 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 C A 169 N1 - C1' - C2' ANGL. DEV. = -7.3 DEGREES REMARK 500 C A 191 N1 - C1' - C2' ANGL. DEV. = 15.8 DEGREES REMARK 500 U A 192 N1 - C1' - C2' ANGL. DEV. = 9.6 DEGREES REMARK 500 U A 192 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 G A 211 C4' - C3' - O3' ANGL. DEV. = -13.2 DEGREES REMARK 500 G A 211 C3' - O3' - P ANGL. DEV. = 28.6 DEGREES REMARK 500 C A 235 OP1 - P - OP2 ANGL. DEV. = -12.4 DEGREES REMARK 500 C A 242 OP1 - P - OP2 ANGL. DEV. = -9.5 DEGREES REMARK 500 C A 261 C3' - O3' - P ANGL. DEV. = -11.3 DEGREES REMARK 500 U A 315 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 U A 321 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 C A 334 N1 - C1' - C2' ANGL. DEV. = 9.1 DEGREES 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 G A 7 0.06 SIDE CHAIN REMARK 500 A A 57 0.08 SIDE CHAIN REMARK 500 C A 105 0.06 SIDE CHAIN REMARK 500 U A 113 0.08 SIDE CHAIN REMARK 500 A A 140 0.09 SIDE CHAIN REMARK 500 C A 150 0.06 SIDE CHAIN REMARK 500 G A 155 0.05 SIDE CHAIN REMARK 500 G A 163 0.06 SIDE CHAIN REMARK 500 G A 179 0.07 SIDE CHAIN REMARK 500 G A 190 0.08 SIDE CHAIN REMARK 500 U A 192 0.06 SIDE CHAIN REMARK 500 A A 278 0.06 SIDE CHAIN REMARK 500 C A 317 0.06 SIDE CHAIN REMARK 500 G A 319 0.06 SIDE CHAIN REMARK 500 U A 324 0.26 SIDE CHAIN 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 OS A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OS A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OS A 1014 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U9S RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE SPECIFICITY DOMAIN OF RIBONUCLEASE P OF REMARK 900 THE A-TYPE REMARK 900 RELATED ID: 1NBS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE SPECIFICITY DOMAIN OF RIBONUCLEASE P OF REMARK 900 THE B-TYPE REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEE REMARK 3, OTHER REFINEMENT REMARKS, FOR REMARK 999 DETAILS REGARDING SOME LONG P-O3* BOND REMARK 999 DISTANCES. DBREF 2A2E A 1 338 PDB 2A2E 2A2E 1 338 SEQRES 1 A 338 G G A G A G G A G C A G G SEQRES 2 A 338 C G G U C G C G G G G G C SEQRES 3 A 338 G C A C A C C U G C G C U SEQRES 4 A 338 U C C C G A G G A A A G U SEQRES 5 A 338 C C G G A C U C U G G A G SEQRES 6 A 338 C G G G G U G C C G G G U SEQRES 7 A 338 A A C G C C C G G G A G G SEQRES 8 A 338 G G U G A C C C U C G G A SEQRES 9 A 338 C A G G G C C A U A G A G SEQRES 10 A 338 A A G A A G A C C G C C C SEQRES 11 A 338 G U U G A G G G C A A G G SEQRES 12 A 338 G U G G A A C G G U G G G SEQRES 13 A 338 G U A A G A G C C C A C C SEQRES 14 A 338 A G C G U C G G G G C A A SEQRES 15 A 338 C C C G G C G G C U U G G SEQRES 16 A 338 C A A C C C C C A C C U G SEQRES 17 A 338 G A G C A A G G C C A A G SEQRES 18 A 338 C A G G G G G U U G G G U SEQRES 19 A 338 C G C U C C C C C U A U U SEQRES 20 A 338 C C C C C G G G U U G G C SEQRES 21 A 338 C G C U U G A G G U G U G SEQRES 22 A 338 C G G U A A C G C A C A C SEQRES 23 A 338 C C C A G A U U G A U G A SEQRES 24 A 338 C C G C C C A C G A C A G SEQRES 25 A 338 A A U C C G G C U U A U G SEQRES 26 A 338 C U C C U C U C C C G U G HET OS A1001 1 HET OS A1002 1 HET OS A1003 1 HET OS A1004 1 HET OS A1005 1 HET OS A1006 1 HET OS A1007 1 HET OS A1008 1 HET OS A1009 1 HET OS A1010 1 HET OS A1011 1 HET OS A1012 1 HET OS A1013 1 HET OS A1014 1 HET OS A1015 1 HET OS A1016 1 HET OS A1017 1 HETNAM OS OSMIUM ION FORMUL 2 OS 17(OS 3+) LINK OP2 C A 125 OS OS A1003 1555 1555 2.65 SITE 1 AC1 1 C A 125 SITE 1 AC2 1 G A 87 SITE 1 AC3 2 G A 75 G A 76 CRYST1 179.277 85.231 101.912 90.00 96.83 90.00 C 1 2 1 4 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 0.005578 0.000000 0.000668 0.00000 SCALE2 0.000000 0.011733 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009883 0.00000