HEADER RNA 03-DEC-02 1NBS TITLE CRYSTAL STRUCTURE OF THE SPECIFICITY DOMAIN OF RIBONUCLEASE P RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE P RNA; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SPECIFICITY-DOMAIN, S-DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 EXPRESSION_SYSTEM: BACILLUS SUBTILIS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 1423; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PUC19; SOURCE 7 OTHER_DETAILS: THE RNA WAS PRODUCED BY VITRO TRANSCRIPTION WITH T7 SOURCE 8 POLYMERASE FROM A PUC19-BASED TEMPLATE WHICH CONTAINED CLONED SOURCE 9 SEQUENCE OF THE S-DOMAIN. KEYWDS RIBONUCLEASE P RNA, P RNA, S-DOMAIN, RNA EXPDTA X-RAY DIFFRACTION AUTHOR A.S.KRASILNIKOV,X.YANG,T.PAN,A.MONDRAGON REVDAT 4 27-OCT-21 1NBS 1 REMARK SEQADV LINK REVDAT 3 24-JUL-19 1NBS 1 REMARK REVDAT 2 24-FEB-09 1NBS 1 VERSN REVDAT 1 18-FEB-03 1NBS 0 JRNL AUTH A.S.KRASILNIKOV,X.YANG,T.PAN,A.MONDRAGON JRNL TITL CRYSTAL STRUCTURE OF THE SPECIFICITY DOMAIN OF RIBONUCLEASE JRNL TITL 2 P JRNL REF NATURE V. 421 760 2003 JRNL REFN ISSN 0028-0836 JRNL PMID 12610630 JRNL DOI 10.1038/NATURE01386 REMARK 2 REMARK 2 RESOLUTION. 3.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 21680 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 + TEST SET) : 0.282 REMARK 3 R VALUE (WORKING SET) : 0.280 REMARK 3 FREE R VALUE : 0.307 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1173 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.24 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1260 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3540 REMARK 3 BIN FREE R VALUE SET COUNT : 66 REMARK 3 BIN FREE R VALUE : 0.3320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 5802 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 66.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 94.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.45000 REMARK 3 B22 (A**2) : -0.56000 REMARK 3 B33 (A**2) : -3.90000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.515 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.857 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.847 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6497 ; 0.008 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10124 ; 1.291 ; 3.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1080 ; 0.139 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2832 ; 0.017 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3164 ; 0.281 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 284 ; 0.161 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 93 ; 0.350 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.174 ; 0.500 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 6497 ; 1.487 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 10124 ; 2.417 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BASES 143-165, 201-212 IN MOLECULE A REMARK 3 AND 121-124 AND 240 IN MOLECULE B ARE DISORDERED; ONLY PHOSPHATE REMARK 3 BACKBONE COULD BE TRACED FOR BASES 99 AND 101 IN BOTH MOLECULES. REMARK 3 CNS WAS ALSO USED IN REFINEMENT. REMARK 4 REMARK 4 1NBS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-DEC-02. REMARK 100 THE DEPOSITION ID IS D_1000017750. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 4 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 5ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9475,0.9293 REMARK 200 MONOCHROMATOR : SI MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA, XDS, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23276 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.150 REMARK 200 RESOLUTION RANGE LOW (A) : 33.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07600 REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.27200 REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ISOPROPANOL, STRONTIUM CHLORIDE, REMARK 280 MAGNESIUM CHLORIDE, SPERMINE, MES, PH 6.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 303K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 72.30000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.30000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 63.25000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 72.65000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 63.25000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 72.65000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 72.30000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 63.25000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 72.65000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 72.30000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 63.25000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 72.65000 REMARK 290 SMTRY3 8 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: MONOMERIC 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 A A 143 REMARK 465 G A 144 REMARK 465 C A 145 REMARK 465 C A 146 REMARK 465 U A 147 REMARK 465 A A 148 REMARK 465 C A 149 REMARK 465 G A 150 REMARK 465 U A 151 REMARK 465 C A 152 REMARK 465 U A 153 REMARK 465 U A 154 REMARK 465 C A 155 REMARK 465 G A 156 REMARK 465 G A 157 REMARK 465 A A 158 REMARK 465 U A 159 REMARK 465 A A 160 REMARK 465 U A 161 REMARK 465 G A 162 REMARK 465 G A 163 REMARK 465 C A 164 REMARK 465 U A 165 REMARK 465 A A 201 REMARK 465 C A 202 REMARK 465 U A 203 REMARK 465 A A 204 REMARK 465 G A 205 REMARK 465 A A 206 REMARK 465 A A 207 REMARK 465 A A 208 REMARK 465 U A 209 REMARK 465 G A 210 REMARK 465 G A 211 REMARK 465 U A 212 REMARK 465 U B 121 REMARK 465 A B 122 REMARK 465 G B 123 REMARK 465 A B 124 REMARK 465 A B 240 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 A A 99 C5' C4' O4' C3' C2' O2' C1' REMARK 480 A A 99 N9 C8 N7 C5 C6 N6 N1 REMARK 480 A A 99 C2 N3 C4 REMARK 480 U A 101 C5' C4' O4' C3' C2' O2' C1' REMARK 480 U A 101 N1 C2 O2 N3 C4 O4 C5 REMARK 480 U A 101 C6 REMARK 480 A B 99 C5' C4' O4' C3' C2' O2' C1' REMARK 480 A B 99 N9 C8 N7 C5 C6 N6 N1 REMARK 480 A B 99 C2 N3 C4 REMARK 480 U B 101 C5' C4' O4' C3' C2' O2' C1' REMARK 480 U B 101 N1 C2 O2 N3 C4 O4 C5 REMARK 480 U B 101 C6 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 O2' G B 190 N1 G B 193 2.15 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 98 N9 - C1' - C2' ANGL. DEV. = 11.4 DEGREES REMARK 500 G A 137 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 A A 167 C2' - C3' - O3' ANGL. DEV. = 15.7 DEGREES REMARK 500 G B 90 N9 - C1' - C2' ANGL. DEV. = 9.8 DEGREES REMARK 500 A B 130 N9 - C1' - C2' ANGL. DEV. = 9.1 DEGREES REMARK 500 C B 134 N1 - C1' - C2' ANGL. DEV. = 9.5 DEGREES REMARK 500 C B 192 C4' - C3' - O3' ANGL. DEV. = -16.1 DEGREES REMARK 500 C B 192 N1 - C1' - C2' ANGL. DEV. = 19.4 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 A A 229 0.05 SIDE CHAIN REMARK 500 C B 134 0.06 SIDE CHAIN REMARK 500 C B 192 0.09 SIDE CHAIN 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 PB A 243 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 86 N7 REMARK 620 2 G A 86 O6 69.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PB A 242 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 132 O6 REMARK 620 2 G A 132 N7 64.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PB A 244 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 134 O2 REMARK 620 2 C A 134 O2' 79.4 REMARK 620 3 U A 181 O4 89.0 149.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PB A 250 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 168 O6 REMARK 620 2 G A 168 N1 42.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PB A 241 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 186 N3 REMARK 620 2 C A 186 N4 43.9 REMARK 620 3 G A 219 O3' 141.0 105.0 REMARK 620 4 G A 220 OP1 162.7 135.5 53.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PB A 249 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 228 O3' REMARK 620 2 A A 231 OP1 68.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PB B 306 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B 101 OP2 REMARK 620 2 C B 102 OP2 69.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PB B 302 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 132 N7 REMARK 620 2 G B 132 O6 62.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PB B 305 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C B 134 O2' REMARK 620 2 C B 134 O2 77.7 REMARK 620 3 U B 181 O4 120.7 66.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PB B 301 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C B 186 N3 REMARK 620 2 C B 186 O2 48.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 241 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 242 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 244 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 245 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 246 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 247 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB A 241 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB A 242 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB A 243 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB A 244 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB A 245 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB A 246 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB A 248 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB A 249 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB A 250 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB A 251 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB A 252 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB B 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB B 312 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NXL RELATED DB: PDB REMARK 900 MODEL WHICH IS COMPOSED OF THE TWO MOLECULES IN THE REMARK 900 CRYSTALLOGRAPHIC ASYMMETRIC UNIT AND REPRESENTS ENTIRE SPECIFICITY REMARK 900 DOMAIN OF RIBONUCLEASE P RNA REMARK 999 REMARK 999 SEQUENCE REMARK 999 BASE A240 IS A TRANSCRIPTIONAL ARTIFACT. DBREF 1NBS A 86 240 GB 143351 M13175 86 240 DBREF 1NBS B 86 240 GB 143351 M13175 86 240 SEQADV 1NBS G A 86 GB 143351 U 86 ENGINEERED MUTATION SEQADV 1NBS A A 89 GB 143351 U 89 ENGINEERED MUTATION SEQADV 1NBS C A 239 GB 143351 A 239 ENGINEERED MUTATION SEQADV 1NBS A A 240 GB 143351 G 240 SEE REMARK 999 SEQADV 1NBS G B 86 GB 143351 U 86 ENGINEERED MUTATION SEQADV 1NBS A B 89 GB 143351 U 89 ENGINEERED MUTATION SEQADV 1NBS C B 239 GB 143351 A 239 ENGINEERED MUTATION SEQADV 1NBS A B 240 GB 143351 G 240 SEE REMARK 999 SEQRES 1 A 155 G C G A G C C U A G C G A SEQRES 2 A 155 A G U C A U A A G C U A G SEQRES 3 A 155 G G C A G U C U U U A G A SEQRES 4 A 155 G G C U G A C G G C A G G SEQRES 5 A 155 A A A A A A G C C U A C G SEQRES 6 A 155 U C U U C G G A U A U G G SEQRES 7 A 155 C U G A G U A U C C U U G SEQRES 8 A 155 A A A G U G C C A C A G U SEQRES 9 A 155 G A C G A A G U C U C A C SEQRES 10 A 155 U A G A A A U G G U G A G SEQRES 11 A 155 A G U G G A A C G C G G U SEQRES 12 A 155 A A A C C C C U C G C A SEQRES 1 B 155 G C G A G C C U A G C G A SEQRES 2 B 155 A G U C A U A A G C U A G SEQRES 3 B 155 G G C A G U C U U U A G A SEQRES 4 B 155 G G C U G A C G G C A G G SEQRES 5 B 155 A A A A A A G C C U A C G SEQRES 6 B 155 U C U U C G G A U A U G G SEQRES 7 B 155 C U G A G U A U C C U U G SEQRES 8 B 155 A A A G U G C C A C A G U SEQRES 9 B 155 G A C G A A G U C U C A C SEQRES 10 B 155 U A G A A A U G G U G A G SEQRES 11 B 155 A G U G G A A C G C G G U SEQRES 12 B 155 A A A C C C C U C G C A HET MG A 2 1 HET MG A 4 1 HET MG A 5 1 HET MG A 6 1 HET MG A 7 1 HET PB A 241 1 HET PB A 242 1 HET PB A 243 1 HET PB A 244 1 HET PB A 245 1 HET PB A 246 1 HET PB A 247 1 HET PB A 248 1 HET PB A 249 1 HET PB A 250 1 HET PB A 251 1 HET PB A 252 1 HET MG B 241 1 HET MG B 242 1 HET MG B 243 1 HET MG B 244 1 HET MG B 245 1 HET MG B 246 1 HET MG B 247 1 HET PB B 301 1 HET PB B 302 1 HET PB B 303 1 HET PB B 304 1 HET PB B 305 1 HET PB B 306 1 HET PB B 307 1 HET PB B 308 1 HET PB B 309 1 HET PB B 310 1 HET PB B 312 1 HETNAM MG MAGNESIUM ION HETNAM PB LEAD (II) ION FORMUL 3 MG 12(MG 2+) FORMUL 8 PB 23(PB 2+) LINK MG MG A 6 O3' C A 134 1555 1555 2.77 LINK MG MG A 7 PB PB A 242 1555 1555 2.72 LINK N7 G A 86 PB PB A 243 1555 1555 2.38 LINK O6 G A 86 PB PB A 243 1555 1555 2.92 LINK OP1 G A 86 PB PB A 252 4556 1555 2.53 LINK O6 G A 97 PB PB A 251 1555 1555 1.45 LINK OP2 C A 102 PB PB A 245 1555 1555 2.70 LINK O6 G A 132 PB PB A 242 1555 1555 2.90 LINK N7 G A 132 PB PB A 242 1555 1555 2.79 LINK O2 C A 134 PB PB A 244 1555 1555 2.27 LINK O2' C A 134 PB PB A 244 1555 1555 3.13 LINK O6 G A 136 PB PB A 248 1555 1555 2.23 LINK O6 G A 168 PB PB A 250 1555 1555 3.38 LINK N1 G A 168 PB PB A 250 1555 1555 2.81 LINK OP1 U A 174 MG MG B 247 2655 1555 3.11 LINK O4 U A 181 PB PB A 244 1555 1555 2.41 LINK N3 C A 186 PB PB A 241 1555 1555 3.28 LINK N4 C A 186 PB PB A 241 1555 1555 2.59 LINK O3' G A 219 PB PB A 241 1555 1555 2.42 LINK O6 G A 219 PB PB A 246 1555 1555 3.43 LINK OP1 G A 220 PB PB A 241 1555 1555 3.04 LINK O3' U A 228 PB PB A 249 1555 1555 3.20 LINK OP1 A A 231 PB PB A 249 1555 1555 3.17 LINK N7 G B 86 PB PB B 303 1555 1555 2.36 LINK O6 G B 97 PB PB B 312 1555 1555 1.45 LINK OP2 U B 101 PB PB B 306 1555 1555 3.23 LINK OP2 C B 102 PB PB B 306 1555 1555 2.66 LINK OP2 A B 106 MG MG B 242 1555 1555 2.97 LINK N7 G B 132 PB PB B 302 1555 1555 3.15 LINK O6 G B 132 PB PB B 302 1555 1555 2.76 LINK O2' C B 134 PB PB B 305 1555 1555 2.43 LINK O2 C B 134 PB PB B 305 1555 1555 3.00 LINK N7 G B 163 PB PB B 304 1555 1555 3.40 LINK O2' A B 167 MG MG B 241 1555 1555 2.38 LINK O4 U B 181 PB PB B 305 1555 1555 2.75 LINK N3 C B 186 PB PB B 301 1555 1555 3.04 LINK O2 C B 186 PB PB B 301 1555 1555 2.42 LINK OP1 A B 191 MG MG B 244 1555 1555 2.39 LINK OP1 G B 193 MG MG B 246 1555 1555 2.99 LINK O6 G B 219 PB PB B 307 1555 1555 3.32 LINK OP1 A B 231 PB PB B 310 1555 1555 2.56 SITE 1 AC1 1 C A 134 SITE 1 AC2 2 A A 230 PB A 242 SITE 1 AC3 2 U B 165 A B 167 SITE 1 AC4 2 A B 106 G B 107 SITE 1 AC5 1 A B 191 SITE 1 AC6 2 A B 135 G B 226 SITE 1 AC7 1 G B 193 SITE 1 AC8 1 U A 174 SITE 1 AC9 3 C A 186 G A 219 G A 220 SITE 1 BC1 2 MG A 7 G A 132 SITE 1 BC2 1 G A 86 SITE 1 BC3 3 C A 134 U A 181 G A 182 SITE 1 BC4 1 C A 102 SITE 1 BC5 1 G A 219 SITE 1 BC6 1 G A 136 SITE 1 BC7 2 U A 228 A A 231 SITE 1 BC8 1 G A 168 SITE 1 BC9 1 G A 97 SITE 1 CC1 1 G A 86 SITE 1 CC2 1 C B 186 SITE 1 CC3 2 G B 90 G B 132 SITE 1 CC4 1 G B 86 SITE 1 CC5 2 A B 160 G B 163 SITE 1 CC6 3 C B 134 U B 181 G B 182 SITE 1 CC7 3 U B 101 C B 102 U B 104 SITE 1 CC8 1 G B 219 SITE 1 CC9 1 A B 231 SITE 1 DC1 1 G B 97 CRYST1 126.500 145.300 144.600 90.00 90.00 90.00 C 2 2 21 16 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 0.007905 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006884 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006915 0.00000 MASTER 580 0 35 0 0 0 28 6 0 0 0 24 END