PDB Short entry for 1M5V HEADER TRANSLATION/RNA 09-JUL-02 1M5V TITLE TRANSITION STATE STABILIZATION BY A CATALYTIC RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA INHIBITOR SUBSTRATE; COMPND 3 CHAIN: A, D; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: FIRST FRAGMENT; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA INHIBITOR SUBSTRATE; COMPND 8 CHAIN: M, P; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: SECOND FRAGMENT; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: RNA HAIRPIN RIBOZYME; COMPND 13 CHAIN: B, E; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A; COMPND 17 CHAIN: C, F; COMPND 18 FRAGMENT: U1A RNA BINDING DOMAIN; COMPND 19 SYNONYM: U1 SNRNP A PROTEIN; U1 SNRNP-SPECIFIC PROTEIN A; COMPND 20 ENGINEERED: YES; COMPND 21 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN SATELLITE TOBACCO SOURCE 4 RINGSPOT VIRUS; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN SATELLITE TOBACCO SOURCE 8 RINGSPOT VIRUS; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN SATELLITE TOBACCO SOURCE 12 RINGSPOT VIRUS; SOURCE 13 MOL_ID: 4; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 GENE: SNRPA; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS HAIRPIN RIBOZYME, CATALYTIC RNA, U1A RNA BINDING PROTEIN 2'3'CYCLIC KEYWDS 2 PHOSPHATE, CLEAVED SUBSTRATE, TRANSLATION-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.B.RUPERT,A.P.MASSEY,S.T.SIGURDSSON,A.R.FERRE-D'AMARE REVDAT 5 14-FEB-24 1M5V 1 REMARK REVDAT 4 27-OCT-21 1M5V 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1M5V 1 VERSN REVDAT 2 22-NOV-02 1M5V 1 JRNL REVDAT 1 12-OCT-02 1M5V 0 JRNL AUTH P.B.RUPERT,A.P.MASSEY,S.T.SIGURDSSON,A.R.FERRE-D'AMARE JRNL TITL TRANSITION STATE STABILIZATION BY A CATALYTIC RNA JRNL REF SCIENCE V. 298 1421 2002 JRNL REFN ISSN 0036-8075 JRNL PMID 12376595 JRNL DOI 10.1126/SCIENCE.1076093 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.B.RUPERT,A.R.FERRE-D'AMARE REMARK 1 TITL CRYSTAL STRUCTURE OF A HAIRPIN RIBOZYME-INHIBITOR COMPLEX REMARK 1 TITL 2 WITH IMPLICATIONS FOR CATALYSIS REMARK 1 REF NATURE V. 410 780 2001 REMARK 1 REFN ISSN 0028-0836 REMARK 1 DOI 10.1038/35071009 REMARK 2 REMARK 2 RESOLUTION. 2.40 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 43428 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) : 0.221 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.400 REMARK 3 FREE R VALUE TEST SET COUNT : 4100 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6524 REMARK 3 BIN R VALUE (WORKING SET) : 0.3110 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 459 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1527 REMARK 3 NUCLEIC ACID ATOMS : 4818 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 237 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 79.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.30000 REMARK 3 B22 (A**2) : -3.20000 REMARK 3 B33 (A**2) : -1.10000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 17.28000 REMARK 3 B23 (A**2) : 0.00000 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) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.32 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.510 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.830 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.580 ; 4.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 6.270 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.310 ; 7.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 52.41 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : DNA-RNA_REPD REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA_RNA_NEW. REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1M5V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUL-02. REMARK 100 THE DEPOSITION ID IS D_1000016636. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-01 REMARK 200 TEMPERATURE (KELVIN) : 150 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43840 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.26500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1HP6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, AMMONIUM CHLORIDE, CALCIUM REMARK 280 CHLORIDE, PH 5.0, VAPOR DIFFUSION, SITTING DROP AT 300K 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 129.32400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.12900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 129.32400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.12900 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, M, B, C 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, P, E, F 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 MET C 1 REMARK 465 ALA C 2 REMARK 465 VAL C 3 REMARK 465 LYS C 98 REMARK 465 GLY C 99 REMARK 465 THR C 100 REMARK 465 MET F 1 REMARK 465 ALA F 2 REMARK 465 VAL F 3 REMARK 465 LYS F 98 REMARK 465 GLY F 99 REMARK 465 THR F 100 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 ASP C 24 CG OD1 OD2 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 B 15 C2' - C3' - O3' ANGL. DEV. = 11.8 DEGREES REMARK 500 C B 40 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 A E 57 C2' - C3' - O3' ANGL. DEV. = 13.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU C 5 31.37 77.76 REMARK 500 THR C 6 140.55 147.76 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 CA E 99 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C M 21 O3' REMARK 620 2 C M 21 O2' 59.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA E 107 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH M 373 O REMARK 620 2 C E 44 OP1 134.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 93 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 22 OP2 REMARK 620 2 A B 22 O5' 46.6 REMARK 620 3 A B 59 OP2 158.6 152.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 94 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B 38 OP1 REMARK 620 2 G B 39 OP1 93.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 100 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C B 45 OP1 REMARK 620 2 HOH B 281 O 138.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 103 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B 58 OP1 REMARK 620 2 U B 58 OP2 54.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA P 32 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G P 13 O3' REMARK 620 2 G P 13 O2' 56.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA E 93 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A E 22 OP2 REMARK 620 2 A E 22 O5' 45.3 REMARK 620 3 A E 59 OP2 149.4 159.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA E 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U E 37 O4 REMARK 620 2 HOH E 397 O 71.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA E 94 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U E 38 OP1 REMARK 620 2 G E 39 OP1 89.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA E 97 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U E 43 O3' REMARK 620 2 U E 43 O5' 88.3 REMARK 620 3 C E 44 OP2 48.0 115.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA E 100 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G E 47 OP2 REMARK 620 2 G E 48 OP2 106.6 REMARK 620 3 HOH E 268 O 127.1 116.8 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 CA E 93 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA E 94 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 93 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 94 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA E 96 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA E 97 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA E 98 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA E 99 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 97 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA E 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA E 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA E 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA E 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA E 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA E 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA D 30 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA E 108 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA P 32 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA E 109 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA E 110 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD C 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD F 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1M5K RELATED DB: PDB REMARK 900 THE SAME RIBOZYME WITH DIFFERENT SUBSTRATE REMARK 900 RELATED ID: 1M5O RELATED DB: PDB REMARK 900 THE SAME RIBOZYME WITH DIFFERENT SUBSTRATE REMARK 900 RELATED ID: 1M5P RELATED DB: PDB REMARK 900 THE SAME RIBOZYME WITH DIFFERENT SUBSTRATE DBREF 1M5V C 1 100 UNP P09012 SNRPA_HUMAN 1 100 DBREF 1M5V F 1 100 UNP P09012 SNRPA_HUMAN 1 100 DBREF 1M5V A 1 12 PDB 1M5V 1M5V 1 12 DBREF 1M5V M 13 21 PDB 1M5V 1M5V 13 21 DBREF 1M5V B 1 92 PDB 1M5V 1M5V 1 92 DBREF 1M5V D 1 12 PDB 1M5V 1M5V 1 12 DBREF 1M5V P 13 21 PDB 1M5V 1M5V 13 21 DBREF 1M5V E 1 92 PDB 1M5V 1M5V 1 92 SEQADV 1M5V HIS C 31 UNP P09012 TYR 31 ENGINEERED MUTATION SEQADV 1M5V ARG C 36 UNP P09012 GLN 36 ENGINEERED MUTATION SEQADV 1M5V HIS F 31 UNP P09012 TYR 31 ENGINEERED MUTATION SEQADV 1M5V ARG F 36 UNP P09012 GLN 36 ENGINEERED MUTATION SEQRES 1 A 12 G G C C A C C U G A C A23 SEQRES 1 M 9 G U C C U C U C C SEQRES 1 B 92 G G A G A G A G A A G U C SEQRES 2 B 92 A A C C A G A G A A A C A SEQRES 3 B 92 C A C C A A C C C A U U G SEQRES 4 B 92 C A C U C C G G G U U G G SEQRES 5 B 92 U G G U A U A U U A C C U SEQRES 6 B 92 G G U A C G G G G G A A A SEQRES 7 B 92 C U U C G U G G U G G C C SEQRES 8 B 92 G SEQRES 1 D 12 G G C C A C C U G A C A23 SEQRES 1 P 9 G U C C U C U C C SEQRES 1 E 92 G G A G A G A G A A G U C SEQRES 2 E 92 A A C C A G A G A A A C A SEQRES 3 E 92 C A C C A A C C C A U U G SEQRES 4 E 92 C A C U C C G G G U U G G SEQRES 5 E 92 U G G U A U A U U A C C U SEQRES 6 E 92 G G U A C G G G G G A A A SEQRES 7 E 92 C U U C G U G G U G G C C SEQRES 8 E 92 G SEQRES 1 C 100 MET ALA VAL PRO GLU THR ARG PRO ASN HIS THR ILE TYR SEQRES 2 C 100 ILE ASN ASN LEU ASN GLU LYS ILE LYS LYS ASP GLU LEU SEQRES 3 C 100 LYS LYS SER LEU HIS ALA ILE PHE SER ARG PHE GLY GLN SEQRES 4 C 100 ILE LEU ASP ILE LEU VAL SER ARG SER LEU LYS MET ARG SEQRES 5 C 100 GLY GLN ALA PHE VAL ILE PHE LYS GLU VAL SER SER ALA SEQRES 6 C 100 THR ASN ALA LEU ARG SER MET GLN GLY PHE PRO PHE TYR SEQRES 7 C 100 ASP LYS PRO MET ARG ILE GLN TYR ALA LYS THR ASP SER SEQRES 8 C 100 ASP ILE ILE ALA LYS MET LYS GLY THR SEQRES 1 F 100 MET ALA VAL PRO GLU THR ARG PRO ASN HIS THR ILE TYR SEQRES 2 F 100 ILE ASN ASN LEU ASN GLU LYS ILE LYS LYS ASP GLU LEU SEQRES 3 F 100 LYS LYS SER LEU HIS ALA ILE PHE SER ARG PHE GLY GLN SEQRES 4 F 100 ILE LEU ASP ILE LEU VAL SER ARG SER LEU LYS MET ARG SEQRES 5 F 100 GLY GLN ALA PHE VAL ILE PHE LYS GLU VAL SER SER ALA SEQRES 6 F 100 THR ASN ALA LEU ARG SER MET GLN GLY PHE PRO PHE TYR SEQRES 7 F 100 ASP LYS PRO MET ARG ILE GLN TYR ALA LYS THR ASP SER SEQRES 8 F 100 ASP ILE ILE ALA LYS MET LYS GLY THR MODRES 1M5V A23 A 12 A MODRES 1M5V A23 D 12 A HET A23 A 12 25 HET A23 D 12 25 HET CA B 93 1 HET CA B 94 1 HET CA B 95 1 HET CA B 96 1 HET CA B 97 1 HET CA B 98 1 HET CA B 99 1 HET CA B 100 1 HET CA B 101 1 HET CA B 102 1 HET CA B 103 1 HET CA B 104 1 HET CA D 23 1 HET CA D 30 1 HET CA P 32 1 HET CA E 93 1 HET CA E 94 1 HET CA E 95 1 HET CA E 96 1 HET CA E 97 1 HET CA E 98 1 HET CA E 99 1 HET CA E 100 1 HET CA E 101 1 HET CA E 102 1 HET CA E 103 1 HET CA E 104 1 HET CA E 105 1 HET CA E 106 1 HET CA E 107 1 HET CA E 108 1 HET CA E 109 1 HET CA E 110 1 HET CA C 101 1 HET MPD C 102 8 HET MPD F 102 8 HETNAM A23 ADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE HETNAM CA CALCIUM ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 1 A23 2(C10 H13 N5 O9 P2) FORMUL 9 CA 34(CA 2+) FORMUL 43 MPD 2(C6 H14 O2) FORMUL 45 HOH *237(H2 O) HELIX 1 1 LYS C 22 SER C 35 1 14 HELIX 2 2 ARG C 36 GLY C 38 5 3 HELIX 3 3 GLU C 61 GLN C 73 1 13 HELIX 4 4 SER C 91 LYS C 96 1 6 HELIX 5 5 LYS F 22 SER F 35 1 14 HELIX 6 6 ARG F 36 GLY F 38 5 3 HELIX 7 7 GLU F 61 GLN F 73 1 13 HELIX 8 8 SER F 91 LYS F 96 1 6 SHEET 1 A 4 ILE C 40 LEU C 44 0 SHEET 2 A 4 GLN C 54 PHE C 59 -1 O PHE C 56 N LEU C 44 SHEET 3 A 4 THR C 11 ASN C 15 -1 N ILE C 14 O ALA C 55 SHEET 4 A 4 ARG C 83 TYR C 86 -1 O GLN C 85 N TYR C 13 SHEET 1 B 2 PRO C 76 PHE C 77 0 SHEET 2 B 2 LYS C 80 PRO C 81 -1 O LYS C 80 N PHE C 77 SHEET 1 C 4 ILE F 40 VAL F 45 0 SHEET 2 C 4 GLN F 54 PHE F 59 -1 O PHE F 56 N LEU F 44 SHEET 3 C 4 THR F 11 ASN F 15 -1 N ILE F 14 O ALA F 55 SHEET 4 C 4 ARG F 83 TYR F 86 -1 O GLN F 85 N TYR F 13 SHEET 1 D 2 PRO F 76 PHE F 77 0 SHEET 2 D 2 LYS F 80 PRO F 81 -1 O LYS F 80 N PHE F 77 LINK O3' C A 11 P A23 A 12 1555 1555 1.61 LINK O3' C D 11 P A23 D 12 1555 1555 1.61 LINK O3' C M 21 CA CA E 99 1556 1555 2.97 LINK O2' C M 21 CA CA E 99 1556 1555 2.81 LINK O HOH M 373 CA CA E 107 1556 1555 2.27 LINK OP2 G B 19 CA CA B 102 1555 1555 2.58 LINK OP2 A B 22 CA CA B 93 1555 1555 2.79 LINK O5' A B 22 CA CA B 93 1555 1555 3.35 LINK OP1 U B 38 CA CA B 94 1555 1555 2.43 LINK OP1 G B 39 CA CA B 94 1555 1555 2.67 LINK OP1 C B 45 CA CA B 100 1555 1555 2.76 LINK OP1 U B 58 CA CA B 103 1555 1555 2.70 LINK OP2 U B 58 CA CA B 103 1555 1555 2.89 LINK OP2 A B 59 CA CA B 93 1555 1555 2.73 LINK OP1 A B 59 CA CA B 97 1555 1555 2.43 LINK CA CA B 100 O HOH B 281 1555 1555 2.58 LINK O HOH B 321 CA CA E 96 4547 1555 2.84 LINK O2C A23 D 12 CA CA D 30 1555 1555 3.02 LINK O3' G P 13 CA CA P 32 1555 1555 2.81 LINK O2' G P 13 CA CA P 32 1555 1555 2.95 LINK N7 G E 2 CA CA E 109 1555 1555 2.77 LINK OP2 G E 19 CA CA E 110 1555 1555 2.75 LINK OP2 A E 22 CA CA E 93 1555 1555 3.08 LINK O5' A E 22 CA CA E 93 1555 1555 3.37 LINK O4 U E 37 CA CA E 101 1555 1555 2.36 LINK OP1 U E 38 CA CA E 94 1555 1555 2.55 LINK OP1 G E 39 CA CA E 94 1555 1555 2.58 LINK O3' U E 43 CA CA E 97 1555 1555 3.03 LINK O5' U E 43 CA CA E 97 1555 1555 3.20 LINK OP2 C E 44 CA CA E 97 1555 1555 3.08 LINK OP1 C E 44 CA CA E 107 1555 1555 2.41 LINK OP2 G E 47 CA CA E 100 1555 1555 3.25 LINK OP2 G E 48 CA CA E 100 1555 1555 3.13 LINK OP1 U E 56 CA CA E 108 1555 1555 2.47 LINK OP2 A E 59 CA CA E 93 1555 1555 2.75 LINK OP1 A E 59 CA CA E 98 1555 1555 2.53 LINK CA CA E 100 O HOH E 268 1555 1555 2.78 LINK CA CA E 101 O HOH E 397 1555 1555 2.91 LINK CA CA E 104 O HOH E 268 1555 1555 2.63 SITE 1 AC1 2 A E 22 A E 59 SITE 1 AC2 2 U E 38 G E 39 SITE 1 AC3 3 A B 22 A B 59 U B 60 SITE 1 AC4 3 U B 38 G B 39 U B 43 SITE 1 AC5 1 HOH B 321 SITE 1 AC6 2 U E 43 C E 44 SITE 1 AC7 1 A E 59 SITE 1 AC8 3 G E 1 ARG F 83 C M 21 SITE 1 AC9 1 A B 59 SITE 1 BC1 3 G E 47 G E 48 HOH E 268 SITE 1 BC2 2 U E 37 HOH E 397 SITE 1 BC3 3 C B 45 HOH B 281 SER C 48 SITE 1 BC4 1 G E 48 SITE 1 BC5 3 G E 47 G E 48 HOH E 268 SITE 1 BC6 1 CA E 109 SITE 1 BC7 1 A B 41 SITE 1 BC8 1 G B 19 SITE 1 BC9 2 C E 44 HOH M 373 SITE 1 CC1 1 U B 58 SITE 1 CC2 2 A23 D 12 A E 7 SITE 1 CC3 1 U E 56 SITE 1 CC4 1 G P 13 SITE 1 CC5 2 G E 2 CA E 106 SITE 1 CC6 1 G E 19 SITE 1 CC7 6 PRO C 76 PHE C 77 TYR C 78 HOH C 427 SITE 2 CC7 6 ARG F 36 HOH F 261 SITE 1 CC8 6 SER F 29 ILE F 33 PRO F 76 PHE F 77 SITE 2 CC8 6 TYR F 78 HOH F 380 CRYST1 258.648 44.258 102.174 90.00 107.69 90.00 C 1 2 1 8 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 0.003866 0.000000 0.001233 0.00000 SCALE2 0.000000 0.022595 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010273 0.00000