PDB Short entry for 3CUN HEADER RNA/RNA BINDING 16-APR-08 3CUN TITLE AMINOACYL-TRNA SYNTHETASE RIBOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (92-MER); COMPND 3 CHAIN: C, D; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: FLEXIZYME; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A; COMPND 8 CHAIN: A, B; COMPND 9 FRAGMENT: UNP RESIDUES 1-98; COMPND 10 SYNONYM: U1 SNRNP PROTEIN A, U1A PROTEIN, U1-A; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 EXPRESSION_SYSTEM: CELL-FREE SYNTHESIS; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 5 ORGANISM_COMMON: HUMAN; SOURCE 6 ORGANISM_TAXID: 9606; SOURCE 7 GENE: SNRPA; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI KEYWDS ARS RIBOZYME CATALYTIC RNA, RNA-RNA BINDING COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.XIAO,H.MURAKAMI,H.SUGA,A.R.FERRE-D'AMARE REVDAT 6 15-NOV-23 3CUN 1 REMARK REVDAT 5 30-AUG-23 3CUN 1 REMARK REVDAT 4 20-OCT-21 3CUN 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 3CUN 1 VERSN REVDAT 2 05-AUG-08 3CUN 1 JRNL REVDAT 1 24-JUN-08 3CUN 0 JRNL AUTH H.XIAO,H.MURAKAMI,H.SUGA,A.R.FERRE-D'AMARE JRNL TITL STRUCTURAL BASIS OF SPECIFIC TRNA AMINOACYLATION BY A SMALL JRNL TITL 2 IN VITRO SELECTED RIBOZYME. JRNL REF NATURE V. 454 358 2008 JRNL REFN ISSN 0028-0836 JRNL PMID 18548004 JRNL DOI 10.1038/NATURE07033 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 185743.740 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 80.8 REMARK 3 NUMBER OF REFLECTIONS : 13610 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) : 0.252 REMARK 3 FREE R VALUE : 0.303 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1355 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.19 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 38.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 954 REMARK 3 BIN R VALUE (WORKING SET) : 0.3790 REMARK 3 BIN FREE R VALUE : 0.4100 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 114 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.038 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1407 REMARK 3 NUCLEIC ACID ATOMS : 3946 REMARK 3 HETEROGEN ATOMS : 11 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) : 100.7 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -40.72000 REMARK 3 B22 (A**2) : 35.40000 REMARK 3 B33 (A**2) : 5.32000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.39 REMARK 3 ESD FROM SIGMAA (A) : 0.52 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.51 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.53 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 12.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.000 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) : 1.930 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.290 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.340 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.600 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 25.00 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : GTN.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : GTN.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3CUN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000047230. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 0.9572 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : SI (111) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13610 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.900 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.8 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.87000 REMARK 200 R SYM (I) : 0.87000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 51.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.50100 REMARK 200 R SYM FOR SHELL (I) : 0.50100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 3CUL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MAGENESIUM FORMATE PH 7.0, 15% REMARK 280 PEG 3000, 1 M LITHIUM CHLORIDE, VAPOR DIFFUSION, TEMPERATURE 295K 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 95.68400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.03800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 95.68400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.03800 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, 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 MSE A 296 REMARK 465 ALA A 297 REMARK 465 VAL A 298 REMARK 465 PRO A 299 REMARK 465 GLU A 300 REMARK 465 THR A 301 REMARK 465 LYS A 393 REMARK 465 MSE B 396 REMARK 465 ALA B 397 REMARK 465 VAL B 398 REMARK 465 PRO B 399 REMARK 465 GLU B 400 REMARK 465 MSE B 492 REMARK 465 LYS B 493 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 ARG A 302 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 317 CG CD CE NZ REMARK 470 ASP A 319 CG OD1 OD2 REMARK 470 LYS A 323 CG CD CE NZ REMARK 470 LYS A 345 CG CD CE NZ REMARK 470 ARG A 365 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 391 CG CD CE NZ REMARK 470 MSE A 392 CG SE CE REMARK 470 THR B 401 OG1 CG2 REMARK 470 ARG B 402 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 415 CG CD CE NZ REMARK 470 LYS B 417 CG CD CE NZ REMARK 470 GLU B 420 CG CD OE1 OE2 REMARK 470 LYS B 423 CG CD CE NZ REMARK 470 GLN B 434 CG CD OE1 NE2 REMARK 470 ARG B 442 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 456 CG CD OE1 OE2 REMARK 470 LYS B 491 CG CD CE NZ 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 GTP C 1 C3' - O3' - P ANGL. DEV. = -20.6 DEGREES REMARK 500 A C 9 C2' - C3' - O3' ANGL. DEV. = 12.9 DEGREES REMARK 500 A C 9 C4' - C3' - C2' ANGL. DEV. = 6.1 DEGREES REMARK 500 U C 32 N1 - C1' - C2' ANGL. DEV. = 8.0 DEGREES REMARK 500 U C 53 C2' - C3' - O3' ANGL. DEV. = 14.2 DEGREES REMARK 500 G D 102 O3' - P - O5' ANGL. DEV. = -22.1 DEGREES REMARK 500 G D 102 O3' - P - OP1 ANGL. DEV. = 9.8 DEGREES REMARK 500 PRO A 303 C - N - CA ANGL. DEV. = 11.3 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 PRO A 303 154.84 -42.19 REMARK 500 ASN A 304 137.97 -174.00 REMARK 500 ASN A 311 40.71 74.07 REMARK 500 LYS A 318 -73.65 -52.17 REMARK 500 ASP A 337 161.10 172.21 REMARK 500 GLN A 368 108.32 -42.54 REMARK 500 ASP A 374 40.12 73.85 REMARK 500 TYR A 381 166.20 -49.25 REMARK 500 ASP A 387 -63.37 -18.77 REMARK 500 ARG B 402 96.07 60.05 REMARK 500 ASN B 411 52.06 87.14 REMARK 500 ASN B 413 103.90 -42.38 REMARK 500 LYS B 418 -70.92 -21.28 REMARK 500 ASP B 437 155.44 177.78 REMARK 500 SER B 443 -178.12 -55.83 REMARK 500 ASN B 462 -74.71 -43.62 REMARK 500 LEU B 464 -78.09 -59.06 REMARK 500 ARG B 465 -59.59 -28.95 REMARK 500 SER B 466 -72.01 -76.59 REMARK 500 PHE B 470 142.79 -35.81 REMARK 500 PHE B 472 93.63 -167.07 REMARK 500 ASP B 474 -11.12 79.69 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 D 166 0.05 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 MG D 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U D 170 OP2 REMARK 620 2 U D 171 O4 96.8 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO B 514 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CUL RELATED DB: PDB REMARK 900 AMINOACYL-TRNA SYNTHETASE RIBOZYME DBREF 3CUN A 301 393 UNP P09012 SNRPA_HUMAN 1 98 DBREF 3CUN B 400 493 UNP P09012 SNRPA_HUMAN 1 98 DBREF 3CUN C 1 92 PDB 3CUN 3CUN 1 92 DBREF 3CUN D 101 192 PDB 3CUN 3CUN 101 192 SEQADV 3CUN HIS A 326 UNP P09012 TYR 31 ENGINEERED MUTATION SEQADV 3CUN ARG A 331 UNP P09012 GLN 36 ENGINEERED MUTATION SEQADV 3CUN HIS B 426 UNP P09012 TYR 31 ENGINEERED MUTATION SEQADV 3CUN ARG B 431 UNP P09012 GLN 36 ENGINEERED MUTATION SEQRES 1 C 92 GTP G A U G G C G A A A G C SEQRES 2 C 92 C A U U U C C G C A G G C SEQRES 3 C 92 C C C A U U G C A C U C C SEQRES 4 C 92 G G G G U A U U G G C G U SEQRES 5 C 92 U A G G U G G U G G U A C SEQRES 6 C 92 G A G G U U C G A A U C C SEQRES 7 C 92 U C G U A C C G C A G C C SEQRES 8 C 92 A SEQRES 1 D 92 GTP G A U G G C G A A A G C SEQRES 2 D 92 C A U U U C C G C A G G C SEQRES 3 D 92 C C C A U U G C A C U C C SEQRES 4 D 92 G G G G U A U U G G C G U SEQRES 5 D 92 U A G G U G G U G G U A C SEQRES 6 D 92 G A G G U U C G A A U C C SEQRES 7 D 92 U C G U A C C G C A G C C SEQRES 8 D 92 A SEQRES 1 A 98 MSE ALA VAL PRO GLU THR ARG PRO ASN HIS THR ILE TYR SEQRES 2 A 98 ILE ASN ASN LEU ASN GLU LYS ILE LYS LYS ASP GLU LEU SEQRES 3 A 98 LYS LYS SER LEU HIS ALA ILE PHE SER ARG PHE GLY GLN SEQRES 4 A 98 ILE LEU ASP ILE LEU VAL SER ARG SER LEU LYS MSE ARG SEQRES 5 A 98 GLY GLN ALA PHE VAL ILE PHE LYS GLU VAL SER SER ALA SEQRES 6 A 98 THR ASN ALA LEU ARG SER MSE GLN GLY PHE PRO PHE TYR SEQRES 7 A 98 ASP LYS PRO MSE ARG ILE GLN TYR ALA LYS THR ASP SER SEQRES 8 A 98 ASP ILE ILE ALA LYS MSE LYS SEQRES 1 B 98 MSE ALA VAL PRO GLU THR ARG PRO ASN HIS THR ILE TYR SEQRES 2 B 98 ILE ASN ASN LEU ASN GLU LYS ILE LYS LYS ASP GLU LEU SEQRES 3 B 98 LYS LYS SER LEU HIS ALA ILE PHE SER ARG PHE GLY GLN SEQRES 4 B 98 ILE LEU ASP ILE LEU VAL SER ARG SER LEU LYS MSE ARG SEQRES 5 B 98 GLY GLN ALA PHE VAL ILE PHE LYS GLU VAL SER SER ALA SEQRES 6 B 98 THR ASN ALA LEU ARG SER MSE GLN GLY PHE PRO PHE TYR SEQRES 7 B 98 ASP LYS PRO MSE ARG ILE GLN TYR ALA LYS THR ASP SER SEQRES 8 B 98 ASP ILE ILE ALA LYS MSE LYS MODRES 3CUN GTP C 1 G GUANOSINE-5'-TRIPHOSPHATE MODRES 3CUN GTP D 101 G GUANOSINE-5'-TRIPHOSPHATE MODRES 3CUN MSE A 346 MET SELENOMETHIONINE MODRES 3CUN MSE A 367 MET SELENOMETHIONINE MODRES 3CUN MSE A 377 MET SELENOMETHIONINE MODRES 3CUN MSE A 392 MET SELENOMETHIONINE MODRES 3CUN MSE B 446 MET SELENOMETHIONINE MODRES 3CUN MSE B 467 MET SELENOMETHIONINE MODRES 3CUN MSE B 477 MET SELENOMETHIONINE HET GTP C 1 32 HET GTP D 101 32 HET MSE A 346 8 HET MSE A 367 8 HET MSE A 377 8 HET MSE A 392 5 HET MSE B 446 8 HET MSE B 467 8 HET MSE B 477 8 HET MG C 501 1 HET MG C 503 1 HET MG C 506 1 HET MG C 507 1 HET MG C 510 1 HET K C 511 1 HET MG D 502 1 HET MG D 504 1 HET MG D 512 1 HET MG D 513 1 HET CO B 514 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM CO COBALT (II) ION FORMUL 1 GTP 2(C10 H16 N5 O14 P3) FORMUL 3 MSE 7(C5 H11 N O2 SE) FORMUL 5 MG 9(MG 2+) FORMUL 10 K K 1+ FORMUL 15 CO CO 2+ HELIX 1 1 LYS A 317 SER A 330 1 14 HELIX 2 2 ARG A 331 GLY A 333 5 3 HELIX 3 3 GLU A 356 GLN A 368 1 13 HELIX 4 4 SER A 386 MSE A 392 1 7 HELIX 5 5 LYS B 417 SER B 430 1 14 HELIX 6 6 GLU B 456 GLN B 468 1 13 HELIX 7 7 SER B 486 LYS B 491 1 6 SHEET 1 A 4 ILE A 335 VAL A 340 0 SHEET 2 A 4 ALA A 350 PHE A 354 -1 O ILE A 353 N ASP A 337 SHEET 3 A 4 THR A 306 ASN A 310 -1 N ILE A 309 O ALA A 350 SHEET 4 A 4 ARG A 378 TYR A 381 -1 O GLN A 380 N TYR A 308 SHEET 1 B 4 ILE B 435 LEU B 439 0 SHEET 2 B 4 GLN B 449 PHE B 454 -1 O ILE B 453 N ASP B 437 SHEET 3 B 4 THR B 406 ASN B 410 -1 N ILE B 409 O ALA B 450 SHEET 4 B 4 ARG B 478 TYR B 481 -1 O GLN B 480 N TYR B 408 SHEET 1 C 2 PRO B 471 PHE B 472 0 SHEET 2 C 2 LYS B 475 PRO B 476 -1 O LYS B 475 N PHE B 472 LINK O3' GTP C 1 P G C 2 1555 1555 1.59 LINK O3' GTP D 101 P G D 102 1555 1555 1.61 LINK C LYS A 345 N MSE A 346 1555 1555 1.32 LINK C MSE A 346 N ARG A 347 1555 1555 1.33 LINK C SER A 366 N MSE A 367 1555 1555 1.33 LINK C MSE A 367 N GLN A 368 1555 1555 1.33 LINK C PRO A 376 N MSE A 377 1555 1555 1.32 LINK C MSE A 377 N ARG A 378 1555 1555 1.32 LINK C LYS A 391 N MSE A 392 1555 1555 1.33 LINK C LYS B 445 N MSE B 446 1555 1555 1.33 LINK C MSE B 446 N ARG B 447 1555 1555 1.32 LINK C SER B 466 N MSE B 467 1555 1555 1.33 LINK C MSE B 467 N GLN B 468 1555 1555 1.32 LINK C PRO B 476 N MSE B 477 1555 1555 1.32 LINK C MSE B 477 N ARG B 478 1555 1555 1.33 LINK O2B GTP C 1 MG MG C 507 1555 1555 1.96 LINK N1 U C 17 K K C 511 1555 1555 2.80 LINK OP2 C D 129 MG MG D 513 1555 1555 2.09 LINK OP2 U D 170 MG MG D 504 1555 1555 2.27 LINK O4 U D 171 MG MG D 504 1555 1555 1.97 SITE 1 AC4 2 HIS B 426 ILE B 435 CRYST1 191.368 48.076 90.645 90.00 93.50 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 0.005226 0.000000 0.000320 0.00000 SCALE2 0.000000 0.020800 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011053 0.00000 HETATM 1 PG GTP C 1 -46.152 0.810 26.722 1.00139.18 P HETATM 2 O1G GTP C 1 -44.845 0.166 27.056 1.00139.05 O HETATM 3 O2G GTP C 1 -46.739 1.517 28.048 1.00135.48 O HETATM 4 O3G GTP C 1 -47.180 -0.321 26.208 1.00139.65 O HETATM 5 O3B GTP C 1 -45.918 1.982 25.507 1.00128.97 O HETATM 6 PB GTP C 1 -45.332 1.255 24.087 1.00118.67 P HETATM 7 O1B GTP C 1 -44.054 0.556 24.371 1.00115.69 O HETATM 8 O2B GTP C 1 -46.422 0.208 23.522 1.00118.13 O HETATM 9 O3A GTP C 1 -45.100 2.434 22.998 1.00116.26 O HETATM 10 PA GTP C 1 -44.562 1.817 21.607 1.00110.62 P HETATM 11 O1A GTP C 1 -43.280 1.113 21.795 1.00108.47 O HETATM 12 O2A GTP C 1 -45.685 0.814 21.020 1.00109.03 O HETATM 13 O5' GTP C 1 -44.326 2.994 20.568 1.00109.21 O HETATM 14 C5' GTP C 1 -45.077 4.034 20.991 1.00 94.38 C HETATM 15 C4' GTP C 1 -45.933 4.956 20.110 1.00 95.39 C HETATM 16 O4' GTP C 1 -45.327 5.083 18.788 1.00 96.47 O HETATM 17 C3' GTP C 1 -47.347 4.452 19.855 1.00 95.29 C HETATM 18 O3' GTP C 1 -48.224 4.947 20.850 1.00 94.85 O HETATM 19 C2' GTP C 1 -47.666 5.022 18.479 1.00 92.68 C HETATM 20 O2' GTP C 1 -48.043 6.382 18.520 1.00 90.55 O HETATM 21 C1' GTP C 1 -46.312 4.886 17.782 1.00 93.43 C HETATM 22 N9 GTP C 1 -46.086 3.562 17.202 1.00 92.41 N HETATM 23 C8 GTP C 1 -44.992 2.765 17.412 1.00 90.48 C HETATM 24 N7 GTP C 1 -45.085 1.603 16.831 1.00 92.18 N HETATM 25 C5 GTP C 1 -46.308 1.638 16.177 1.00 92.10 C HETATM 26 C6 GTP C 1 -46.957 0.651 15.379 1.00 91.43 C HETATM 27 O6 GTP C 1 -46.568 -0.490 15.089 1.00 91.54 O HETATM 28 N1 GTP C 1 -48.181 1.102 14.905 1.00 89.87 N HETATM 29 C2 GTP C 1 -48.717 2.335 15.158 1.00 90.13 C HETATM 30 N2 GTP C 1 -49.905 2.579 14.605 1.00 89.65 N HETATM 31 N3 GTP C 1 -48.129 3.261 15.900 1.00 94.08 N HETATM 32 C4 GTP C 1 -46.933 2.847 16.377 1.00 92.56 C