PDB Short entry for 3CUL HEADER RNA/RNA BINDING 16-APR-08 3CUL TITLE AMINOACYL-TRNA SYNTHETASE RIBOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (92-MER); COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: FLEXIZYME; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (92-MER); COMPND 8 CHAIN: D; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: FLEXIZYME; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A; COMPND 13 CHAIN: A, B; COMPND 14 FRAGMENT: UNP RESIDUES 1-98; COMPND 15 SYNONYM: U1 SNRNP PROTEIN A, U1A PROTEIN, U1-A; COMPND 16 ENGINEERED: YES; COMPND 17 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 EXPRESSION_SYSTEM: CELL-FREE SYNTHESIS; SOURCE 3 MOL_ID: 2; SOURCE 4 EXPRESSION_SYSTEM: CELL-FREE SYNTHESIS; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 GENE: SNRPA; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI KEYWDS CATALYTIC RNA RIBOZYME ARS, RNA-RNA BINDING COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.XIAO,H.MURAKAMI,H.SUGA,A.R.FERRE-D'AMARE REVDAT 4 20-OCT-21 3CUL 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 3CUL 1 VERSN REVDAT 2 05-AUG-08 3CUL 1 JRNL REVDAT 1 24-JUN-08 3CUL 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. 2.80 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1429168.810 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 36041 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) : 0.227 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4011 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3109 REMARK 3 BIN R VALUE (WORKING SET) : 0.4600 REMARK 3 BIN FREE R VALUE : 0.5290 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 344 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.029 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1394 REMARK 3 NUCLEIC ACID ATOMS : 3929 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 10 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 0.44 REMARK 3 ESD FROM SIGMAA (A) : 0.65 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) : 0.54 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.73 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 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) : 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 : 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 3CUL 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_1000047228. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 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) : 0.9795, 0.9792, 1.2157 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL 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 : 36041 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.37200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MAGNESIUM FORMATE, 15% PEG REMARK 280 3000, 1 M LITHIUM CHLORIDE, PH 7.0, VAPOR DIFFUSION, TEMPERATURE REMARK 280 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 96.07550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.36250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 96.07550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.36250 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 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 U C 60 N1 C2 O2 N3 C4 O4 C5 REMARK 470 U C 60 C6 REMARK 470 THR A 301 OG1 CG2 REMARK 470 ARG A 302 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 315 CD CE NZ REMARK 470 LYS A 317 CG CD CE NZ REMARK 470 ASP A 319 CG OD1 OD2 REMARK 470 GLU A 320 CG CD OE1 OE2 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 ASP B 419 CG OD1 OD2 REMARK 470 GLU B 420 CG CD OE1 OE2 REMARK 470 LYS B 423 CG CD CE NZ REMARK 470 ARG B 442 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 455 CE NZ REMARK 470 GLU B 456 CG CD OE1 OE2 REMARK 470 ARG B 478 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 483 CG CD CE NZ REMARK 470 LYS B 491 CG CD CE NZ 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 GTP C 1 O3' G C 2 P -0.123 REMARK 500 G C 2 O3' A C 3 P -0.114 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 C 2 O3' - P - OP2 ANGL. DEV. = 33.2 DEGREES REMARK 500 G C 2 O3' - P - OP1 ANGL. DEV. = -45.0 DEGREES REMARK 500 C C 34 N1 - C1' - C2' ANGL. DEV. = 11.4 DEGREES REMARK 500 U C 53 C2' - C3' - O3' ANGL. DEV. = 13.6 DEGREES REMARK 500 C D 134 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 PRO A 303 127.09 -24.74 REMARK 500 ASN A 311 35.17 73.63 REMARK 500 ARG A 331 30.13 -98.97 REMARK 500 ASP A 337 148.49 -176.04 REMARK 500 PHE A 372 -32.83 -141.38 REMARK 500 TYR A 373 54.11 -171.46 REMARK 500 ASP A 385 151.84 -43.85 REMARK 500 ASN B 411 39.11 75.17 REMARK 500 LEU B 464 -70.94 -46.12 REMARK 500 PHE B 472 106.86 -171.16 REMARK 500 ASP B 474 0.75 81.03 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 C 30 0.06 SIDE CHAIN REMARK 500 G D 108 0.07 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 C 507 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GTP C 1 O2B REMARK 620 2 HOH C 609 O 103.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 505 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U C 70 OP2 REMARK 620 2 U C 71 O4 123.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 602 O REMARK 620 2 HOH C 603 O 162.1 REMARK 620 N 1 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 96.5 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 C 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K C 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CUN RELATED DB: PDB REMARK 900 AMINOACYL-TRNA SYNTHETASE RIBOZYME DBREF 3CUL A 300 391 UNP P09012 SNRPA_HUMAN 1 98 DBREF 3CUL B 400 491 UNP P09012 SNRPA_HUMAN 1 98 DBREF 3CUL C 1 92 PDB 3CUL 3CUL 1 92 DBREF 3CUL D 101 192 PDB 3CUL 3CUL 101 192 SEQADV 3CUL HIS A 326 UNP P09012 TYR 31 ENGINEERED MUTATION SEQADV 3CUL ARG A 331 UNP P09012 GLN 36 ENGINEERED MUTATION SEQADV 3CUL HIS B 426 UNP P09012 TYR 31 ENGINEERED MUTATION SEQADV 3CUL 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 G 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 3CUL GTP C 1 G GUANOSINE-5'-TRIPHOSPHATE MODRES 3CUL MSE A 346 MET SELENOMETHIONINE MODRES 3CUL MSE A 367 MET SELENOMETHIONINE MODRES 3CUL MSE A 377 MET SELENOMETHIONINE MODRES 3CUL MSE A 392 MET SELENOMETHIONINE MODRES 3CUL MSE B 446 MET SELENOMETHIONINE MODRES 3CUL MSE B 467 MET SELENOMETHIONINE MODRES 3CUL MSE B 477 MET SELENOMETHIONINE HET GTP C 1 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 505 1 HET MG C 506 1 HET MG C 507 1 HET MG C 508 1 HET MG C 509 1 HET MG C 510 1 HET K C 511 1 HET MG D 502 1 HET MG D 504 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 3 MSE 7(C5 H11 N O2 SE) FORMUL 5 MG 10(MG 2+) FORMUL 13 K K 1+ FORMUL 16 HOH *10(H2 O) HELIX 1 1 LYS A 317 SER A 330 1 14 HELIX 2 2 GLU A 356 GLN A 368 1 13 HELIX 3 3 SER A 386 MSE A 392 1 7 HELIX 4 4 LYS B 417 SER B 430 1 14 HELIX 5 5 ARG B 431 GLY B 433 5 3 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 VAL B 440 0 SHEET 2 B 4 ALA B 450 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 1.48 LINK C LYS A 345 N MSE A 346 1555 1555 1.33 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 1.33 LINK C SER B 466 N MSE B 467 1555 1555 1.32 LINK C MSE B 467 N GLN B 468 1555 1555 1.33 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 2.14 LINK O1B GTP C 1 MG MG C 510 1555 1555 2.44 LINK OP2 G C 8 MG MG C 509 1555 1555 2.31 LINK OP2 U C 70 MG MG C 505 1555 1555 2.06 LINK O4 U C 71 MG MG C 505 1555 1555 2.02 LINK MG MG C 501 O HOH C 601 1555 1555 1.92 LINK MG MG C 503 O HOH C 602 1555 1555 1.85 LINK MG MG C 503 O HOH C 603 1555 1555 2.05 LINK MG MG C 506 O HOH C 604 1555 1555 2.03 LINK MG MG C 507 O HOH C 609 1555 1555 2.01 LINK OP2 U D 170 MG MG D 504 1555 1555 2.36 LINK O4 U D 171 MG MG D 504 1555 1555 2.04 LINK MG MG D 502 O HOH D 610 1555 1555 2.10 SITE 1 AC1 2 G C 5 HOH C 601 SITE 1 AC2 2 HOH C 602 HOH C 603 SITE 1 AC3 2 U C 70 U C 71 SITE 1 AC4 2 A C 75 HOH C 604 SITE 1 AC5 3 GTP C 1 G C 2 HOH C 609 SITE 1 AC6 1 C C 22 SITE 1 AC7 2 C C 7 G C 8 SITE 1 AC8 2 GTP C 1 C C 13 SITE 1 AC9 2 U C 17 C C 19 SITE 1 BC1 1 HOH D 610 SITE 1 BC2 2 U D 170 U D 171 CRYST1 192.151 48.725 90.515 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 0.005204 0.000000 0.000318 0.00000 SCALE2 0.000000 0.020523 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011069 0.00000 HETATM 1 PG GTP C 1 -46.047 0.044 26.926 1.00110.02 P HETATM 2 O1G GTP C 1 -44.786 -0.415 27.555 1.00107.05 O HETATM 3 O2G GTP C 1 -46.894 0.864 28.021 1.00104.42 O HETATM 4 O3G GTP C 1 -46.902 -1.237 26.433 1.00106.94 O HETATM 5 O3B GTP C 1 -45.727 1.063 25.598 1.00 98.38 O HETATM 6 PB GTP C 1 -44.853 0.300 24.334 1.00 86.98 P HETATM 7 O1B GTP C 1 -43.573 -0.278 24.794 1.00 85.32 O HETATM 8 O2B GTP C 1 -45.764 -0.838 23.664 1.00 89.90 O HETATM 9 O3A GTP C 1 -44.633 1.447 23.243 1.00 90.02 O HETATM 10 PA GTP C 1 -43.781 1.005 21.948 1.00 84.71 P HETATM 11 O1A GTP C 1 -42.408 0.663 22.317 1.00 87.07 O HETATM 12 O2A GTP C 1 -44.478 -0.228 21.179 1.00 86.15 O HETATM 13 O5' GTP C 1 -43.719 2.300 21.050 1.00 89.25 O HETATM 14 C5' GTP C 1 -44.474 3.337 21.475 1.00 74.13 C HETATM 15 C4' GTP C 1 -45.339 4.212 20.586 1.00 72.40 C HETATM 16 O4' GTP C 1 -44.747 4.317 19.265 1.00 75.72 O HETATM 17 C3' GTP C 1 -46.741 3.682 20.347 1.00 75.05 C HETATM 18 O3' GTP C 1 -47.626 4.138 21.347 1.00 81.84 O HETATM 19 C2' GTP C 1 -47.081 4.245 18.977 1.00 74.03 C HETATM 20 O2' GTP C 1 -47.442 5.602 19.020 1.00 71.59 O HETATM 21 C1' GTP C 1 -45.738 4.115 18.266 1.00 74.37 C HETATM 22 N9 GTP C 1 -45.507 2.792 17.688 1.00 76.11 N HETATM 23 C8 GTP C 1 -44.442 1.970 17.969 1.00 78.69 C HETATM 24 N7 GTP C 1 -44.490 0.827 17.342 1.00 79.83 N HETATM 25 C5 GTP C 1 -45.653 0.894 16.593 1.00 80.01 C HETATM 26 C6 GTP C 1 -46.215 -0.049 15.715 1.00 76.54 C HETATM 27 O6 GTP C 1 -45.781 -1.146 15.408 1.00 75.44 O HETATM 28 N1 GTP C 1 -47.402 0.406 15.159 1.00 75.46 N HETATM 29 C2 GTP C 1 -47.973 1.628 15.408 1.00 75.03 C HETATM 30 N2 GTP C 1 -49.124 1.883 14.759 1.00 69.83 N HETATM 31 N3 GTP C 1 -47.450 2.536 16.230 1.00 78.73 N HETATM 32 C4 GTP C 1 -46.295 2.103 16.786 1.00 79.03 C