PDB Short entry for 1ZZN HEADER STRUCTURAL PROTEIN/RNA 14-JUN-05 1ZZN TITLE CRYSTAL STRUCTURE OF A GROUP I INTRON/TWO EXON COMPLEX THAT INCLUDES TITLE 2 ALL CATALYTIC METAL ION LIGANDS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 197-MER; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: GROUP I INTRON; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*AP*GP*AP*CP COMPND 8 *GP*GP*CP*C)-3'; COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: GROUP I INTRON, 3'-EXON; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-R(*CP*AP*(5MU))-3'; COMPND 14 CHAIN: D; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: 5'-EXON, U-1DEOXY5MU; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A RNA BINDING DOMAIN; COMPND 19 CHAIN: A; COMPND 20 FRAGMENT: RRM 1; COMPND 21 SYNONYM: U1 SNRNP PROTEIN A, U1A PROTEIN, U1-A; COMPND 22 ENGINEERED: YES; COMPND 23 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA WAS IS TRANSCRIBED BY T7 RNA POLYMERASE. SEQUENCE SOURCE 4 FROM AZOARCUS GROUP I INTRON; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: SOLID PHASE SYTHESIS. SEQUENCE FROM AZOARCUS INTRON SOURCE 8 AND EXON SEQUENCE.; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: SOLID PHASE SYNTHESIS. SEQUENCE FROM AZOARCUS GROUP I SOURCE 12 INTRON 5'-EXON SEQUENCE.; 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 BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 20 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PET11 KEYWDS RNA STRUCTURE, RIBOZYME, SELF-SPLICING INTRON, AZOARCUS, TWO-METAL- KEYWDS 2 ION MECHANISM, STRUCTURAL PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.R.STAHLEY,S.A.STROBEL REVDAT 6 23-AUG-23 1ZZN 1 REMARK REVDAT 5 20-OCT-21 1ZZN 1 REMARK SEQADV LINK REVDAT 4 11-OCT-17 1ZZN 1 REMARK REVDAT 3 24-FEB-09 1ZZN 1 VERSN REVDAT 2 13-SEP-05 1ZZN 1 JRNL REVDAT 1 30-AUG-05 1ZZN 0 JRNL AUTH M.R.STAHLEY,S.A.STROBEL JRNL TITL STRUCTURAL EVIDENCE FOR A TWO-METAL-ION MECHANISM OF GROUP I JRNL TITL 2 INTRON SPLICING. JRNL REF SCIENCE V. 309 1587 2005 JRNL REFN ISSN 0036-8075 JRNL PMID 16141079 JRNL DOI 10.1126/SCIENCE.1114994 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.L.ADAMS,M.R.STAHLEY,A.B.KOSEK,J.WANG,S.A.STROBEL REMARK 1 TITL CRYSTAL STRUCTURE OF A SELF-SPLICING GROUP I INTRON WITH REMARK 1 TITL 2 BOTH EXONS REMARK 1 REF NATURE V. 430 45 2004 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 15175762 REMARK 1 DOI 10.1038/NATURE02642 REMARK 1 REFERENCE 2 REMARK 1 AUTH P.L.ADAMS,M.R.STAHLEY,M.L.GILL,A.B.KOSEK,J.WANG,S.A.STROBEL REMARK 1 TITL CRYSTAL STRUCTURE OF A GROUP I INTRON SPLICING INTERMEDIATE REMARK 1 REF RNA V. 10 1867 2004 REMARK 1 REFN ISSN 1355-8382 REMARK 1 PMID 15547134 REMARK 1 DOI 10.1261/RNA.7140504 REMARK 1 REFERENCE 3 REMARK 1 AUTH T.R.CECH,A.J.ZAUG,P.J.GRABOWASKI REMARK 1 TITL IN VITRO SPLICING OF THE RIBOSOMAL RNA PRECURSOR OF REMARK 1 TITL 2 TETRAHYMENA: INVOLVEMENT OF A GUANOSINE NUCLEOTIDE IN THE REMARK 1 TITL 3 EXCISION OF INTERVENING SEQUENCE REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 27 487 1981 REMARK 1 REFN ISSN 0092-8674 REMARK 1 PMID 6101203 REMARK 1 DOI 10.1016/0092-8674(81)90390-1 REMARK 1 REFERENCE 4 REMARK 1 AUTH B.REINHOLD-HUREK,D.A.SHUB REMARK 1 TITL SELF-SPLICING INTRON IN TRNA GENES OF WIDELY DIVERGENT REMARK 1 TITL 2 BACTERIA REMARK 1 REF NATURE V. 357 173 1992 REMARK 1 REFN ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. 3.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : CNS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 198973.330 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 84.8 REMARK 3 NUMBER OF REFLECTIONS : 18224 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) : 0.269 REMARK 3 FREE R VALUE : 0.307 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.400 REMARK 3 FREE R VALUE TEST SET COUNT : 801 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 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) : 3.37 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.58 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2379 REMARK 3 BIN R VALUE (WORKING SET) : 0.3810 REMARK 3 BIN FREE R VALUE : 0.4110 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 109 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.039 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 775 REMARK 3 NUCLEIC ACID ATOMS : 4768 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 54 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) : 5.88000 REMARK 3 B22 (A**2) : 5.88000 REMARK 3 B33 (A**2) : -11.76000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.51 REMARK 3 ESD FROM SIGMAA (A) : 0.69 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) : 0.60 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.69 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 15.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.710 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) : 2.460 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.610 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.000 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.180 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.05 REMARK 3 BSOL : 10.00 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 : RNA_DNA_MODIFIED.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM 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_MODIFIED.TOP 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: EXPERIMENTAL PHASES FROM 1U6B STRUCTURE REMARK 3 WERE USED FOLLOWED BY MAXIMUM LIKELIHOOD REFINEMENT. OCTAHEDRAL REMARK 3 PARAMETERS FOR MG2+ COORDINATION WERE USED TO REFINE M1 AND M2 REMARK 3 IN THE FINAL ROUND OF REFINEMENT ONLY REMARK 4 REMARK 4 1ZZN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000033309. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20658 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.370 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.100 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 1U6B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, SODIUM CACODYLATE, MAGNESIUM REMARK 280 ACETATE, POTASSIUM CHLORIDE, COBALT HEXIMINE, PH 6.8, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 2 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 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 123.20000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 61.60000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 184.80000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 123.20000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 184.80000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 61.60000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: B, C, D, A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 VAL A 3 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 5MU D 1 O2' REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 G B 170 C5' G B 170 C4' -0.044 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 B 10 O4' - C4' - C3' ANGL. DEV. = -6.5 DEGREES REMARK 500 U B 11 N1 - C1' - C2' ANGL. DEV. = -6.7 DEGREES REMARK 500 C B 31 O3' - P - OP2 ANGL. DEV. = 6.8 DEGREES REMARK 500 C B 33 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 G B 37 N9 - C1' - C2' ANGL. DEV. = 10.9 DEGREES REMARK 500 G B 83 O5' - P - OP2 ANGL. DEV. = -5.9 DEGREES REMARK 500 G B 107 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 C B 112 N1 - C1' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 G B 128 C5' - C4' - C3' ANGL. DEV. = 9.9 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 8 147.86 -29.42 REMARK 500 ASN A 9 128.77 -178.51 REMARK 500 HIS A 10 5.07 -56.41 REMARK 500 ASN A 16 94.86 64.34 REMARK 500 GLU A 19 -25.69 -38.85 REMARK 500 LYS A 20 -28.12 -39.79 REMARK 500 SER A 29 32.79 -72.14 REMARK 500 LEU A 30 -41.82 -157.42 REMARK 500 HIS A 31 -43.86 -28.90 REMARK 500 SER A 35 82.18 -166.32 REMARK 500 GLN A 39 -177.81 -63.05 REMARK 500 ASP A 42 136.02 179.95 REMARK 500 ILE A 43 71.02 -103.02 REMARK 500 LEU A 49 1.40 -56.25 REMARK 500 PHE A 59 -152.06 -106.51 REMARK 500 LYS A 60 -34.80 -135.13 REMARK 500 SER A 71 12.84 -58.98 REMARK 500 MET A 72 -14.40 -157.51 REMARK 500 PRO A 76 100.29 -59.61 REMARK 500 PRO A 81 -156.08 -48.47 REMARK 500 GLN A 85 130.90 -177.28 REMARK 500 TYR A 86 152.33 -49.28 REMARK 500 ASP A 90 106.02 -40.85 REMARK 500 SER A 91 146.05 -23.27 REMARK 500 ASP A 92 33.97 -68.51 REMARK 500 MET A 97 -73.17 -79.21 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 B 19 0.05 SIDE CHAIN REMARK 500 U B 62 0.08 SIDE CHAIN REMARK 500 G B 135 0.06 SIDE CHAIN REMARK 500 A B 161 0.11 SIDE CHAIN REMARK 500 A B 168 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 B 3 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B 173 OP2 REMARK 620 2 A B 174 OP2 73.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 4 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 149 O2' REMARK 620 2 G B 151 N7 93.1 REMARK 620 3 G B 151 O6 71.2 77.5 REMARK 620 4 G B 152 O6 137.5 77.5 66.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1015 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C B 88 OP1 REMARK 620 2 G B 170 OP1 84.3 REMARK 620 3 A B 172 OP1 90.8 91.8 REMARK 620 4 A C 1 OP2 98.7 175.3 91.8 REMARK 620 5 5MU D 1 O3' 86.0 90.5 175.8 86.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1016 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 127 OP2 REMARK 620 2 C B 171 OP2 106.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 207 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 128 OP1 REMARK 620 2 A B 172 OP2 91.0 REMARK 620 3 A C 1 OP2 175.8 90.1 REMARK 620 4 G C 206 O3' 98.7 168.2 80.7 REMARK 620 5 G C 206 O2' 84.6 95.1 99.4 79.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1015 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1016 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1017 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U6B RELATED DB: PDB REMARK 900 GROUP I INTRON STRUCTURE WITH BOTH EXONS. DG206, DA205, DA+1 REMARK 900 SUBSTITUTIONS IN PDB 1U6B ARE RIBOSE IN THIS NEW STRUCTURE. REMARK 999 REMARK 999 SEQUENCE REMARK 999 NUCLEOTIDES 1001B TO 1014B BELONG TO AN ENGINEERED REMARK 999 U1A LOOP AND ARE INSERTED BETWEEN GUA-107B AND REMARK 999 CYT-112B. THERE ARE NO NUCLEOTIDES BETWEEN GUA-1B REMARK 999 AND GUA-5B DUE TO A CLONING DESIGN. CHAINS B AND REMARK 999 C ARE TWO PARTS OF THE ORIGINAL ONE INTRON SEQUENCE REMARK 999 BECAUSE OF AN EXPERIMENTAL DESIGN. THE FIRST THREE REMARK 999 RESIDUES IN U1A PROTEIN WERE MISSING IN THE STRUCTURE. DBREF 1ZZN A 2 98 UNP P09012 SNRPA_HUMAN 1 97 DBREF 1ZZN B 1 190 PDB 1ZZN 1ZZN 1 190 DBREF 1ZZN C 191 6 PDB 1ZZN 1ZZN 191 6 DBREF 1ZZN D 3 1 PDB 1ZZN 1ZZN 3 1 SEQADV 1ZZN MET A 1 UNP P09012 INITIATING METHIONINE SEQADV 1ZZN HIS A 31 UNP P09012 TYR 30 ENGINEERED MUTATION SEQADV 1ZZN ARG A 36 UNP P09012 GLN 35 ENGINEERED MUTATION SEQRES 1 B 197 GTP G C C G U G U G C C U U SEQRES 2 B 197 G C G C C G G G A A A C C SEQRES 3 B 197 A C G C A A G G G A U G G SEQRES 4 B 197 U G U C A A A U U C G G C SEQRES 5 B 197 G A A A C C U A A G C G C SEQRES 6 B 197 C C G C C C G G G C G U A SEQRES 7 B 197 U G G C A A C G C C G A G SEQRES 8 B 197 C C A A G C U U C G C A G SEQRES 9 B 197 C C A U U G C A C U C C G SEQRES 10 B 197 G C U G C G A U G A A G G SEQRES 11 B 197 U G U A G A G A C U A G A SEQRES 12 B 197 C G G C A C C C A C C U A SEQRES 13 B 197 A G G C A A A C G C U A U SEQRES 14 B 197 G G U G A A G G C A U A G SEQRES 15 B 197 U C C A G G G A G U G G C SEQRES 16 B 197 G A23 SEQRES 1 C 22 A A G C C A C A C A A A C SEQRES 2 C 22 C A G A C G G C C SEQRES 1 D 3 C A 5MU SEQRES 1 A 98 MET 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 MET 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 MET GLN GLY PHE PRO PHE TYR SEQRES 7 A 98 ASP LYS PRO MET ARG ILE GLN TYR ALA LYS THR ASP SER SEQRES 8 A 98 ASP ILE ILE ALA LYS MET LYS MODRES 1ZZN GTP B 1 G GUANOSINE-5'-TRIPHOSPHATE MODRES 1ZZN A23 B 190 A MODRES 1ZZN 5MU D 1 U 5-METHYLURIDINE 5'-MONOPHOSPHATE HET GTP B 1 32 HET A23 B 190 25 HET 5MU D 1 21 HET MG B1015 1 HET MG B 3 1 HET K B 4 1 HET MG B1016 1 HET MG B1017 1 HET MG C 207 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM A23 ADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE HETNAM 5MU 5-METHYLURIDINE 5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 1 A23 C10 H13 N5 O9 P2 FORMUL 3 5MU C10 H15 N2 O9 P FORMUL 5 MG 5(MG 2+) FORMUL 7 K K 1+ FORMUL 11 HOH *54(H2 O) HELIX 1 1 LYS A 22 ALA A 32 1 11 HELIX 2 2 GLU A 61 MET A 72 1 12 HELIX 3 3 PRO A 76 LYS A 80 5 5 HELIX 4 4 ILE A 93 LYS A 98 1 6 SHEET 1 A 3 THR A 11 ASN A 15 0 SHEET 2 A 3 GLN A 54 ILE A 58 -1 O VAL A 57 N ILE A 12 SHEET 3 A 3 LEU A 44 SER A 46 -1 N LEU A 44 O PHE A 56 LINK O3' GTP B 1 P G B 5 1555 1555 1.63 LINK O3' G B 189 P A23 B 190 1555 1555 1.62 LINK P 5MU D 1 O3' A D 2 1555 1555 1.59 LINK P A D 2 O3' C D 3 1555 1555 1.60 LINK MG MG B 3 OP2 U B 173 1555 1555 2.14 LINK MG MG B 3 OP2 A B 174 1555 1555 1.90 LINK K K B 4 O2' A B 149 1555 1555 2.40 LINK K K B 4 N7 G B 151 1555 1555 2.50 LINK K K B 4 O6 G B 151 1555 1555 2.33 LINK K K B 4 O6 G B 152 1555 1555 2.78 LINK OP1 C B 88 MG MG B1015 1555 1555 2.19 LINK OP2 A B 127 MG MG B1016 1555 1555 2.37 LINK OP1 G B 128 MG MG C 207 1555 1555 2.02 LINK OP1 G B 170 MG MG B1015 1555 1555 2.11 LINK OP2 C B 171 MG MG B1016 1555 1555 2.21 LINK OP1 A B 172 MG MG B1015 1555 1555 2.17 LINK OP2 A B 172 MG MG C 207 1555 1555 2.18 LINK MG MG B1015 OP2 A C 1 1555 1555 2.17 LINK MG MG B1015 O3' 5MU D 1 1555 1555 2.08 LINK MG MG B1017 O HOH B1065 1555 1555 2.20 LINK OP2 A C 1 MG MG C 207 1555 1555 1.95 LINK O3' G C 206 MG MG C 207 1555 1555 2.08 LINK O2' G C 206 MG MG C 207 1555 1555 2.16 SITE 1 AC1 5 C B 88 G B 170 A B 172 A C 1 SITE 2 AC1 5 5MU D 1 SITE 1 AC2 5 A B 127 G B 128 A B 172 A C 1 SITE 2 AC2 5 G C 206 SITE 1 AC3 3 A B 172 U B 173 A B 174 SITE 1 AC4 6 A B 149 A B 150 G B 151 G B 152 SITE 2 AC4 6 C B 159 U B 160 SITE 1 AC5 5 U B 124 G B 125 U B 126 A B 127 SITE 2 AC5 5 C B 171 SITE 1 AC6 2 U B 15 HOH B1065 CRYST1 108.466 108.466 246.400 90.00 90.00 90.00 P 41 2 2 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 0.009219 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009219 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004058 0.00000 HETATM 1 PG GTP B 1 66.047 74.777 48.752 1.00201.87 P HETATM 2 O1G GTP B 1 65.096 74.402 49.836 1.00202.42 O HETATM 3 O2G GTP B 1 66.950 75.787 48.575 1.00201.50 O HETATM 4 O3G GTP B 1 65.513 74.794 47.410 1.00200.60 O HETATM 5 O3B GTP B 1 67.453 74.292 49.346 1.00197.81 O HETATM 6 PB GTP B 1 68.160 74.877 50.714 1.00194.05 P HETATM 7 O1B GTP B 1 69.356 74.923 49.875 1.00194.36 O HETATM 8 O2B GTP B 1 67.230 73.863 51.291 1.00194.36 O HETATM 9 O3A GTP B 1 69.100 74.162 51.828 1.00186.33 O HETATM 10 PA GTP B 1 68.872 73.243 53.174 1.00179.01 P HETATM 11 O1A GTP B 1 69.701 73.672 54.173 1.00179.28 O HETATM 12 O2A GTP B 1 67.437 73.098 53.516 1.00180.60 O HETATM 13 O5' GTP B 1 69.541 71.787 52.829 1.00175.28 O HETATM 14 C5' GTP B 1 70.964 72.007 52.484 1.00167.86 C HETATM 15 C4' GTP B 1 72.092 72.045 53.528 1.00162.72 C HETATM 16 O4' GTP B 1 73.271 72.637 52.906 1.00158.04 O HETATM 17 C3' GTP B 1 71.886 72.891 54.788 1.00161.62 C HETATM 18 O3' GTP B 1 72.526 72.335 55.972 1.00161.56 O HETATM 19 C2' GTP B 1 72.299 74.285 54.325 1.00159.85 C HETATM 20 O2' GTP B 1 72.554 75.166 55.412 1.00159.90 O HETATM 21 C1' GTP B 1 73.489 73.944 53.425 1.00155.62 C HETATM 22 N9 GTP B 1 73.820 74.818 52.303 1.00148.28 N HETATM 23 C8 GTP B 1 73.017 75.202 51.254 1.00146.58 C HETATM 24 N7 GTP B 1 73.677 75.809 50.307 1.00143.86 N HETATM 25 C5 GTP B 1 74.977 75.873 50.787 1.00142.33 C HETATM 26 C6 GTP B 1 76.140 76.395 50.200 1.00141.66 C HETATM 27 O6 GTP B 1 76.272 76.908 49.091 1.00143.61 O HETATM 28 N1 GTP B 1 77.241 76.265 51.039 1.00139.73 N HETATM 29 C2 GTP B 1 77.222 75.698 52.284 1.00137.71 C HETATM 30 N2 GTP B 1 78.391 75.673 52.949 1.00138.70 N HETATM 31 N3 GTP B 1 76.144 75.194 52.838 1.00137.28 N HETATM 32 C4 GTP B 1 75.066 75.311 52.038 1.00142.45 C