PDB Short entry for 1VBY HEADER TRANSLATION/RNA 03-MAR-04 1VBY TITLE CRYSTAL STRUCTURE OF THE HEPATITIS DELTA VIRUS GEMONIC RIBOZYME TITLE 2 PRECURSOR, WITH C75U MUTAION, AND MN2+ BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEPATITIS DELTA VIRUS RIBOZYME; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A; COMPND 8 CHAIN: A; COMPND 9 FRAGMENT: U1A_RBD(RESIDUES 1-100); 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 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA OCCURS FROM HAPATITIS DELTA VIRUS PATHOGEN, IN SOURCE 4 VITRO TRANSCRIPTION WITH PUC19; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS HDV, RIBOZYME, RNA, U1A, PRECURSOR, TRANSLATION-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.KE,K.ZHOU,F.DING,J.H.D.CATE,J.A.DOUDNA REVDAT 4 27-DEC-23 1VBY 1 REMARK REVDAT 3 10-NOV-21 1VBY 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1VBY 1 VERSN REVDAT 1 18-MAY-04 1VBY 0 JRNL AUTH A.KE,K.ZHOU,F.DING,J.H.D.CATE,J.A.DOUDNA JRNL TITL A CONFORMATIONAL SWITCH CONTROLS HEPATITIS DELTA VIRUS JRNL TITL 2 RIBOZYME CATALYSIS JRNL REF NATURE V. 429 201 2004 JRNL REFN ISSN 0028-0836 JRNL PMID 15141216 JRNL DOI 10.1038/NATURE02522 REMARK 2 REMARK 2 RESOLUTION. 2.90 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2315411.180 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 9690 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) : 0.239 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 963 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1429 REMARK 3 BIN R VALUE (WORKING SET) : 0.3470 REMARK 3 BIN FREE R VALUE : 0.3690 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 135 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.032 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 762 REMARK 3 NUCLEIC ACID ATOMS : 1552 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 14 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 149.5 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 74.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -12.95000 REMARK 3 B22 (A**2) : -12.95000 REMARK 3 B33 (A**2) : 25.90000 REMARK 3 B12 (A**2) : 2.83000 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) : 0.37 REMARK 3 ESD FROM SIGMAA (A) : 0.58 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) : 0.43 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.61 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 28.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.620 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) : 1.440 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.810 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.500 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.330 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.28 REMARK 3 BSOL : 24.45 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-MULTI-ENDO.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 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1VBY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000006445. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-03 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0781 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10698 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 42.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MNCL2, NACL, MPD, SODIUM CACODYLATE, REMARK 280 SPERMINE-HCL, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 54.29450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 31.34694 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 63.50633 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 54.29450 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 31.34694 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 63.50633 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 54.29450 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 31.34694 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 63.50633 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 54.29450 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 31.34694 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 63.50633 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 54.29450 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 31.34694 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 63.50633 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 54.29450 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 31.34694 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 63.50633 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 62.69389 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 127.01267 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 62.69389 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 127.01267 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 62.69389 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 127.01267 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 62.69389 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 127.01267 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 62.69389 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 127.01267 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 62.69389 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 127.01267 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 G B 98 REMARK 465 A B 99 REMARK 465 U B 173 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 VAL A 3 REMARK 465 GLY A 99 REMARK 465 THR A 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 U B 100 P OP1 OP2 REMARK 470 GLU A 5 CG CD OE1 OE2 REMARK 470 LYS A 20 CG CD CE NZ REMARK 470 LYS A 98 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O4 U B 120 O6 G B 125 2.06 REMARK 500 N3 U B 120 O6 G B 125 2.08 REMARK 500 OP1 C B 121 O2' G B 162 2.13 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 C B 152 C2' - C3' - O3' ANGL. DEV. = 18.8 DEGREES REMARK 500 G B 162 N9 - C1' - C2' ANGL. DEV. = -7.0 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 A 5 173.15 -52.67 REMARK 500 LYS A 96 25.84 -59.37 REMARK 500 MET A 97 -90.15 -155.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DRZ RELATED DB: PDB REMARK 900 CLEAVED HDV RIBOZYME REMARK 900 RELATED ID: 1CX0 RELATED DB: PDB REMARK 900 CLEAVED HDV RIBOZYME REMARK 900 RELATED ID: 1VBX RELATED DB: PDB REMARK 900 THE SAME PROTEIN/RNA(C75U) COMPLEX IN EDTA SOLUTION REMARK 900 RELATED ID: 1VBZ RELATED DB: PDB REMARK 900 THE SAME PROTEIN/RNA(C75U) COMPLEX IN BA2+ SOLUTION REMARK 900 RELATED ID: 1VC0 RELATED DB: PDB REMARK 900 THE SAME PROTEIN/RNA(C75U) COMPLEX IN IMIDAZOLE AND SR2+ SOLUTIONS REMARK 900 RELATED ID: 1SJF RELATED DB: PDB REMARK 900 THE SAME PROTEIN/RNA(C75U) COMPLEX IN COBALT HEXAMMINE SOLUTION REMARK 900 RELATED ID: 1VC5 RELATED DB: PDB REMARK 900 THE SAME PROTEIN/RNA(WILD TYPE) COMPLEX IN EDTA SOLUTION REMARK 900 RELATED ID: 1VC6 RELATED DB: PDB REMARK 900 THE SAME PROTEIN/RNA(C75U) COMPLEX IN IMIDAZOLE AND MG2+ SOLUTIONS REMARK 900 RELATED ID: 1VC7 RELATED DB: PDB REMARK 900 THE SAME PROTEIN/RNA(C75U) COMPLEX IN SR2+ SOLUTION DBREF 1VBY A 1 100 UNP P09012 SNRPA_HUMAN 1 100 DBREF 1VBY B 98 173 PDB 1VBY 1VBY 98 173 SEQADV 1VBY HIS A 31 UNP P09012 TYR 31 ENGINEERED MUTATION SEQADV 1VBY ARG A 36 UNP P09012 GLN 36 ENGINEERED MUTATION SEQRES 1 B 76 G A U G G C C G G C A U G SEQRES 2 B 76 G U C C C A G C C U C C U SEQRES 3 B 76 C G C U G G C G C C G G C SEQRES 4 B 76 U G G G C A A C A C C A U SEQRES 5 B 76 U G C A C U C C G G U G G SEQRES 6 B 76 U G A A U G G G A C U SEQRES 1 A 100 MET ALA VAL PRO GLU THR ARG PRO ASN HIS THR ILE TYR SEQRES 2 A 100 ILE ASN ASN LEU ASN GLU LYS ILE LYS LYS ASP GLU LEU SEQRES 3 A 100 LYS LYS SER LEU HIS ALA ILE PHE SER ARG PHE GLY GLN SEQRES 4 A 100 ILE LEU ASP ILE LEU VAL SER ARG SER LEU LYS MET ARG SEQRES 5 A 100 GLY GLN ALA PHE VAL ILE PHE LYS GLU VAL SER SER ALA SEQRES 6 A 100 THR ASN ALA LEU ARG SER MET GLN GLY PHE PRO PHE TYR SEQRES 7 A 100 ASP LYS PRO MET ARG ILE GLN TYR ALA LYS THR ASP SER SEQRES 8 A 100 ASP ILE ILE ALA LYS MET LYS GLY THR HET MN B 201 1 HET MN B 202 1 HET NA B 203 1 HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION FORMUL 3 MN 2(MN 2+) FORMUL 5 NA NA 1+ FORMUL 6 HOH *14(H2 O) HELIX 1 1 LYS A 22 SER A 35 1 14 HELIX 2 2 ARG A 36 GLY A 38 5 3 HELIX 3 3 GLU A 61 GLN A 73 1 13 HELIX 4 4 SER A 91 LYS A 96 1 6 SHEET 1 A 4 ILE A 40 VAL A 45 0 SHEET 2 A 4 GLN A 54 PHE A 59 -1 O ILE A 58 N LEU A 41 SHEET 3 A 4 THR A 11 ASN A 15 -1 N ILE A 14 O ALA A 55 SHEET 4 A 4 ARG A 83 TYR A 86 -1 O GLN A 85 N TYR A 13 SHEET 1 B 2 PRO A 76 PHE A 77 0 SHEET 2 B 2 LYS A 80 PRO A 81 -1 O LYS A 80 N PHE A 77 LINK O4 U B 163 MN MN B 201 1555 1555 2.46 LINK OP2 A B 166 MN MN B 202 1555 1555 1.87 SITE 1 AC1 4 G B 101 U B 120 U B 123 U B 163 SITE 1 AC2 2 A B 165 A B 166 CRYST1 108.589 108.589 190.519 90.00 90.00 120.00 H 3 2 18 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 0.009209 0.005317 0.000000 0.00000 SCALE2 0.000000 0.010634 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005249 0.00000