HEADER RNA BINDING PROTEIN 21-JAN-00 1DVK TITLE CRYSTAL STRUCTURE OF THE FUNCTIONAL DOMAIN OF THE SPLICING FACTOR TITLE 2 PRP18 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRP18; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS PRE-MRNA SPLICING FACTOR, PRP18, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.JIANG,D.S.HOROWITZ,R.M.XU REVDAT 3 07-FEB-24 1DVK 1 REMARK REVDAT 2 24-FEB-09 1DVK 1 VERSN REVDAT 1 05-APR-00 1DVK 0 JRNL AUTH J.JIANG,D.S.HOROWITZ,R.M.XU JRNL TITL CRYSTAL STRUCTURE OF THE FUNCTIONAL DOMAIN OF THE SPLICING JRNL TITL 2 FACTOR PRP18. JRNL REF PROC.NATL.ACAD.SCI.USA V. 97 3022 2000 JRNL REFN ISSN 0027-8424 JRNL PMID 10737784 JRNL DOI 10.1073/PNAS.97.7.3022 REMARK 2 REMARK 2 RESOLUTION. 2.15 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 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) (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 17517 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1759 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2427 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 219 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.59 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) : 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) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DVK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-00. REMARK 100 THE DEPOSITION ID IS D_1000010409. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X26C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.09 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17664 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 200 DATA REDUNDANCY : 10.70 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 55.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.09700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM MES 6.0, 25% PEG8000, 10% REMARK 280 GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K, PH 6.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 85.59550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 85.59550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 24.96750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.58350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 24.96750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.58350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 85.59550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.96750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.58350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 85.59550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 24.96750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 39.58350 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: A, 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 THR A 198 REMARK 465 SER A 199 REMARK 465 VAL A 200 REMARK 465 GLY A 201 REMARK 465 ILE A 202 REMARK 465 HIS A 203 REMARK 465 ALA A 204 REMARK 465 ARG A 205 REMARK 465 SER A 206 REMARK 465 ALA A 207 REMARK 465 HIS A 208 REMARK 465 SER A 209 REMARK 465 LYS A 210 REMARK 465 ILE A 211 REMARK 465 GLN A 212 REMARK 465 GLY A 213 REMARK 465 GLY A 214 REMARK 465 ARG A 215 REMARK 465 ASN A 216 REMARK 465 ALA A 217 REMARK 465 ASP A 248 REMARK 465 SER A 249 REMARK 465 LEU A 250 REMARK 465 ALA A 251 REMARK 465 SER B 199 REMARK 465 VAL B 200 REMARK 465 GLY B 201 REMARK 465 ILE B 202 REMARK 465 HIS B 203 REMARK 465 ALA B 204 REMARK 465 ARG B 205 REMARK 465 SER B 206 REMARK 465 ALA B 207 REMARK 465 HIS B 208 REMARK 465 SER B 209 REMARK 465 LYS B 210 REMARK 465 ILE B 211 REMARK 465 GLN B 212 REMARK 465 GLY B 213 REMARK 465 GLY B 214 REMARK 465 ARG B 215 REMARK 465 ASN B 216 REMARK 465 ALA B 217 REMARK 465 ASP B 248 REMARK 465 SER B 249 REMARK 465 LEU B 250 REMARK 465 ALA B 251 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 HIS A 132 65.73 29.37 REMARK 500 ASN A 246 71.54 -111.66 REMARK 500 HIS B 132 64.06 17.71 REMARK 500 REMARK 500 REMARK: NULL DBREF 1DVK A 79 251 UNP P33411 PRP18_YEAST 79 251 DBREF 1DVK B 79 251 UNP P33411 PRP18_YEAST 79 251 SEQADV 1DVK MET A 79 UNP P33411 GLU 79 SEE REMARK 999 SEQADV 1DVK MET B 79 UNP P33411 GLU 79 SEE REMARK 999 SEQRES 1 A 173 MET ARG ILE GLN GLU ALA ILE ALA GLN ASP LYS THR ILE SEQRES 2 A 173 SER VAL ILE ILE ASP PRO SER GLN ILE GLY SER THR GLU SEQRES 3 A 173 GLY LYS PRO LEU LEU SER MET LYS CYS ASN LEU TYR ILE SEQRES 4 A 173 HIS GLU ILE LEU SER ARG TRP LYS ALA SER LEU GLU ALA SEQRES 5 A 173 TYR HIS PRO GLU LEU PHE LEU ASP THR LYS LYS ALA LEU SEQRES 6 A 173 PHE PRO LEU LEU LEU GLN LEU ARG ARG ASN GLN LEU ALA SEQRES 7 A 173 PRO ASP LEU LEU ILE SER LEU ALA THR VAL LEU TYR HIS SEQRES 8 A 173 LEU GLN GLN PRO LYS GLU ILE ASN LEU ALA VAL GLN SER SEQRES 9 A 173 TYR MET LYS LEU SER ILE GLY ASN VAL ALA TRP PRO ILE SEQRES 10 A 173 GLY VAL THR SER VAL GLY ILE HIS ALA ARG SER ALA HIS SEQRES 11 A 173 SER LYS ILE GLN GLY GLY ARG ASN ALA ALA ASN ILE MET SEQRES 12 A 173 ILE ASP GLU ARG THR ARG LEU TRP ILE THR SER ILE LYS SEQRES 13 A 173 ARG LEU ILE THR PHE GLU GLU TRP TYR THR SER ASN HIS SEQRES 14 A 173 ASP SER LEU ALA SEQRES 1 B 173 MET ARG ILE GLN GLU ALA ILE ALA GLN ASP LYS THR ILE SEQRES 2 B 173 SER VAL ILE ILE ASP PRO SER GLN ILE GLY SER THR GLU SEQRES 3 B 173 GLY LYS PRO LEU LEU SER MET LYS CYS ASN LEU TYR ILE SEQRES 4 B 173 HIS GLU ILE LEU SER ARG TRP LYS ALA SER LEU GLU ALA SEQRES 5 B 173 TYR HIS PRO GLU LEU PHE LEU ASP THR LYS LYS ALA LEU SEQRES 6 B 173 PHE PRO LEU LEU LEU GLN LEU ARG ARG ASN GLN LEU ALA SEQRES 7 B 173 PRO ASP LEU LEU ILE SER LEU ALA THR VAL LEU TYR HIS SEQRES 8 B 173 LEU GLN GLN PRO LYS GLU ILE ASN LEU ALA VAL GLN SER SEQRES 9 B 173 TYR MET LYS LEU SER ILE GLY ASN VAL ALA TRP PRO ILE SEQRES 10 B 173 GLY VAL THR SER VAL GLY ILE HIS ALA ARG SER ALA HIS SEQRES 11 B 173 SER LYS ILE GLN GLY GLY ARG ASN ALA ALA ASN ILE MET SEQRES 12 B 173 ILE ASP GLU ARG THR ARG LEU TRP ILE THR SER ILE LYS SEQRES 13 B 173 ARG LEU ILE THR PHE GLU GLU TRP TYR THR SER ASN HIS SEQRES 14 B 173 ASP SER LEU ALA FORMUL 3 HOH *219(H2 O) HELIX 1 1 ILE A 81 ALA A 86 1 6 HELIX 2 2 ASP A 96 ILE A 100 5 5 HELIX 3 3 GLY A 105 SER A 127 1 23 HELIX 4 4 LEU A 128 TYR A 131 5 4 HELIX 5 5 LEU A 135 ASN A 153 1 19 HELIX 6 6 ALA A 156 GLN A 171 1 16 HELIX 7 7 GLN A 172 LYS A 174 5 3 HELIX 8 8 GLU A 175 ILE A 188 1 14 HELIX 9 9 ASP A 223 ASN A 246 1 24 HELIX 10 10 ARG B 80 ASP B 88 1 9 HELIX 11 11 ASP B 96 ILE B 100 5 5 HELIX 12 12 GLY B 105 SER B 127 1 23 HELIX 13 13 HIS B 132 GLU B 134 5 3 HELIX 14 14 LEU B 135 ARG B 152 1 18 HELIX 15 15 ALA B 156 GLN B 172 1 17 HELIX 16 16 GLU B 175 ILE B 188 1 14 HELIX 17 17 ASP B 223 ASN B 246 1 24 CRYST1 49.935 79.167 171.191 90.00 90.00 90.00 C 2 2 21 16 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 0.020026 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012632 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005841 0.00000