HEADER SPLICING 30-SEP-11 3U1M TITLE STRUCTURE OF THE MRNA SPLICING COMPLEX COMPONENT CWC2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRE-MRNA-SPLICING FACTOR CWC2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-240; COMPND 5 SYNONYM: MRNA SPLICING COMPLEX COMPONENT CWC2, COMPLEXED WITH CEF1 COMPND 6 PROTEIN 2, PRP19-ASSOCIATED COMPLEX PROTEIN 40, SYNTHETIC LETHAL WITH COMPND 7 CLF1 PROTEIN 3; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: CWC2, NTC40, SLC3, YDL209C, D1041; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS CSMP, ZINC FINGER, MRNA SPLICING, SPLICING EXPDTA X-RAY DIFFRACTION AUTHOR P.LU,G.LU,C.YAN,L.WANG,W.LI,P.YIN REVDAT 3 01-NOV-23 3U1M 1 REMARK LINK REVDAT 2 05-FEB-14 3U1M 1 JRNL REVDAT 1 16-NOV-11 3U1M 0 JRNL AUTH P.LU,G.LU,C.YAN,L.WANG,W.LI,P.YIN JRNL TITL STRUCTURE OF THE MRNA SPLICING COMPLEX COMPONENT CWC2: JRNL TITL 2 INSIGHTS INTO RNA RECOGNITION JRNL REF BIOCHEM.J. V. 441 591 2012 JRNL REFN ISSN 0264-6021 JRNL PMID 21957909 JRNL DOI 10.1042/BJ20111385 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.3_473) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 13.460 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 20239 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1038 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.3499 - 3.7262 0.99 2920 150 0.1696 0.2105 REMARK 3 2 3.7262 - 2.9585 0.99 2784 167 0.1541 0.1796 REMARK 3 3 2.9585 - 2.5848 0.98 2704 151 0.1612 0.1885 REMARK 3 4 2.5848 - 2.3485 0.98 2700 144 0.1596 0.1800 REMARK 3 5 2.3485 - 2.1803 0.99 2742 133 0.1466 0.1865 REMARK 3 6 2.1803 - 2.0518 1.00 2729 150 0.1431 0.1762 REMARK 3 7 2.0518 - 1.9490 0.97 2622 143 0.1656 0.2144 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 64.17 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.870 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.38 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.60140 REMARK 3 B22 (A**2) : 2.37690 REMARK 3 B33 (A**2) : -3.97830 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 1818 REMARK 3 ANGLE : 1.081 2445 REMARK 3 CHIRALITY : 0.086 249 REMARK 3 PLANARITY : 0.005 319 REMARK 3 DIHEDRAL : 13.128 675 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 20.7648 34.6120 41.3055 REMARK 3 T TENSOR REMARK 3 T11: 0.0779 T22: 0.0910 REMARK 3 T33: 0.0831 T12: 0.0113 REMARK 3 T13: -0.0056 T23: -0.0064 REMARK 3 L TENSOR REMARK 3 L11: 0.1358 L22: 0.2904 REMARK 3 L33: 0.3461 L12: 0.1238 REMARK 3 L13: -0.1575 L23: 0.0207 REMARK 3 S TENSOR REMARK 3 S11: -0.0092 S12: 0.0246 S13: -0.0167 REMARK 3 S21: -0.0143 S22: 0.0032 S23: -0.0001 REMARK 3 S31: -0.0036 S32: -0.0509 S33: 0.0003 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3U1M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000068191. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20478 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 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 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3U1L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5, 21% PEG 3350, 200MM REMARK 280 (NH4)2HCITRATE, 100MM NA3CITRATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 22.35950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.69050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.17000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.69050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.35950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.17000 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 ILE A 127 REMARK 465 GLY A 128 REMARK 465 SER A 129 REMARK 465 PHE A 130 REMARK 465 ARG A 131 REMARK 465 GLU A 228 REMARK 465 ASP A 229 REMARK 465 PRO A 230 REMARK 465 ASP A 231 REMARK 465 PRO A 232 REMARK 465 ALA A 233 REMARK 465 ALA A 234 REMARK 465 GLN A 235 REMARK 465 LYS A 236 REMARK 465 ARG A 237 REMARK 465 LEU A 238 REMARK 465 GLN A 239 REMARK 465 GLU A 240 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 91 65.26 -118.53 REMARK 500 LYS A 133 85.64 60.00 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 ZN A 241 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 73 SG REMARK 620 2 CYS A 81 SG 112.6 REMARK 620 3 CYS A 87 SG 109.8 119.9 REMARK 620 4 HIS A 91 NE2 107.2 105.7 100.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 241 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3U1L RELATED DB: PDB DBREF 3U1M A 1 240 UNP Q12046 CWC2_YEAST 1 240 SEQRES 1 A 240 MET THR SER TRP ARG ASP LYS SER ALA LYS VAL GLN VAL SEQRES 2 A 240 LYS GLU SER GLU LEU PRO SER SER ILE PRO ALA GLN THR SEQRES 3 A 240 GLY LEU THR PHE ASN ILE TRP TYR ASN LYS TRP SER GLN SEQRES 4 A 240 GLY PHE ALA GLY ASN THR ARG PHE VAL SER PRO PHE ALA SEQRES 5 A 240 LEU GLN PRO GLN LEU HIS SER GLY LYS THR ARG GLY ASP SEQRES 6 A 240 ASN ASP GLY GLN LEU PHE PHE CYS LEU PHE PHE ALA LYS SEQRES 7 A 240 GLY MET CYS CYS LEU GLY PRO LYS CYS GLU TYR LEU HIS SEQRES 8 A 240 HIS ILE PRO ASP GLU GLU ASP ILE GLY LYS LEU ALA LEU SEQRES 9 A 240 ARG THR GLU VAL LEU ASP CYS PHE GLY ARG GLU LYS PHE SEQRES 10 A 240 ALA ASP TYR ARG GLU ASP MET GLY GLY ILE GLY SER PHE SEQRES 11 A 240 ARG LYS LYS ASN LYS THR LEU TYR VAL GLY GLY ILE ASP SEQRES 12 A 240 GLY ALA LEU ASN SER LYS HIS LEU LYS PRO ALA GLN ILE SEQRES 13 A 240 GLU SER ARG ILE ARG PHE VAL PHE SER ARG LEU GLY ASP SEQRES 14 A 240 ILE ASP ARG ILE ARG TYR VAL GLU SER LYS ASN CYS GLY SEQRES 15 A 240 PHE VAL LYS PHE LYS TYR GLN ALA ASN ALA GLU PHE ALA SEQRES 16 A 240 LYS GLU ALA MET SER ASN GLN THR LEU LEU LEU PRO SER SEQRES 17 A 240 ASP LYS GLU TRP ASP ASP ARG ARG GLU GLY THR GLY LEU SEQRES 18 A 240 LEU VAL LYS TRP ALA ASN GLU ASP PRO ASP PRO ALA ALA SEQRES 19 A 240 GLN LYS ARG LEU GLN GLU HET ZN A 241 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *326(H2 O) HELIX 1 1 SER A 3 LYS A 7 5 5 HELIX 2 2 LYS A 14 LEU A 18 5 5 HELIX 3 3 THR A 29 GLY A 40 1 12 HELIX 4 4 GLN A 54 SER A 59 1 6 HELIX 5 5 THR A 62 ASP A 67 1 6 HELIX 6 6 CYS A 73 LYS A 78 1 6 HELIX 7 7 LEU A 83 CYS A 87 5 5 HELIX 8 8 ASP A 95 THR A 106 1 12 HELIX 9 9 LYS A 116 TYR A 120 5 5 HELIX 10 10 GLY A 141 LEU A 146 1 6 HELIX 11 11 LYS A 152 ARG A 166 1 15 HELIX 12 12 GLU A 177 ASN A 180 5 4 HELIX 13 13 TYR A 188 SER A 200 1 13 HELIX 14 14 GLU A 211 GLY A 218 5 8 SHEET 1 A 4 ILE A 170 VAL A 176 0 SHEET 2 A 4 CYS A 181 PHE A 186 -1 O CYS A 181 N VAL A 176 SHEET 3 A 4 THR A 136 GLY A 140 -1 N LEU A 137 O VAL A 184 SHEET 4 A 4 LEU A 222 TRP A 225 -1 O LEU A 222 N GLY A 140 LINK SG CYS A 73 ZN ZN A 241 1555 1555 2.34 LINK SG CYS A 81 ZN ZN A 241 1555 1555 2.34 LINK SG CYS A 87 ZN ZN A 241 1555 1555 2.48 LINK NE2 HIS A 91 ZN ZN A 241 1555 1555 2.11 CISPEP 1 ALA A 42 GLY A 43 0 -24.23 SITE 1 AC1 4 CYS A 73 CYS A 81 CYS A 87 HIS A 91 CRYST1 44.719 54.340 111.381 90.00 90.00 90.00 P 21 21 21 4 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 0.022362 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018403 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008978 0.00000