HEADER RNA BINDING PROTEIN/DNA 16-MAY-18 6DG0 TITLE MEC-8 C-TERMINAL RRM DOMAIN BOUND TO AGCACA COMPND MOL_ID: 1; COMPND 2 MOLECULE: MEC-8 PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*AP*GP*CP*AP*CP*A)-3'); COMPND 8 CHAIN: C, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 GENE: MEC-8; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PLYSY; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-GB1A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 13 ORGANISM_TAXID: 6239 KEYWDS RNA RECOGNITION MOTIF, SPLICING FACTOR, RNA-BINDING, RNA BINDING KEYWDS 2 PROTEIN, RNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.D.MACKERETH,H.SOUFARI REVDAT 2 11-OCT-23 6DG0 1 REMARK REVDAT 1 21-AUG-19 6DG0 0 JRNL AUTH H.SOUFARI,C.D.MACKERETH JRNL TITL STRUCTURE OF MEC-8 RRM2 IN COMPLEX WITH AGCACA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 8221 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 413 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 28.0835 - 3.5415 0.95 2650 139 0.2024 0.2284 REMARK 3 2 3.5415 - 2.8119 0.99 2732 141 0.2615 0.3519 REMARK 3 3 2.8119 - 2.4567 0.89 2426 133 0.2913 0.3764 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.75 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 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 : 0.003 1571 REMARK 3 ANGLE : 0.779 2161 REMARK 3 CHIRALITY : 0.032 244 REMARK 3 PLANARITY : 0.002 243 REMARK 3 DIHEDRAL : 17.758 573 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6DG0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1000233189. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 FR-X REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8221 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.457 REMARK 200 RESOLUTION RANGE LOW (A) : 28.082 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : 0.05359 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.21210 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.560 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1URN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1MM MES PH6.5, PEG 8000 25%, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K 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 36.03750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.35700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.03750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.35700 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: A, D 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: B, C 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 213 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 217 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 225 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 238 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 241 LIES ON A SPECIAL POSITION. 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 SER A 18 REMARK 465 ILE A 83 REMARK 465 ASN A 104 REMARK 465 GLY A 105 REMARK 465 ILE B 83 REMARK 465 VAL B 103 REMARK 465 ASN B 104 REMARK 465 GLY B 105 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 LYS A 55 CG CD CE NZ REMARK 470 ASN A 56 CG OD1 ND2 REMARK 470 GLU B 31 CG CD OE1 OE2 REMARK 470 LYS B 55 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 ND2 ASN A 27 O GLY A 90 2.15 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 LYS A 55 -108.92 -124.22 REMARK 500 ASN A 86 -62.67 -104.06 REMARK 500 ALA B 19 57.81 -100.99 REMARK 500 LYS B 55 -121.48 -124.74 REMARK 500 ALA B 85 -89.47 -106.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 6DG0 A 20 105 UNP Q22039 Q22039_CAEEL 227 312 DBREF 6DG0 B 20 105 UNP Q22039 Q22039_CAEEL 227 312 DBREF 6DG0 C 0 5 PDB 6DG0 6DG0 0 5 DBREF 6DG0 D 0 5 PDB 6DG0 6DG0 0 5 SEQADV 6DG0 SER A 18 UNP Q22039 EXPRESSION TAG SEQADV 6DG0 ALA A 19 UNP Q22039 EXPRESSION TAG SEQADV 6DG0 ALA A 20 UNP Q22039 CYS 227 ENGINEERED MUTATION SEQADV 6DG0 ALA A 59 UNP Q22039 CYS 266 ENGINEERED MUTATION SEQADV 6DG0 SER B 18 UNP Q22039 EXPRESSION TAG SEQADV 6DG0 ALA B 19 UNP Q22039 EXPRESSION TAG SEQADV 6DG0 ALA B 20 UNP Q22039 CYS 227 ENGINEERED MUTATION SEQADV 6DG0 ALA B 59 UNP Q22039 CYS 266 ENGINEERED MUTATION SEQRES 1 A 88 SER ALA ALA SER THR LEU PHE VAL ALA ASN LEU SER ALA SEQRES 2 A 88 GLU VAL ASN GLU ASP THR LEU ARG GLY VAL PHE LYS ALA SEQRES 3 A 88 PHE SER GLY PHE THR ARG LEU ARG LEU HIS ASN LYS ASN SEQRES 4 A 88 GLY SER ALA VAL ALA PHE VAL GLU TYR SER ASP LEU GLN SEQRES 5 A 88 LYS ALA THR GLN ALA MET ILE SER LEU GLN GLY PHE GLN SEQRES 6 A 88 ILE THR ALA ASN ASP ARG GLY GLY LEU ARG ILE GLU TYR SEQRES 7 A 88 ALA ARG ASN LYS MET ALA ASP VAL ASN GLY SEQRES 1 B 88 SER ALA ALA SER THR LEU PHE VAL ALA ASN LEU SER ALA SEQRES 2 B 88 GLU VAL ASN GLU ASP THR LEU ARG GLY VAL PHE LYS ALA SEQRES 3 B 88 PHE SER GLY PHE THR ARG LEU ARG LEU HIS ASN LYS ASN SEQRES 4 B 88 GLY SER ALA VAL ALA PHE VAL GLU TYR SER ASP LEU GLN SEQRES 5 B 88 LYS ALA THR GLN ALA MET ILE SER LEU GLN GLY PHE GLN SEQRES 6 B 88 ILE THR ALA ASN ASP ARG GLY GLY LEU ARG ILE GLU TYR SEQRES 7 B 88 ALA ARG ASN LYS MET ALA ASP VAL ASN GLY SEQRES 1 C 6 DA DG DC DA DC DA SEQRES 1 D 6 DA DG DC DA DC DA FORMUL 5 HOH *102(H2 O) HELIX 1 AA1 ASN A 33 LYS A 42 1 10 HELIX 2 AA2 ASP A 67 GLN A 79 1 13 HELIX 3 AA3 ASN B 33 LYS B 42 1 10 HELIX 4 AA4 ASP B 67 GLN B 79 1 13 SHEET 1 AA1 4 PHE A 47 ASN A 54 0 SHEET 2 AA1 4 ALA A 59 TYR A 65 -1 O GLU A 64 N ARG A 49 SHEET 3 AA1 4 SER A 21 LEU A 28 -1 N LEU A 23 O VAL A 63 SHEET 4 AA1 4 ARG A 92 TYR A 95 -1 O GLU A 94 N PHE A 24 SHEET 1 AA2 4 PHE B 47 ASN B 54 0 SHEET 2 AA2 4 ALA B 59 TYR B 65 -1 O GLU B 64 N ARG B 49 SHEET 3 AA2 4 SER B 21 LEU B 28 -1 N LEU B 23 O VAL B 63 SHEET 4 AA2 4 ARG B 92 TYR B 95 -1 O GLU B 94 N PHE B 24 CRYST1 72.075 68.714 57.531 90.00 122.40 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 0.013874 0.000000 0.008804 0.00000 SCALE2 0.000000 0.014553 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020586 0.00000