HEADER RNA-BINDING PROTEIN 22-NOV-10 2XZ2 TITLE CRYSTAL STRUCTURE OF CSTF-50 HOMODIMERIZATION DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CSTF-50, ISOFORM B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-65; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS RNA-BINDING PROTEIN, 3' END MRNA MATURATION, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR M.MORENO-MORCILLO,S.FRIBOURG REVDAT 2 06-APR-11 2XZ2 1 JRNL REVDAT 1 26-JAN-11 2XZ2 0 JRNL AUTH M.MORENO-MORCILLO,L.MINVIELLE-SEBASTIA,C.MACKERETH, JRNL AUTH 2 S.FRIBOURG JRNL TITL HEXAMERIC ARCHITECTURE OF CSTF SUPPORTED BY CSTF- 50 JRNL TITL 2 HOMODIMERIZATION DOMAIN STRUCTURE. JRNL REF RNA V. 17 412 2011 JRNL REFN ISSN 1355-8382 JRNL PMID 21233223 JRNL DOI 10.1261/RNA.2481011 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.8.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SMART,VONRHEIN,WOMACK, REMARK 3 : MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 7738 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 + TEST SET) : 0.2012 REMARK 3 R VALUE (WORKING SET) : 0.1989 REMARK 3 FREE R VALUE : 0.2452 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.03 REMARK 3 FREE R VALUE TEST SET COUNT : 702 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 : 7 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.51 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2804 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2149 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2658 REMARK 3 BIN R VALUE (WORKING SET) : 0.2142 REMARK 3 BIN FREE R VALUE : 0.2282 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.21 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 146 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 : 552 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 40 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.5921 REMARK 3 B22 (A**2) : 1.2175 REMARK 3 B33 (A**2) : -0.6254 REMARK 3 B12 (A**2) : 0.0000 REMARK 3 B13 (A**2) : 0.0000 REMARK 3 B23 (A**2) : 0.0000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.168 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.9489 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.8930 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 568 ; 2.00 ; HARMONIC REMARK 3 BOND ANGLES : 762 ; 2.00 ; HARMONIC REMARK 3 TORSION ANGLES : 217 ; 2.00 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 14 ; 2.00 ; HARMONIC REMARK 3 GENERAL PLANES : 81 ; 5.00 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 568 ; 20.00 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 5 ; 5.00 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 72 ; 5.00 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 718 ; 4.00 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.99 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.01 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.14 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2XZ2 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-NOV-10. REMARK 100 THE PDBE ID CODE IS EBI-46346. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13968 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.40 REMARK 200 RESOLUTION RANGE LOW (A) : 30.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.52 REMARK 200 R MERGE (I) : 0.04 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.56 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.19 REMARK 200 R MERGE FOR SHELL (I) : 0.28 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.13 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXCD REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 0.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES PH 7.5, 3% PEG400, REMARK 280 1.4 M AMMONIUM SULFATE, 15% GLYCEROL 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 28.92500 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 28.92500 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 23.11500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.11500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 23.11500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.11500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.92500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 23.11500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 26.11500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 28.92500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 23.11500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 26.11500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -128.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 46.23000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 28.92500 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 MET A 1 CG SD CE 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 NA A1066 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 50 O REMARK 620 2 LEU A 21 O 115.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1067 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 14 OD1 REMARK 620 2 HOH A2005 O 126.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1069 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 15 NE REMARK 620 2 ASP A 29 OD1 127.9 REMARK 620 3 GLU A 51 OE1 84.9 128.1 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A1066 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A1067 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A1068 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A1069 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A1070 DBREF 2XZ2 A 1 65 UNP Q8IMG2 Q8IMG2_DROME 1 65 SEQADV 2XZ2 HIS A 0 UNP Q8IMG2 EXPRESSION TAG SEQRES 1 A 66 HIS MET ARG ASP GLU ILE LEU ASP PRO SER ASN LEU VAL SEQRES 2 A 66 LYS ASN ARG GLU ILE LEU TYR ARG LEU MET ILE SER GLN SEQRES 3 A 66 LEU MET TYR ASP GLY LEU GLU LYS PHE ALA MET GLU LEU SEQRES 4 A 66 SER MET LEU VAL LYS ALA ASP GLN CYS ALA PRO SER GLU SEQRES 5 A 66 ARG LEU LEU HIS VAL MET ILE ALA GLY MET GLN THR LEU SEQRES 6 A 66 SER HET NA A1066 1 HET NA A1067 1 HET NA A1068 1 HET NA A1069 1 HET PEG A1070 7 HETNAM NA SODIUM ION HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 NA 4(NA 1+) FORMUL 3 PEG C4 H10 O3 FORMUL 4 HOH *40(H2 O) HELIX 1 1 HIS A 0 GLU A 4 5 5 HELIX 2 2 ASN A 10 ASP A 29 1 20 HELIX 3 3 LEU A 31 LYS A 43 1 13 HELIX 4 4 GLU A 51 SER A 65 1 15 LINK NA NA A1066 O SER A 50 1555 1555 2.93 LINK NA NA A1066 O LEU A 21 1555 1555 2.90 LINK NA NA A1067 OD1 ASN A 14 1555 1555 2.79 LINK NA NA A1067 O HOH A2005 1555 1555 2.80 LINK NA NA A1068 OD2 ASP A 7 1555 1555 2.63 LINK NA NA A1069 OD1 ASP A 29 1555 1555 2.85 LINK NA NA A1069 OE1 GLU A 51 1555 1555 2.88 LINK NA NA A1069 NE ARG A 15 1555 3655 2.97 SITE 1 AC1 6 LEU A 21 SER A 24 GLN A 25 SER A 50 SITE 2 AC1 6 ARG A 52 LEU A 53 SITE 1 AC2 5 LEU A 6 ASP A 7 LYS A 13 ASN A 14 SITE 2 AC2 5 HOH A2005 SITE 1 AC3 2 ASP A 7 ASN A 10 SITE 1 AC4 4 ARG A 15 GLN A 25 ASP A 29 GLU A 51 SITE 1 AC5 4 TYR A 19 ASP A 29 HOH A2038 HOH A2039 CRYST1 46.230 52.230 57.850 90.00 90.00 90.00 C 2 2 21 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 0.021631 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019146 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017286 0.00000