HEADER TRANSCRIPTION/RNA 06-JAN-10 2X1A TITLE STRUCTURE OF RNA15 RRM WITH RNA BOUND (G) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MRNA 3'-END-PROCESSING PROTEIN RNA15; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RNA RECOGNITION MODULE, RESIDUES 16-111; COMPND 5 SYNONYM: RNA15 RRM; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-R(*GP*UP*UP*GP*UP)-3'; COMPND 9 CHAIN: B 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES KEYWDS TRANSCRIPTION-RNA COMPLEX, TRANSLATION, NUCLEUS, KEYWDS 2 RNA-BINDING, MRNA PROCESSING EXPDTA X-RAY DIFFRACTION AUTHOR C.PANCEVAC,D.C.GOLDSTONE,A.RAMOS,I.A.TAYLOR REVDAT 2 26-MAY-10 2X1A 1 JRNL REMARK REVDAT 1 02-FEB-10 2X1A 0 JRNL AUTH C.PANCEVAC,D.C.GOLDSTONE,A.RAMOS,I.A.TAYLOR JRNL TITL STRUCTURE OF THE RNA15 RRM-RNA COMPLEX REVEALS THE JRNL TITL 2 MOLECULAR BASIS OF GU SPECIFICITY IN JRNL TITL 3 TRANSCRIPTIONAL 3-END PROCESSING FACTORS. JRNL REF NUCLEIC ACIDS RES. V. 38 3119 2010 JRNL REFN ISSN 0305-1048 JRNL PMID 20097654 JRNL DOI 10.1093/NAR/GKQ002 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0088 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 99.51 REMARK 3 NUMBER OF REFLECTIONS : 5604 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) : 0.20837 REMARK 3 R VALUE (WORKING SET) : 0.20615 REMARK 3 FREE R VALUE : 0.25807 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.5 REMARK 3 FREE R VALUE TEST SET COUNT : 265 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.050 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.103 REMARK 3 REFLECTION IN BIN (WORKING SET) : 392 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.316 REMARK 3 BIN FREE R VALUE SET COUNT : 18 REMARK 3 BIN FREE R VALUE : 0.418 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 666 REMARK 3 NUCLEIC ACID ATOMS : 24 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 44 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.8 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.647 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.74 REMARK 3 B22 (A**2) : -1.93 REMARK 3 B33 (A**2) : 3.68 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.226 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.195 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.143 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.546 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.905 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 704 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 477 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 954 ; 1.107 ; 2.018 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1159 ; 0.767 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 86 ; 5.177 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 31 ;34.396 ;23.871 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 113 ;12.630 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;17.341 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 103 ; 0.064 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 779 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 144 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 429 ; 0.442 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 178 ; 0.072 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 686 ; 0.874 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 275 ; 1.576 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 268 ; 2.815 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. REMARK 4 REMARK 4 2X1A COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JAN-10. REMARK 100 THE PDBE ID CODE IS EBI-42321. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5957 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.05 REMARK 200 RESOLUTION RANGE LOW (A) : 25.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.3 REMARK 200 R MERGE (I) : 0.11 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.80 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 18.51850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.48350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.51850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.48350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 VAL A 102 REMARK 465 SER A 103 REMARK 465 GLN A 104 REMARK 465 GLN A 105 REMARK 465 GLN A 106 REMARK 465 GLN A 107 REMARK 465 GLN A 108 REMARK 465 GLN A 109 REMARK 465 TYR A 110 REMARK 465 ASN A 111 REMARK 465 G B -1 REMARK 465 U B 0 REMARK 465 U B 3 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 GLU A 32 CG CD OE1 OE2 REMARK 470 U B 1 P OP1 OP2 O5' C5' C4' O4' C3' REMARK 470 U B 1 C2' O2' C1' N1 C2 O2 N3 C4 REMARK 470 U B 1 O4 C5 C6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2X1B RELATED DB: PDB REMARK 900 STRUCTURE OF RNA15 RRM REMARK 900 RELATED ID: 2X1F RELATED DB: PDB REMARK 900 STRUCTURE OF RNA15 RRM WITH BOUND RNA (GU) DBREF 2X1A A 15 15 PDB 2X1A 2X1A 15 15 DBREF 2X1A A 16 111 UNP P25299 RNA15_YEAST 16 111 DBREF 2X1A B -1 3 PDB 2X1A 2X1A -1 3 SEQRES 1 A 97 GLY PRO SER ARG VAL VAL TYR LEU GLY SER ILE PRO TYR SEQRES 2 A 97 ASP GLN THR GLU GLU GLN ILE LEU ASP LEU CYS SER ASN SEQRES 3 A 97 VAL GLY PRO VAL ILE ASN LEU LYS MET MET PHE ASP PRO SEQRES 4 A 97 GLN THR GLY ARG SER LYS GLY TYR ALA PHE ILE GLU PHE SEQRES 5 A 97 ARG ASP LEU GLU SER SER ALA SER ALA VAL ARG ASN LEU SEQRES 6 A 97 ASN GLY TYR GLN LEU GLY SER ARG PHE LEU LYS CYS GLY SEQRES 7 A 97 TYR SER SER ASN SER ASP ILE SER GLY VAL SER GLN GLN SEQRES 8 A 97 GLN GLN GLN GLN TYR ASN SEQRES 1 B 5 G U U G U HET MG A1102 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG MG 2+ FORMUL 4 HOH *44(H2 O) HELIX 1 1 THR A 30 GLY A 42 1 13 HELIX 2 2 ASP A 68 ASN A 80 1 13 SHEET 1 AA 4 VAL A 44 ASP A 52 0 SHEET 2 AA 4 ARG A 57 PHE A 66 -1 O ARG A 57 N ASP A 52 SHEET 3 AA 4 VAL A 19 GLY A 23 -1 O VAL A 20 N ILE A 64 SHEET 4 AA 4 LYS A 90 TYR A 93 -1 O LYS A 90 N GLY A 23 SHEET 1 AB 2 GLN A 83 LEU A 84 0 SHEET 2 AB 2 ARG A 87 PHE A 88 -1 O ARG A 87 N LEU A 84 LINK MG MG A1102 OP1 G B 2 1555 1555 2.70 SITE 1 AC1 3 SER A 24 GLY A 60 G B 2 CRYST1 37.037 74.967 31.508 90.00 90.00 90.00 P 21 21 2 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 0.027000 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013339 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031738 0.00000