HEADER RNA BINDING PROTEIN/DNA 29-DEC-11 3VAF TITLE STRUCTURE OF U2AF65 VARIANT WITH BRU3 DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPLICING FACTOR U2AF 65 KDA SUBUNIT; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RNA BINDING DOMAINS 1 AND 2; COMPND 5 SYNONYM: U2 AUXILIARY FACTOR 65 KDA SUBUNIT, HU2AF(65), HU2AF65, U2 COMPND 6 SNRNP AUXILIARY FACTOR LARGE SUBUNIT; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA 5'-D(*UP*UP*(BRU)P*(BRU)P*UP*UP*U)-3'; COMPND 10 CHAIN: P, E; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: BRU3 DNA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: U2AF2, U2AF65; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: DNA KEYWDS RNA SPLICING FACTOR, RNA RECOGNITION MOTIF, RNA BINDING PROTEIN-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.L.JENKINS,C.L.KIELKOPF REVDAT 4 13-SEP-23 3VAF 1 REMARK SEQADV LINK REVDAT 3 16-AUG-17 3VAF 1 SOURCE REMARK REVDAT 2 22-MAY-13 3VAF 1 JRNL REVDAT 1 13-FEB-13 3VAF 0 JRNL AUTH J.L.JENKINS,A.A.AGRAWAL,A.GUPTA,M.R.GREEN,C.L.KIELKOPF JRNL TITL U2AF65 ADAPTS TO DIVERSE PRE-MRNA SPLICE SITES THROUGH JRNL TITL 2 CONFORMATIONAL SELECTION OF SPECIFIC AND PROMISCUOUS RNA JRNL TITL 3 RECOGNITION MOTIFS. JRNL REF NUCLEIC ACIDS RES. V. 41 3859 2013 JRNL REFN ISSN 0305-1048 JRNL PMID 23376934 JRNL DOI 10.1093/NAR/GKT046 REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 16380 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) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1617 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) : 2.49 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 REFLECTION IN BIN (WORKING SET) : 963 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.3710 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.4590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2675 REMARK 3 NUCLEIC ACID ATOMS : 226 REMARK 3 HETEROGEN ATOMS : 87 REMARK 3 SOLVENT ATOMS : 119 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.64000 REMARK 3 B22 (A**2) : 0.23000 REMARK 3 B33 (A**2) : 1.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.50000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.705 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.349 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.229 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.959 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.908 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.869 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3068 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2044 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4187 ; 1.401 ; 2.089 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4992 ; 1.093 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 346 ; 6.179 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 131 ;35.579 ;24.885 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 461 ;16.179 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;16.232 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 454 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3215 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 563 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 582 ; 0.216 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2091 ; 0.196 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1463 ; 0.188 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1588 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 102 ; 0.150 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.041 ; 0.200 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): 25 ; 0.194 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 58 ; 0.174 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.160 ; 0.200 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): 2194 ; 0.509 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 709 ; 0.082 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2738 ; 0.633 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1589 ; 1.149 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1448 ; 1.793 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 143 A 237 REMARK 3 ORIGIN FOR THE GROUP (A): 13.1127 90.3588 111.3416 REMARK 3 T TENSOR REMARK 3 T11: -0.1760 T22: -0.1834 REMARK 3 T33: -0.1179 T12: -0.0497 REMARK 3 T13: 0.0296 T23: -0.0855 REMARK 3 L TENSOR REMARK 3 L11: 2.5672 L22: 2.0747 REMARK 3 L33: 5.0989 L12: 1.2567 REMARK 3 L13: 0.8647 L23: -0.0047 REMARK 3 S TENSOR REMARK 3 S11: -0.1687 S12: 0.0848 S13: -0.2822 REMARK 3 S21: -0.0414 S22: -0.0678 S23: 0.0407 REMARK 3 S31: 0.1759 S32: 0.0048 S33: 0.2365 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 258 A 336 REMARK 3 ORIGIN FOR THE GROUP (A): -8.1753 115.5543 107.0935 REMARK 3 T TENSOR REMARK 3 T11: -0.0964 T22: -0.1393 REMARK 3 T33: 0.0194 T12: -0.1424 REMARK 3 T13: 0.1095 T23: -0.1166 REMARK 3 L TENSOR REMARK 3 L11: 7.8313 L22: 2.4570 REMARK 3 L33: 4.6975 L12: 1.8796 REMARK 3 L13: 1.7168 L23: -0.1869 REMARK 3 S TENSOR REMARK 3 S11: -0.0276 S12: 0.0689 S13: 0.0398 REMARK 3 S21: -0.2196 S22: 0.2429 S23: -0.0119 REMARK 3 S31: -0.3348 S32: 0.1414 S33: -0.2154 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 145 B 237 REMARK 3 ORIGIN FOR THE GROUP (A): 50.0680 82.1884 109.2609 REMARK 3 T TENSOR REMARK 3 T11: -0.1823 T22: -0.1538 REMARK 3 T33: -0.1908 T12: -0.0580 REMARK 3 T13: -0.0156 T23: 0.0051 REMARK 3 L TENSOR REMARK 3 L11: 5.4416 L22: 5.9848 REMARK 3 L33: 3.7806 L12: 0.4345 REMARK 3 L13: 0.4735 L23: -0.8736 REMARK 3 S TENSOR REMARK 3 S11: -0.2528 S12: 0.0135 S13: 0.0561 REMARK 3 S21: -0.4338 S22: 0.2985 S23: 0.2382 REMARK 3 S31: 0.2330 S32: -0.2285 S33: -0.0457 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 258 B 336 REMARK 3 ORIGIN FOR THE GROUP (A): 29.0005 106.1984 94.3352 REMARK 3 T TENSOR REMARK 3 T11: -0.1099 T22: -0.0643 REMARK 3 T33: -0.2476 T12: -0.0509 REMARK 3 T13: -0.0179 T23: 0.0105 REMARK 3 L TENSOR REMARK 3 L11: 6.3499 L22: 4.5845 REMARK 3 L33: 6.0914 L12: 1.9353 REMARK 3 L13: 2.0314 L23: -0.4405 REMARK 3 S TENSOR REMARK 3 S11: -0.2877 S12: 0.5156 S13: 0.0466 REMARK 3 S21: -0.3186 S22: 0.1226 S23: -0.0789 REMARK 3 S31: -0.4136 S32: 0.0100 S33: 0.1652 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3VAF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000069797. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.960 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17441 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.13400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.45500 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 2G4B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M AMMONIUM SULFATE, 10% DIOXANE, REMARK 280 0.1M MES PH 6.5, DEOXY-BIG CHAP, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K 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 82.14800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.49050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 82.14800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.49050 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, P, E 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 GLY B 143 REMARK 465 PRO B 144 REMARK 465 DU P 8 REMARK 465 DU E 8 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DU P 2 C5' - C4' - O4' ANGL. DEV. = 21.6 DEGREES 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 ALA B 181 176.94 178.49 REMARK 500 GLN B 220 56.74 37.96 REMARK 500 SER B 281 -8.51 -58.39 REMARK 500 LEU B 325 79.70 -108.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 CPQ B 401 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DIO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DIO A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPQ B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DIO B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DIO B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 P 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2G4B RELATED DB: PDB REMARK 900 U2AF65 VARIANT WITH POLYURIDINE TRACT REMARK 900 RELATED ID: 2HZC RELATED DB: PDB REMARK 900 N-TERMINAL RRM OF U2AF65 REMARK 900 RELATED ID: 3VAG RELATED DB: PDB REMARK 900 RELATED ID: 3VAH RELATED DB: PDB REMARK 900 RELATED ID: 3VAI RELATED DB: PDB REMARK 900 RELATED ID: 3VAJ RELATED DB: PDB REMARK 900 RELATED ID: 3VAK RELATED DB: PDB REMARK 900 RELATED ID: 3VAL RELATED DB: PDB REMARK 900 RELATED ID: 3VAM RELATED DB: PDB REMARK 900 RELATED ID: 3VAN RELATED DB: PDB REMARK 900 RELATED ID: 3VAO RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 PROTEIN WAS COCRYSTALIZED WITH A DNA 7MER (5'-D(*UP*UP*(BRU)P*UP*UP* REMARK 999 UP*U)-3') BUT THE PROTEIN BOUND THE DNA IN DIFFERENT REGISTERS REMARK 999 RESULTING IN THE BRU APPEARING IN MORE THAN ONE POSITION IN THE REMARK 999 STRUCTURE DBREF 3VAF A 148 237 UNP P26368 U2AF2_HUMAN 148 237 DBREF 3VAF A 258 336 UNP P26368 U2AF2_HUMAN 258 336 DBREF 3VAF B 148 237 UNP P26368 U2AF2_HUMAN 148 237 DBREF 3VAF B 258 336 UNP P26368 U2AF2_HUMAN 258 336 DBREF 3VAF P 2 8 PDB 3VAF 3VAF 2 8 DBREF 3VAF E 2 8 PDB 3VAF 3VAF 2 8 SEQADV 3VAF GLY A 143 UNP P26368 EXPRESSION TAG SEQADV 3VAF PRO A 144 UNP P26368 EXPRESSION TAG SEQADV 3VAF LEU A 145 UNP P26368 EXPRESSION TAG SEQADV 3VAF GLY A 146 UNP P26368 EXPRESSION TAG SEQADV 3VAF SER A 147 UNP P26368 EXPRESSION TAG SEQADV 3VAF GLY B 143 UNP P26368 EXPRESSION TAG SEQADV 3VAF PRO B 144 UNP P26368 EXPRESSION TAG SEQADV 3VAF LEU B 145 UNP P26368 EXPRESSION TAG SEQADV 3VAF GLY B 146 UNP P26368 EXPRESSION TAG SEQADV 3VAF SER B 147 UNP P26368 EXPRESSION TAG SEQRES 1 A 174 GLY PRO LEU GLY SER ALA ARG ARG LEU TYR VAL GLY ASN SEQRES 2 A 174 ILE PRO PHE GLY ILE THR GLU GLU ALA MET MET ASP PHE SEQRES 3 A 174 PHE ASN ALA GLN MET ARG LEU GLY GLY LEU THR GLN ALA SEQRES 4 A 174 PRO GLY ASN PRO VAL LEU ALA VAL GLN ILE ASN GLN ASP SEQRES 5 A 174 LYS ASN PHE ALA PHE LEU GLU PHE ARG SER VAL ASP GLU SEQRES 6 A 174 THR THR GLN ALA MET ALA PHE ASP GLY ILE ILE PHE GLN SEQRES 7 A 174 GLY GLN SER LEU LYS ILE ARG ARG PRO HIS ASP TYR GLN SEQRES 8 A 174 PRO LEU PRO GLY ALA HIS LYS LEU PHE ILE GLY GLY LEU SEQRES 9 A 174 PRO ASN TYR LEU ASN ASP ASP GLN VAL LYS GLU LEU LEU SEQRES 10 A 174 THR SER PHE GLY PRO LEU LYS ALA PHE ASN LEU VAL LYS SEQRES 11 A 174 ASP SER ALA THR GLY LEU SER LYS GLY TYR ALA PHE CYS SEQRES 12 A 174 GLU TYR VAL ASP ILE ASN VAL THR ASP GLN ALA ILE ALA SEQRES 13 A 174 GLY LEU ASN GLY MET GLN LEU GLY ASP LYS LYS LEU LEU SEQRES 14 A 174 VAL GLN ARG ALA SER SEQRES 1 B 174 GLY PRO LEU GLY SER ALA ARG ARG LEU TYR VAL GLY ASN SEQRES 2 B 174 ILE PRO PHE GLY ILE THR GLU GLU ALA MET MET ASP PHE SEQRES 3 B 174 PHE ASN ALA GLN MET ARG LEU GLY GLY LEU THR GLN ALA SEQRES 4 B 174 PRO GLY ASN PRO VAL LEU ALA VAL GLN ILE ASN GLN ASP SEQRES 5 B 174 LYS ASN PHE ALA PHE LEU GLU PHE ARG SER VAL ASP GLU SEQRES 6 B 174 THR THR GLN ALA MET ALA PHE ASP GLY ILE ILE PHE GLN SEQRES 7 B 174 GLY GLN SER LEU LYS ILE ARG ARG PRO HIS ASP TYR GLN SEQRES 8 B 174 PRO LEU PRO GLY ALA HIS LYS LEU PHE ILE GLY GLY LEU SEQRES 9 B 174 PRO ASN TYR LEU ASN ASP ASP GLN VAL LYS GLU LEU LEU SEQRES 10 B 174 THR SER PHE GLY PRO LEU LYS ALA PHE ASN LEU VAL LYS SEQRES 11 B 174 ASP SER ALA THR GLY LEU SER LYS GLY TYR ALA PHE CYS SEQRES 12 B 174 GLU TYR VAL ASP ILE ASN VAL THR ASP GLN ALA ILE ALA SEQRES 13 B 174 GLY LEU ASN GLY MET GLN LEU GLY ASP LYS LYS LEU LEU SEQRES 14 B 174 VAL GLN ARG ALA SER SEQRES 1 P 7 DU DU BRU BRU DU DU DU SEQRES 1 E 7 DU DU BRU BRU DU DU DU MODRES 3VAF BRU P 4 DU MODRES 3VAF BRU P 5 DU MODRES 3VAF BRU E 4 DU MODRES 3VAF BRU E 5 DU HET BRU P 4 20 HET BRU P 5 20 HET BRU E 4 20 HET BRU E 5 20 HET DIO A 401 6 HET DIO A 402 6 HET SO4 A 403 5 HET SO4 A 404 5 HET GOL A 405 6 HET CPQ B 401 27 HET DIO B 402 6 HET DIO B 403 6 HET SO4 B 404 5 HET SO4 B 405 5 HET SO4 B 406 5 HET SO4 P 101 5 HETNAM BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM DIO 1,4-DIETHYLENE DIOXIDE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM CPQ N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN CPQ DEOXY-BIGCHAP FORMUL 3 BRU 4(C9 H12 BR N2 O8 P) FORMUL 5 DIO 4(C4 H8 O2) FORMUL 7 SO4 6(O4 S 2-) FORMUL 9 GOL C3 H8 O3 FORMUL 10 CPQ C42 H75 N3 O15 FORMUL 17 HOH *119(H2 O) HELIX 1 1 THR A 161 GLY A 176 1 16 HELIX 2 2 SER A 204 MET A 212 1 9 HELIX 3 3 ALA A 213 ASP A 215 5 3 HELIX 4 4 ASN A 271 SER A 281 1 11 HELIX 5 5 ASN A 311 ASN A 321 1 11 HELIX 6 6 GLY B 146 ALA B 148 5 3 HELIX 7 7 THR B 161 GLY B 177 1 17 HELIX 8 8 SER B 204 MET B 212 1 9 HELIX 9 9 ALA B 213 ASP B 215 5 3 HELIX 10 10 ASN B 271 SER B 281 1 11 HELIX 11 11 ASP B 309 ASN B 311 5 3 HELIX 12 12 VAL B 312 ASN B 321 1 10 SHEET 1 A 4 VAL A 186 ASN A 192 0 SHEET 2 A 4 PHE A 197 PHE A 202 -1 O GLU A 201 N LEU A 187 SHEET 3 A 4 ARG A 150 GLY A 154 -1 N VAL A 153 O ALA A 198 SHEET 4 A 4 LYS A 225 ARG A 227 -1 O LYS A 225 N GLY A 154 SHEET 1 B 2 ILE A 218 PHE A 219 0 SHEET 2 B 2 GLN A 222 SER A 223 -1 O GLN A 222 N PHE A 219 SHEET 1 C 4 LEU A 285 LYS A 292 0 SHEET 2 C 4 SER A 299 TYR A 307 -1 O GLU A 306 N LYS A 286 SHEET 3 C 4 LEU A 261 GLY A 264 -1 N LEU A 261 O CYS A 305 SHEET 4 C 4 LEU A 331 ARG A 334 -1 O LEU A 331 N GLY A 264 SHEET 1 D 2 GLN A 324 LEU A 325 0 SHEET 2 D 2 LYS A 328 LYS A 329 -1 O LYS A 328 N LEU A 325 SHEET 1 E 4 VAL B 186 ASN B 192 0 SHEET 2 E 4 PHE B 197 PHE B 202 -1 O GLU B 201 N ALA B 188 SHEET 3 E 4 ARG B 150 GLY B 154 -1 N VAL B 153 O ALA B 198 SHEET 4 E 4 LYS B 225 ARG B 227 -1 O LYS B 225 N GLY B 154 SHEET 1 F 2 ILE B 218 PHE B 219 0 SHEET 2 F 2 GLN B 222 SER B 223 -1 O GLN B 222 N PHE B 219 SHEET 1 G 4 LEU B 285 LYS B 292 0 SHEET 2 G 4 SER B 299 TYR B 307 -1 O PHE B 304 N ASN B 289 SHEET 3 G 4 LEU B 261 GLY B 264 -1 N LEU B 261 O CYS B 305 SHEET 4 G 4 LEU B 331 ARG B 334 -1 O GLN B 333 N PHE B 262 SHEET 1 H 2 GLN B 324 LEU B 325 0 SHEET 2 H 2 LYS B 328 LYS B 329 -1 O LYS B 328 N LEU B 325 LINK O3' DU P 3 P BRU P 4 1555 1555 1.61 LINK O3' BRU P 4 P BRU P 5 1555 1555 1.58 LINK O3' BRU P 5 P DU P 6 1555 1555 1.59 LINK O3' DU E 3 P BRU E 4 1555 1555 1.59 LINK O3' BRU E 4 P BRU E 5 1555 1555 1.59 LINK O3' BRU E 5 P DU E 6 1555 1555 1.60 CISPEP 1 GLY A 143 PRO A 144 0 -11.83 SITE 1 AC1 3 LYS A 292 HOH A 519 HOH A 534 SITE 1 AC2 4 PRO A 144 TYR A 232 GLN A 233 LEU A 325 SITE 1 AC3 2 LYS A 225 ARG A 227 SITE 1 AC4 4 ARG A 228 TYR A 232 ILE A 310 HOH A 502 SITE 1 AC5 4 ILE A 191 GLN A 193 ASP A 194 LYS B 329 SITE 1 AC6 3 TYR B 269 GLU B 277 GLY B 326 SITE 1 AC7 3 LYS B 276 LEU B 285 LYS B 286 SITE 1 AC8 3 ARG B 174 GLY B 183 HIS B 259 SITE 1 AC9 3 ARG B 149 SER B 204 VAL B 205 SITE 1 BC1 3 LYS B 225 ARG B 227 HOH E 110 SITE 1 BC2 2 MET B 212 ARG B 228 SITE 1 BC3 5 ARG A 150 GLU A 201 SER A 281 DU P 7 SITE 2 BC3 5 HOH P 202 CRYST1 164.296 36.981 99.431 90.00 125.67 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 0.006087 0.000000 0.004368 0.00000 SCALE2 0.000000 0.027041 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012379 0.00000