HEADER PRE-MRNA PROCESSING PROTEIN 04-MAY-04 1T5I TITLE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF UAP56 COMPND MOL_ID: 1; COMPND 2 MOLECULE: C_TERMINAL DOMAIN OF A PROBABLE ATP-DEPENDENT RNA HELICASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN (RESIDUES 259-428); COMPND 5 SYNONYM: U2AF65 ASSOCIATED PROTEIN 56, UAP56; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BAT1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: XA90; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-KG KEYWDS RECA-LIKE FOLD, PRE-MRNA PROCESSING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.ZHAO,M.R.GREEN,J.SHEN REVDAT 4 14-FEB-24 1T5I 1 SEQADV REVDAT 3 24-FEB-09 1T5I 1 VERSN REVDAT 2 08-FEB-05 1T5I 1 SCALE1 SCALE2 SCALE3 REVDAT 1 31-AUG-04 1T5I 0 JRNL AUTH R.ZHAO,J.SHEN,M.R.GREEN,M.MACMORRIS,T.BLUMENTHAL JRNL TITL CRYSTAL STRUCTURE OF UAP56, A "DEXD/H-BOX" PROTEIN INVOLVED JRNL TITL 2 IN PRE-MRNA SPLICING AND MRNA EXPORT JRNL REF STRUCTURE V. 12 1373 2004 JRNL REFN ISSN 0969-2126 JRNL PMID 15296731 JRNL DOI 10.1016/J.STR.2004.06.006 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 9595 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : RFREE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT : 690 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 : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 64.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 625 REMARK 3 BIN R VALUE (WORKING SET) : 0.2873 REMARK 3 BIN FREE R VALUE : 0.2485 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 45 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 : 1311 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 87 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.00 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.19 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.37 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.830 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.186 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.527 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 3.588 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.683 ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 43.31 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1T5I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1000022337. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-03; 10-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; APS REMARK 200 BEAMLINE : 19-BM; 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934, 0.97949, 0.96411; REMARK 200 1.03320 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : NULL; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9977 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.25800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MOPS, NACL, SODIUM PHOSPHATE, REMARK 280 POTASSIUM PHOSPHATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 59.53750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 89.30625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.76875 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 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 GLY A 257 REMARK 465 SER A 258 REMARK 465 LEU A 259 REMARK 465 HIS A 260 REMARK 465 ASP A 416 REMARK 465 GLU A 417 REMARK 465 ILE A 418 REMARK 465 ASP A 419 REMARK 465 ILE A 420 REMARK 465 SER A 421 REMARK 465 SER A 422 REMARK 465 TYR A 423 REMARK 465 ILE A 424 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 CG GLU A 425 NH2 ARG A 428 1.96 REMARK 500 O HOH A 36 O HOH A 69 1.98 REMARK 500 N SER A 296 O HOH A 74 2.00 REMARK 500 OD2 ASP A 405 O HOH A 66 2.08 REMARK 500 O HOH A 38 O HOH A 77 2.15 REMARK 500 NE2 GLN A 264 O HOH A 72 2.16 REMARK 500 O HOH A 45 O HOH A 75 2.16 REMARK 500 N PHE A 293 O HOH A 71 2.16 REMARK 500 O HOH A 24 O HOH A 83 2.17 REMARK 500 NH1 ARG A 428 O HOH A 54 2.18 REMARK 500 NH2 ARG A 338 O HOH A 68 2.18 REMARK 500 O HOH A 19 O HOH A 80 2.18 REMARK 500 OE1 GLN A 264 O HOH A 72 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU A 425 O HOH A 57 3654 1.89 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 LEU A 262 78.57 45.20 REMARK 500 ASN A 288 -78.11 -100.51 REMARK 500 PRO A 313 79.25 -60.46 REMARK 500 PHE A 347 -152.21 -112.99 REMARK 500 MET A 351 45.55 -84.37 REMARK 500 ASP A 352 69.39 -60.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1T6N RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF UAP56 DBREF 1T5I A 259 428 UNP Q13838 UAP56_HUMAN 259 428 SEQADV 1T5I GLY A 257 UNP Q13838 CLONING ARTIFACT SEQADV 1T5I SER A 258 UNP Q13838 CLONING ARTIFACT SEQRES 1 A 172 GLY SER LEU HIS GLY LEU GLN GLN TYR TYR VAL LYS LEU SEQRES 2 A 172 LYS ASP ASN GLU LYS ASN ARG LYS LEU PHE ASP LEU LEU SEQRES 3 A 172 ASP VAL LEU GLU PHE ASN GLN VAL VAL ILE PHE VAL LYS SEQRES 4 A 172 SER VAL GLN ARG CYS ILE ALA LEU ALA GLN LEU LEU VAL SEQRES 5 A 172 GLU GLN ASN PHE PRO ALA ILE ALA ILE HIS ARG GLY MET SEQRES 6 A 172 PRO GLN GLU GLU ARG LEU SER ARG TYR GLN GLN PHE LYS SEQRES 7 A 172 ASP PHE GLN ARG ARG ILE LEU VAL ALA THR ASN LEU PHE SEQRES 8 A 172 GLY ARG GLY MET ASP ILE GLU ARG VAL ASN ILE ALA PHE SEQRES 9 A 172 ASN TYR ASP MET PRO GLU ASP SER ASP THR TYR LEU HIS SEQRES 10 A 172 ARG VAL ALA ARG ALA GLY ARG PHE GLY THR LYS GLY LEU SEQRES 11 A 172 ALA ILE THR PHE VAL SER ASP GLU ASN ASP ALA LYS ILE SEQRES 12 A 172 LEU ASN ASP VAL GLN ASP ARG PHE GLU VAL ASN ILE SER SEQRES 13 A 172 GLU LEU PRO ASP GLU ILE ASP ILE SER SER TYR ILE GLU SEQRES 14 A 172 GLN THR ARG FORMUL 2 HOH *87(H2 O) HELIX 1 1 LYS A 270 ASN A 272 5 3 HELIX 2 2 GLU A 273 LEU A 285 1 13 HELIX 3 3 SER A 296 GLN A 310 1 15 HELIX 4 4 PRO A 322 ASP A 335 1 14 HELIX 5 5 ASP A 352 VAL A 356 5 5 HELIX 6 6 ASP A 367 GLY A 379 1 13 HELIX 7 7 ARG A 380 THR A 383 5 4 HELIX 8 8 ASP A 393 GLU A 408 1 16 SHEET 1 A 7 ALA A 314 ILE A 317 0 SHEET 2 A 7 ILE A 340 ALA A 343 1 O VAL A 342 N ILE A 315 SHEET 3 A 7 VAL A 290 PHE A 293 1 N ILE A 292 O LEU A 341 SHEET 4 A 7 ILE A 358 ASN A 361 1 O PHE A 360 N PHE A 293 SHEET 5 A 7 LEU A 386 VAL A 391 1 O ILE A 388 N ASN A 361 SHEET 6 A 7 GLN A 263 LYS A 268 1 N GLN A 263 O ALA A 387 SHEET 7 A 7 ILE A 411 GLU A 413 1 O SER A 412 N TYR A 266 CRYST1 33.582 33.582 119.075 90.00 90.00 90.00 P 43 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 0.029778 0.000000 0.000000 0.00000 SCALE2 0.000000 0.029778 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008398 0.00000