HEADER GENE REGULATION/DNA 10-JUL-98 2UP1 TITLE STRUCTURE OF UP1-TELOMERIC DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PROTEIN (HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1); COMPND 7 CHAIN: A; COMPND 8 FRAGMENT: THE TWO RNA-RECOGNITION MOTIF DOMAIN, 1 - 196; COMPND 9 SYNONYM: HNRNP A1, UP1, HELIX-DESTABILIZING PROTEIN, SINGLE-STRAND COMPND 10 BINDING PROTEIN, HNRNP CORE PROTEIN A1 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 5 ORGANISM_COMMON: HUMAN; SOURCE 6 ORGANISM_TAXID: 9606 KEYWDS COMPLEX (RIBONUCLEOPROTEIN-DNA), HETEROGENEOUS NUCLEAR KEYWDS 2 RIBONUCLEOPROTEIN A1, GENE REGULATION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.DING,M.K.HAYASHI,A.R.KRAINER,R.-M.XU REVDAT 4 30-AUG-23 2UP1 1 REMARK REVDAT 3 22-NOV-17 2UP1 1 REMARK REVDAT 2 24-FEB-09 2UP1 1 VERSN REVDAT 1 10-NOV-99 2UP1 0 JRNL AUTH J.DING,M.K.HAYASHI,Y.ZHANG,L.MANCHE,A.R.KRAINER,R.M.XU JRNL TITL CRYSTAL STRUCTURE OF THE TWO-RRM DOMAIN OF HNRNP A1 (UP1) JRNL TITL 2 COMPLEXED WITH SINGLE-STRANDED TELOMERIC DNA. JRNL REF GENES DEV. V. 13 1102 1999 JRNL REFN ISSN 0890-9369 JRNL PMID 10323862 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.3 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 83.4 REMARK 3 NUMBER OF REFLECTIONS : 11767 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 SET) : 0.195 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1214 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 63.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1303 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 143 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1466 REMARK 3 NUCLEIC ACID ATOMS : 234 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 144 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.34000 REMARK 3 B22 (A**2) : -6.34000 REMARK 3 B33 (A**2) : 12.67000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.12 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) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.25 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.990 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.960 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.940 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.060 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2UP1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000178722. 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 : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.15 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRANDEIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14247 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.21800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: PHASER, AMORE, PHASES REMARK 200 STARTING MODEL: PDB ENTRY 1UP1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 85.54500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.60000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.60000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 128.31750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.60000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.60000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 42.77250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.60000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.60000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 128.31750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.60000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.60000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 42.77250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 85.54500 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 APPLY THE FOLLOWING TO CHAINS: B, 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 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 CYS A 43 115.20 -162.21 REMARK 500 LYS A 52 -11.49 66.69 REMARK 500 REMARK 500 REMARK: NULL DBREF 2UP1 A 8 190 UNP P09651 ROA1_HUMAN 8 190 DBREF 2UP1 B 202 212 PDB 2UP1 2UP1 202 212 SEQRES 1 B 11 DT DA DG DG DG DT DT DA DG DG DG SEQRES 1 A 183 LYS GLU PRO GLU GLN LEU ARG LYS LEU PHE ILE GLY GLY SEQRES 2 A 183 LEU SER PHE GLU THR THR ASP GLU SER LEU ARG SER HIS SEQRES 3 A 183 PHE GLU GLN TRP GLY THR LEU THR ASP CYS VAL VAL MET SEQRES 4 A 183 ARG ASP PRO ASN THR LYS ARG SER ARG GLY PHE GLY PHE SEQRES 5 A 183 VAL THR TYR ALA THR VAL GLU GLU VAL ASP ALA ALA MET SEQRES 6 A 183 ASN ALA ARG PRO HIS LYS VAL ASP GLY ARG VAL VAL GLU SEQRES 7 A 183 PRO LYS ARG ALA VAL SER ARG GLU ASP SER GLN ARG PRO SEQRES 8 A 183 GLY ALA HIS LEU THR VAL LYS LYS ILE PHE VAL GLY GLY SEQRES 9 A 183 ILE LYS GLU ASP THR GLU GLU HIS HIS LEU ARG ASP TYR SEQRES 10 A 183 PHE GLU GLN TYR GLY LYS ILE GLU VAL ILE GLU ILE MET SEQRES 11 A 183 THR ASP ARG GLY SER GLY LYS LYS ARG GLY PHE ALA PHE SEQRES 12 A 183 VAL THR PHE ASP ASP HIS ASP SER VAL ASP LYS ILE VAL SEQRES 13 A 183 ILE GLN LYS TYR HIS THR VAL ASN GLY HIS ASN CYS GLU SEQRES 14 A 183 VAL ARG LYS ALA LEU SER LYS GLN GLU MET ALA SER ALA SEQRES 15 A 183 SER FORMUL 3 HOH *144(H2 O) HELIX 1 1 GLU A 11 ARG A 14 1 4 HELIX 2 2 ASP A 27 TRP A 37 1 11 HELIX 3 3 VAL A 65 ALA A 74 1 10 HELIX 4 4 ASP A 94 GLN A 96 5 3 HELIX 5 5 GLU A 118 TYR A 128 1 11 HELIX 6 6 HIS A 156 VAL A 163 1 8 HELIX 7 7 LYS A 183 SER A 188 1 6 SHEET 1 A 4 GLU A 85 ARG A 88 0 SHEET 2 A 4 LYS A 15 GLY A 19 -1 N GLY A 19 O GLU A 85 SHEET 3 A 4 PHE A 57 TYR A 62 -1 N VAL A 60 O LEU A 16 SHEET 4 A 4 LEU A 40 MET A 46 -1 N MET A 46 O PHE A 57 SHEET 1 B 4 GLU A 176 LYS A 179 0 SHEET 2 B 4 LYS A 106 GLY A 110 -1 N GLY A 110 O GLU A 176 SHEET 3 B 4 PHE A 148 PHE A 153 -1 N VAL A 151 O ILE A 107 SHEET 4 B 4 ILE A 131 ILE A 136 -1 N GLU A 135 O PHE A 150 CISPEP 1 ARG A 75 PRO A 76 0 0.13 CRYST1 51.200 51.200 171.090 90.00 90.00 90.00 P 43 21 2 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 0.019531 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019531 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005845 0.00000