HEADER RNA BINDING PROTEIN 30-JUN-23 8PNK TITLE CRYSTAL STRUCTURE OF THE DED1P RECA1 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT RNA HELICASE DED1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DEAD BOX PROTEIN 1,DEFINES ESSENTIAL DOMAIN PROTEIN 1; COMPND 5 EC: 3.6.4.13; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: DED1, SPP81, YOR204W; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DED1P, HELICASE, RECA, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.HUEBNER,R.SPRANGERS REVDAT 1 16-AUG-23 8PNK 0 JRNL AUTH J.HUEBNER,R.SPRANGERS JRNL TITL CRYSTAL STRUCTURE OF THE DED1P RECA1 DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 18431 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 922 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 47.6300 - 4.2100 1.00 2571 136 0.1661 0.1830 REMARK 3 2 4.2100 - 3.3400 1.00 2514 133 0.1868 0.2209 REMARK 3 3 3.3400 - 2.9200 1.00 2504 132 0.2177 0.3081 REMARK 3 4 2.9200 - 2.6500 1.00 2492 131 0.2129 0.2523 REMARK 3 5 2.6500 - 2.4600 1.00 2513 132 0.2069 0.2401 REMARK 3 6 2.4600 - 2.3200 1.00 2492 131 0.2110 0.2802 REMARK 3 7 2.3200 - 2.2000 0.98 2423 127 0.2292 0.2528 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.206 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.512 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.99 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 2025 REMARK 3 ANGLE : 0.541 2745 REMARK 3 CHIRALITY : 0.043 306 REMARK 3 PLANARITY : 0.005 360 REMARK 3 DIHEDRAL : 4.514 274 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8PNK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1292131579. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000036 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18435 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 47.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.04857 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.6900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.71150 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.480 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.0, 30% JEFFAMINE ED REMARK 280 -2001 PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 17.40000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.80000 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 26.10000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 43.50000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 8.70000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 81 REMARK 465 GLY A 82 REMARK 465 ARG A 83 REMARK 465 SER A 84 REMARK 465 VAL A 109 REMARK 465 PRO A 110 REMARK 465 GLU A 111 REMARK 465 ASP A 112 REMARK 465 PRO A 113 REMARK 465 ASN A 114 REMARK 465 PHE A 115 REMARK 465 GLN A 116 REMARK 465 SER A 117 REMARK 465 SER A 118 REMARK 465 GLY A 119 REMARK 465 ILE A 120 REMARK 465 ASN A 121 REMARK 465 PHE A 122 REMARK 465 ASP A 123 REMARK 465 ASN A 124 REMARK 465 TYR A 125 REMARK 465 ASP A 126 REMARK 465 SER A 215 REMARK 465 GLN A 216 REMARK 465 GLY A 217 REMARK 465 SER A 218 REMARK 465 PHE A 219 REMARK 465 TYR A 220 REMARK 465 GLN A 221 REMARK 465 ARG A 366 REMARK 465 VAL A 367 REMARK 465 GLY A 368 REMARK 465 SER A 369 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 ARG A 251 -3.71 77.99 REMARK 500 CYS A 327 -156.74 -94.28 REMARK 500 ASP A 358 57.10 39.33 REMARK 500 REMARK 500 REMARK: NULL DBREF 8PNK A 82 369 UNP P06634 DED1_YEAST 82 369 SEQADV 8PNK GLY A 81 UNP P06634 EXPRESSION TAG SEQRES 1 A 289 GLY GLY ARG SER GLY GLY ARG TRP ILE ASP GLY LYS HIS SEQRES 2 A 289 VAL PRO ALA PRO ARG ASN GLU LYS ALA GLU ILE ALA ILE SEQRES 3 A 289 PHE GLY VAL PRO GLU ASP PRO ASN PHE GLN SER SER GLY SEQRES 4 A 289 ILE ASN PHE ASP ASN TYR ASP ASP ILE PRO VAL ASP ALA SEQRES 5 A 289 SER GLY LYS ASP VAL PRO GLU PRO ILE THR GLU PHE THR SEQRES 6 A 289 SER PRO PRO LEU ASP GLY LEU LEU LEU GLU ASN ILE LYS SEQRES 7 A 289 LEU ALA ARG PHE THR LYS PRO THR PRO VAL GLN LYS TYR SEQRES 8 A 289 SER VAL PRO ILE VAL ALA ASN GLY ARG ASP LEU MET ALA SEQRES 9 A 289 CYS ALA GLN THR GLY SER GLY LYS THR GLY GLY PHE LEU SEQRES 10 A 289 PHE PRO VAL LEU SER GLU SER PHE LYS THR GLY PRO SER SEQRES 11 A 289 PRO GLN PRO GLU SER GLN GLY SER PHE TYR GLN ARG LYS SEQRES 12 A 289 ALA TYR PRO THR ALA VAL ILE MET ALA PRO THR ARG GLU SEQRES 13 A 289 LEU ALA THR GLN ILE PHE ASP GLU ALA LYS LYS PHE THR SEQRES 14 A 289 TYR ARG SER TRP VAL LYS ALA CYS VAL VAL TYR GLY GLY SEQRES 15 A 289 SER PRO ILE GLY ASN GLN LEU ARG GLU ILE GLU ARG GLY SEQRES 16 A 289 CYS ASP LEU LEU VAL ALA THR PRO GLY ARG LEU ASN ASP SEQRES 17 A 289 LEU LEU GLU ARG GLY LYS ILE SER LEU ALA ASN VAL LYS SEQRES 18 A 289 TYR LEU VAL LEU ASP GLU ALA ASP ARG MET LEU ASP MET SEQRES 19 A 289 GLY PHE GLU PRO GLN ILE ARG HIS ILE VAL GLU ASP CYS SEQRES 20 A 289 ASP MET THR PRO VAL GLY GLU ARG GLN THR LEU MET PHE SEQRES 21 A 289 SER ALA THR PHE PRO ALA ASP ILE GLN HIS LEU ALA ARG SEQRES 22 A 289 ASP PHE LEU SER ASP TYR ILE PHE LEU SER VAL GLY ARG SEQRES 23 A 289 VAL GLY SER FORMUL 2 HOH *45(H2 O) HELIX 1 AA1 ASN A 99 PHE A 107 1 9 HELIX 2 AA2 ASP A 150 ALA A 160 1 11 HELIX 3 AA3 VAL A 168 ASN A 178 1 11 HELIX 4 AA4 GLN A 187 SER A 190 5 4 HELIX 5 AA5 GLY A 191 GLY A 208 1 18 HELIX 6 AA6 THR A 234 THR A 249 1 16 HELIX 7 AA7 PRO A 264 ARG A 274 1 11 HELIX 8 AA8 THR A 282 ARG A 292 1 11 HELIX 9 AA9 GLU A 307 MET A 314 1 8 HELIX 10 AB1 PHE A 316 ASP A 326 1 11 HELIX 11 AB2 PRO A 345 LEU A 356 1 12 SHEET 1 AA1 2 ARG A 87 ILE A 89 0 SHEET 2 AA1 2 LYS A 92 VAL A 94 -1 O VAL A 94 N ARG A 87 SHEET 1 AA2 8 VAL A 130 SER A 133 0 SHEET 2 AA2 8 ILE A 360 VAL A 364 -1 O SER A 363 N ASP A 131 SHEET 3 AA2 8 LEU A 182 CYS A 185 1 N CYS A 185 O LEU A 362 SHEET 4 AA2 8 GLN A 336 PHE A 340 1 O MET A 339 N ALA A 184 SHEET 5 AA2 8 TYR A 302 LEU A 305 1 N LEU A 305 O PHE A 340 SHEET 6 AA2 8 ALA A 228 MET A 231 1 N VAL A 229 O VAL A 304 SHEET 7 AA2 8 LEU A 278 ALA A 281 1 O LEU A 279 N ILE A 230 SHEET 8 AA2 8 ALA A 256 VAL A 259 1 N CYS A 257 O VAL A 280 CRYST1 110.000 110.000 52.200 90.00 90.00 120.00 P 61 6 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 0.009091 0.005249 0.000000 0.00000 SCALE2 0.000000 0.010497 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019157 0.00000