HEADER DNA BINDING PROTEIN/DNA 11-SEP-19 6UBF TITLE ROLE OF BETA-HAIRPIN MOTIFS IN THE DNA DUPLEX OPENING BY THE RAD4/XPC TITLE 2 NUCLEOTIDE EXCISION REPAIR COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA REPAIR PROTEIN RAD4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 101-632; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: UV EXCISION REPAIR PROTEIN RAD23; COMPND 8 CHAIN: X; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*(G47) COMPND 12 P*AP*CP*AP*TP*CP*CP*C*GP*CP*TP*AP*CP*AP*A)-3'); COMPND 13 CHAIN: W; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'- COMPND 17 D(*AP*TP*TP*GP*TP*AP*GP*CP*GP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A)- COMPND 18 3'); COMPND 19 CHAIN: Y; COMPND 20 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 ATCC: 204508 / S288C; SOURCE 6 GENE: RAD4, YER162C; SOURCE 7 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 8 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 12 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 13 ORGANISM_TAXID: 4932; SOURCE 14 GENE: RAD23, YEL037C, SYGP-ORF29; SOURCE 15 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 16 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 18 MOL_ID: 3; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 21 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 22 ORGANISM_TAXID: 4932; SOURCE 23 MOL_ID: 4; SOURCE 24 SYNTHETIC: YES; SOURCE 25 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 26 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 27 ORGANISM_TAXID: 4932 KEYWDS DNA DAMAGE REPAIR, BETA HAIRPIN MOTIF, CHEMICAL CROSSLINKING, DNA KEYWDS 2 BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.PAUL,J.H.MIN REVDAT 2 11-OCT-23 6UBF 1 REMARK REVDAT 1 14-OCT-20 6UBF 0 JRNL AUTH X.CHEN,Y.VELMURUGU,G.ZHENG,B.PARK,Y.SHIM,Y.KIM,L.LIU, JRNL AUTH 2 B.VAN HOUTEN,C.HE,A.ANSARI,J.H.MIN JRNL TITL KINETIC GATING MECHANISM OF DNA DAMAGE RECOGNITION BY JRNL TITL 2 RAD4/XPC. JRNL REF NAT COMMUN V. 6 5849 2015 JRNL REFN ESSN 2041-1723 JRNL PMID 25562780 JRNL DOI 10.1038/NCOMMS6849 REMARK 2 REMARK 2 RESOLUTION. 4.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 4.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.6 REMARK 3 NUMBER OF REFLECTIONS : 6576 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.316 REMARK 3 R VALUE (WORKING SET) : 0.314 REMARK 3 FREE R VALUE : 0.356 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.640 REMARK 3 FREE R VALUE TEST SET COUNT : 305 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 48.7400 - 5.7897 1.00 3830 173 0.2961 0.3410 REMARK 3 2 5.7897 - 4.6000 0.68 2441 132 0.3983 0.4137 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.660 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 45.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 198.4 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 279.9 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 : 0.009 5428 REMARK 3 ANGLE : 1.415 7490 REMARK 3 CHIRALITY : 0.082 818 REMARK 3 PLANARITY : 0.009 801 REMARK 3 DIHEDRAL : 16.201 3140 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 6UBF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1000244288. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97919 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7782 REMARK 200 RESOLUTION RANGE HIGH (A) : 4.000 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.70 REMARK 200 R MERGE (I) : 0.26700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.10 REMARK 200 R MERGE FOR SHELL (I) : 0.92600 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 4YIR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM BTP-HCL, 150 MM SODIUM CHLORIDE, REMARK 280 12% ISOPROPANOL, PH 6.8, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 201.91200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.36150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.36150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 100.95600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.36150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.36150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 302.86800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.36150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.36150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 100.95600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.36150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.36150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 302.86800 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 201.91200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, X, W, Y 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 95 REMARK 465 SER A 96 REMARK 465 SER A 97 REMARK 465 ARG A 98 REMARK 465 ALA A 99 REMARK 465 MET A 100 REMARK 465 GLY A 101 REMARK 465 ASN A 102 REMARK 465 GLU A 103 REMARK 465 VAL A 104 REMARK 465 ALA A 105 REMARK 465 GLY A 106 REMARK 465 VAL A 107 REMARK 465 GLU A 108 REMARK 465 ASP A 109 REMARK 465 ILE A 110 REMARK 465 SER A 111 REMARK 465 VAL A 112 REMARK 465 GLU A 113 REMARK 465 ILE A 114 REMARK 465 THR A 115 REMARK 465 PRO A 116 REMARK 465 SER A 117 REMARK 465 SER A 118 REMARK 465 LYS A 119 REMARK 465 ARG A 120 REMARK 465 ASN A 121 REMARK 465 SER A 122 REMARK 465 ASP A 123 REMARK 465 ALA A 124 REMARK 465 ARG A 125 REMARK 465 LYS A 240 REMARK 465 ARG A 241 REMARK 465 LYS A 242 REMARK 465 THR A 505 REMARK 465 GLY A 506 REMARK 465 SER A 507 REMARK 465 ARG A 508 REMARK 465 CYS A 509 REMARK 465 LYS A 510 REMARK 465 LYS A 511 REMARK 465 VAL A 517 REMARK 465 GLY A 518 REMARK 465 ARG A 519 REMARK 465 PRO A 520 REMARK 465 LYS A 521 REMARK 465 GLY A 522 REMARK 465 GLU A 523 REMARK 465 ALA A 524 REMARK 465 PHE A 604 REMARK 465 LYS A 605 REMARK 465 PHE A 606 REMARK 465 GLY X 228 REMARK 465 SER X 229 REMARK 465 GLY X 230 REMARK 465 ASN X 231 REMARK 465 ALA X 232 REMARK 465 SER X 233 REMARK 465 SER X 234 REMARK 465 GLY X 235 REMARK 465 ALA X 236 REMARK 465 LEU X 237 REMARK 465 GLY X 238 REMARK 465 THR X 239 REMARK 465 THR X 240 REMARK 465 GLY X 241 REMARK 465 GLY X 242 REMARK 465 ALA X 243 REMARK 465 THR X 244 REMARK 465 ASP X 245 REMARK 465 ALA X 246 REMARK 465 ALA X 247 REMARK 465 GLN X 248 REMARK 465 GLY X 249 REMARK 465 GLY X 250 REMARK 465 PRO X 251 REMARK 465 PRO X 252 REMARK 465 GLY X 253 REMARK 465 SER X 254 REMARK 465 ILE X 255 REMARK 465 VAL X 309 REMARK 465 GLY X 310 REMARK 465 ASP X 311 REMARK 465 ASN X 312 REMARK 465 MET X 313 REMARK 465 GLN X 314 REMARK 465 ASP X 315 REMARK 465 VAL X 316 REMARK 465 MET X 317 REMARK 465 GLU X 318 REMARK 465 GLY X 319 REMARK 465 ALA X 320 REMARK 465 ASP X 321 REMARK 465 ASP X 322 REMARK 465 MET X 323 REMARK 465 VAL X 324 REMARK 465 GLU X 325 REMARK 465 GLY X 326 REMARK 465 GLU X 327 REMARK 465 ASP X 328 REMARK 465 ILE X 329 REMARK 465 GLU X 330 REMARK 465 VAL X 331 REMARK 465 THR X 332 REMARK 465 GLY X 333 REMARK 465 GLU X 334 REMARK 465 ALA X 335 REMARK 465 ALA X 336 REMARK 465 ALA X 337 REMARK 465 ALA X 338 REMARK 465 GLY X 339 REMARK 465 LEU X 340 REMARK 465 GLY X 341 REMARK 465 GLN X 342 REMARK 465 GLY X 343 REMARK 465 GLU X 344 REMARK 465 GLY X 345 REMARK 465 GLU X 346 REMARK 465 GLY X 347 REMARK 465 SER X 348 REMARK 465 PHE X 349 REMARK 465 GLN X 350 REMARK 465 VAL X 351 REMARK 465 ASP X 352 REMARK 465 TYR X 353 REMARK 465 THR X 354 REMARK 465 PRO X 355 REMARK 465 GLU X 356 REMARK 465 ASP X 357 REMARK 465 ASP X 358 REMARK 465 GLN X 359 REMARK 465 ALA X 360 REMARK 465 ILE X 361 REMARK 465 SER X 362 REMARK 465 ARG X 363 REMARK 465 LEU X 364 REMARK 465 CYS X 365 REMARK 465 GLU X 366 REMARK 465 LEU X 367 REMARK 465 GLY X 368 REMARK 465 PHE X 369 REMARK 465 GLU X 370 REMARK 465 ARG X 371 REMARK 465 ASP X 372 REMARK 465 LEU X 373 REMARK 465 VAL X 374 REMARK 465 ILE X 375 REMARK 465 GLN X 376 REMARK 465 VAL X 377 REMARK 465 TYR X 378 REMARK 465 PHE X 379 REMARK 465 ALA X 380 REMARK 465 CYS X 381 REMARK 465 ASP X 382 REMARK 465 LYS X 383 REMARK 465 ASN X 384 REMARK 465 GLU X 385 REMARK 465 GLU X 386 REMARK 465 ALA X 387 REMARK 465 ALA X 388 REMARK 465 ALA X 389 REMARK 465 ASN X 390 REMARK 465 ILE X 391 REMARK 465 LEU X 392 REMARK 465 PHE X 393 REMARK 465 SER X 394 REMARK 465 ASP X 395 REMARK 465 HIS X 396 REMARK 465 ALA X 397 REMARK 465 ASP X 398 REMARK 465 DC W 16 REMARK 465 DC W 17 REMARK 465 DG Y 10 REMARK 465 DG Y 11 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 DG W 18 P OP1 OP2 REMARK 470 DG Y 9 C4' O4' C3' O3' C2' C1' N9 REMARK 470 DG Y 9 C8 N7 C5 C6 O6 N1 C2 REMARK 470 DG Y 9 N2 N3 C4 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 O LYS A 244 HD21 ASN X 272 1.39 REMARK 500 HE1 TRP A 230 O ASP A 290 1.48 REMARK 500 O2 DC W 19 H22 DG Y 7 1.50 REMARK 500 H2 G47 W 8 O2 DC Y 18 1.53 REMARK 500 H SER A 492 OE1 GLN A 495 1.54 REMARK 500 O2 DC W 7 H22 DG Y 19 1.56 REMARK 500 OE1 GLN A 287 H MET A 359 1.56 REMARK 500 HE21 GLN A 457 OD1 ASP A 489 1.58 REMARK 500 OE2 GLU A 232 HH22 ARG A 357 1.59 REMARK 500 H VAL A 438 OP1 DA W 4 1.59 REMARK 500 HH11 ARG X 266 O LEU X 305 1.60 REMARK 500 NH1 ARG X 266 O LEU X 305 2.16 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 HO5' DT W 1 O3' DA W 24 1565 1.35 REMARK 500 O5' DT W 1 O3' DA W 24 1565 1.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DT W 2 O3' DT W 2 C3' -0.061 REMARK 500 DG W 3 O3' DG W 3 C3' -0.055 REMARK 500 DT W 12 C1' DT W 12 N1 0.084 REMARK 500 DA W 21 O3' DA W 21 C3' -0.098 REMARK 500 DC W 22 O4' DC W 22 C4' 0.072 REMARK 500 DC W 22 C1' DC W 22 N1 0.176 REMARK 500 DA W 23 P DA W 23 O5' 0.064 REMARK 500 DT Y 2 C1' DT Y 2 N1 0.130 REMARK 500 REMARK 500 REMARK: NULL 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 DT W 1 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG W 3 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC W 10 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA W 24 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT Y 5 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA Y 14 O4' - C1' - N9 ANGL. DEV. = 1.9 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 ARG A 129 71.71 52.15 REMARK 500 ASN A 222 -136.20 48.69 REMARK 500 ASN A 238 -74.08 -51.01 REMARK 500 LEU A 246 -67.31 -108.31 REMARK 500 LYS A 247 -172.59 53.01 REMARK 500 GLN A 287 72.92 -116.46 REMARK 500 TRP A 316 -167.18 -162.00 REMARK 500 ASN A 334 -79.16 -80.84 REMARK 500 ARG A 342 -82.37 -110.88 REMARK 500 VAL A 352 -36.75 -134.08 REMARK 500 ARG A 361 -51.14 -137.28 REMARK 500 SER A 385 -77.30 -98.53 REMARK 500 ALA A 563 142.73 -171.46 REMARK 500 ASN A 576 132.61 -173.29 REMARK 500 THR X 258 -176.59 -67.25 REMARK 500 VAL X 302 -70.09 -51.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 PHE A 243 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 THR A 245 -12.09 REMARK 500 REMARK 500 REMARK: NULL DBREF 6UBF A 101 632 UNP P14736 RAD4_YEAST 101 632 DBREF 6UBF X 230 398 UNP P32628 RAD23_YEAST 230 398 DBREF 6UBF W 1 24 PDB 6UBF 6UBF 1 24 DBREF 6UBF Y 1 24 PDB 6UBF 6UBF 1 24 SEQADV 6UBF GLY A 95 UNP P14736 EXPRESSION TAG SEQADV 6UBF SER A 96 UNP P14736 EXPRESSION TAG SEQADV 6UBF SER A 97 UNP P14736 EXPRESSION TAG SEQADV 6UBF ARG A 98 UNP P14736 EXPRESSION TAG SEQADV 6UBF ALA A 99 UNP P14736 EXPRESSION TAG SEQADV 6UBF MET A 100 UNP P14736 EXPRESSION TAG SEQADV 6UBF THR A 115 UNP P14736 LYS 115 CONFLICT SEQADV 6UBF CYS A 131 UNP P14736 VAL 131 CONFLICT SEQADV 6UBF SER A 132 UNP P14736 CYS 132 CONFLICT SEQADV 6UBF GLU A 223 UNP P14736 VAL 223 CONFLICT SEQADV 6UBF ARG A 427 UNP P14736 GLN 427 CONFLICT SEQADV 6UBF A UNP P14736 GLU 600 DELETION SEQADV 6UBF A UNP P14736 ARG 601 DELETION SEQADV 6UBF A UNP P14736 GLY 602 DELETION SEQADV 6UBF A UNP P14736 SER 603 DELETION SEQADV 6UBF A UNP P14736 THR 604 DELETION SEQADV 6UBF A UNP P14736 VAL 605 DELETION SEQADV 6UBF A UNP P14736 LYS 606 DELETION SEQADV 6UBF GLY X 228 UNP P32628 EXPRESSION TAG SEQADV 6UBF SER X 229 UNP P32628 EXPRESSION TAG SEQRES 1 A 531 GLY SER SER ARG ALA MET GLY ASN GLU VAL ALA GLY VAL SEQRES 2 A 531 GLU ASP ILE SER VAL GLU ILE THR PRO SER SER LYS ARG SEQRES 3 A 531 ASN SER ASP ALA ARG ARG THR SER ARG ASN CYS SER SER SEQRES 4 A 531 ASN GLU GLU ARG LYS ARG ARG LYS TYR PHE HIS MET LEU SEQRES 5 A 531 TYR LEU VAL CYS LEU MET VAL HIS GLY PHE ILE ARG ASN SEQRES 6 A 531 GLU TRP ILE ASN SER LYS ARG LEU SER ARG LYS LEU SER SEQRES 7 A 531 ASN LEU VAL PRO GLU LYS VAL PHE GLU LEU LEU HIS PRO SEQRES 8 A 531 GLN LYS ASP GLU GLU LEU PRO LEU ARG SER THR ARG LYS SEQRES 9 A 531 LEU LEU ASP GLY LEU LYS LYS CYS MET GLU LEU TRP GLN SEQRES 10 A 531 LYS HIS TRP LYS ILE THR LYS LYS TYR ASP ASN GLU GLY SEQRES 11 A 531 LEU TYR MET ARG THR TRP LYS GLU ILE GLU MET SER ALA SEQRES 12 A 531 ASN ASN LYS ARG LYS PHE LYS THR LEU LYS ARG SER ASP SEQRES 13 A 531 PHE LEU ARG ALA VAL SER LYS GLY HIS GLY ASP PRO ASP SEQRES 14 A 531 ILE SER VAL GLN GLY PHE VAL ALA MET LEU ARG ALA CYS SEQRES 15 A 531 ASN VAL ASN ALA ARG LEU ILE MET SER CYS GLN PRO PRO SEQRES 16 A 531 ASP PHE THR ASN MET LYS ILE ASP THR SER LEU ASN GLY SEQRES 17 A 531 ASN ASN ALA TYR LYS ASP MET VAL LYS TYR PRO ILE PHE SEQRES 18 A 531 TRP CYS GLU VAL TRP ASP LYS PHE SER LYS LYS TRP ILE SEQRES 19 A 531 THR VAL ASP PRO VAL ASN LEU LYS THR ILE GLU GLN VAL SEQRES 20 A 531 ARG LEU HIS SER LYS LEU ALA PRO LYS GLY VAL ALA CYS SEQRES 21 A 531 CYS GLU ARG ASN MET LEU ARG TYR VAL ILE ALA TYR ASP SEQRES 22 A 531 ARG LYS TYR GLY CYS ARG ASP VAL THR ARG ARG TYR ALA SEQRES 23 A 531 GLN TRP MET ASN SER LYS VAL ARG LYS ARG ARG ILE THR SEQRES 24 A 531 LYS ASP ASP PHE GLY GLU LYS TRP PHE ARG LYS VAL ILE SEQRES 25 A 531 THR ALA LEU HIS HIS ARG LYS ARG THR LYS ILE ASP ASP SEQRES 26 A 531 TYR GLU ASP GLN TYR PHE PHE ARG ARG ASP GLU SER GLU SEQRES 27 A 531 GLY ILE PRO ASP SER VAL GLN ASP LEU LYS ASN HIS PRO SEQRES 28 A 531 TYR TYR VAL LEU GLU GLN ASP ILE LYS GLN THR GLN ILE SEQRES 29 A 531 VAL LYS PRO GLY CYS LYS GLU CYS GLY TYR LEU LYS VAL SEQRES 30 A 531 HIS GLY LYS VAL GLY LYS VAL LEU LYS VAL TYR ALA LYS SEQRES 31 A 531 ARG ASP ILE ALA ASP LEU LYS SER ALA ARG GLN TRP TYR SEQRES 32 A 531 MET ASN GLY ARG ILE LEU LYS THR GLY SER ARG CYS LYS SEQRES 33 A 531 LYS VAL ILE LYS ARG THR VAL GLY ARG PRO LYS GLY GLU SEQRES 34 A 531 ALA GLU GLU GLU ASP GLU ARG LEU TYR SER PHE GLU ASP SEQRES 35 A 531 THR GLU LEU TYR ILE PRO PRO LEU ALA SER ALA SER GLY SEQRES 36 A 531 GLU ILE THR LYS ASN THR PHE GLY ASN ILE GLU VAL PHE SEQRES 37 A 531 ALA PRO THR MET ILE PRO GLY ASN CYS CYS LEU VAL GLU SEQRES 38 A 531 ASN PRO VAL ALA ILE LYS ALA ALA ARG PHE LEU GLY VAL SEQRES 39 A 531 GLU PHE ALA PRO ALA VAL THR SER PHE LYS PHE PRO VAL SEQRES 40 A 531 LEU SER GLY ILE VAL VAL ALA LYS TRP LEU ARG GLU ALA SEQRES 41 A 531 ILE GLU THR ALA ILE ASP GLY ILE GLU PHE ILE SEQRES 1 X 171 GLY SER GLY ASN ALA SER SER GLY ALA LEU GLY THR THR SEQRES 2 X 171 GLY GLY ALA THR ASP ALA ALA GLN GLY GLY PRO PRO GLY SEQRES 3 X 171 SER ILE GLY LEU THR VAL GLU ASP LEU LEU SER LEU ARG SEQRES 4 X 171 GLN VAL VAL SER GLY ASN PRO GLU ALA LEU ALA PRO LEU SEQRES 5 X 171 LEU GLU ASN ILE SER ALA ARG TYR PRO GLN LEU ARG GLU SEQRES 6 X 171 HIS ILE MET ALA ASN PRO GLU VAL PHE VAL SER MET LEU SEQRES 7 X 171 LEU GLU ALA VAL GLY ASP ASN MET GLN ASP VAL MET GLU SEQRES 8 X 171 GLY ALA ASP ASP MET VAL GLU GLY GLU ASP ILE GLU VAL SEQRES 9 X 171 THR GLY GLU ALA ALA ALA ALA GLY LEU GLY GLN GLY GLU SEQRES 10 X 171 GLY GLU GLY SER PHE GLN VAL ASP TYR THR PRO GLU ASP SEQRES 11 X 171 ASP GLN ALA ILE SER ARG LEU CYS GLU LEU GLY PHE GLU SEQRES 12 X 171 ARG ASP LEU VAL ILE GLN VAL TYR PHE ALA CYS ASP LYS SEQRES 13 X 171 ASN GLU GLU ALA ALA ALA ASN ILE LEU PHE SER ASP HIS SEQRES 14 X 171 ALA ASP SEQRES 1 W 24 DT DT DG DA DC DT DC G47 DA DC DA DT DC SEQRES 2 W 24 DC DC DC DC DG DC DT DA DC DA DA SEQRES 1 Y 24 DA DT DT DG DT DA DG DC DG DG DG DG DG SEQRES 2 Y 24 DA DT DG DT DC DG DA DG DT DC DA HET G47 W 8 39 HETNAM G47 N2-ETHANETHIOL-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 3 G47 C12 H18 N5 O7 P S HELIX 1 AA1 SER A 133 SER A 164 1 32 HELIX 2 AA2 SER A 164 ASN A 173 1 10 HELIX 3 AA3 PRO A 176 HIS A 184 1 9 HELIX 4 AA4 LEU A 191 TRP A 214 1 24 HELIX 5 AA5 THR A 229 ALA A 237 1 9 HELIX 6 AA6 LEU A 246 GLY A 258 1 13 HELIX 7 AA7 ASP A 261 CYS A 276 1 16 HELIX 8 AA8 ASN A 304 VAL A 310 1 7 HELIX 9 AA9 VAL A 375 ALA A 380 1 6 HELIX 10 AB1 LYS A 386 LYS A 394 5 9 HELIX 11 AB2 ASP A 395 HIS A 410 1 16 HELIX 12 AB3 THR A 415 GLU A 432 1 18 HELIX 13 AB4 VAL A 438 LYS A 442 5 5 HELIX 14 AB5 GLN A 451 ILE A 453 5 3 HELIX 15 AB6 SER A 492 MET A 498 1 7 HELIX 16 AB7 ALA A 563 ILE A 567 5 5 HELIX 17 AB8 VAL A 578 GLY A 587 1 10 HELIX 18 AB9 LEU A 618 GLY A 628 1 11 HELIX 19 AC1 ILE A 629 ILE A 632 5 4 HELIX 20 AC2 VAL X 259 ASN X 272 1 14 HELIX 21 AC3 ALA X 275 TYR X 287 1 13 HELIX 22 AC4 GLN X 289 ASN X 297 1 9 HELIX 23 AC5 ASN X 297 ALA X 308 1 12 SHEET 1 AA1 2 ILE A 216 THR A 217 0 SHEET 2 AA1 2 HIS A 259 GLY A 260 1 O GLY A 260 N ILE A 216 SHEET 1 AA2 6 THR A 337 GLU A 339 0 SHEET 2 AA2 6 LYS A 326 ASP A 331 -1 N ASP A 331 O THR A 337 SHEET 3 AA2 6 PHE A 315 ASP A 321 -1 N VAL A 319 O ILE A 328 SHEET 4 AA2 6 ALA A 280 CYS A 286 -1 N ILE A 283 O TRP A 316 SHEET 5 AA2 6 TYR A 362 TYR A 366 -1 O ILE A 364 N MET A 284 SHEET 6 AA2 6 CYS A 372 ASP A 374 -1 O ARG A 373 N ALA A 365 SHEET 1 AA3 3 TYR A 447 LEU A 449 0 SHEET 2 AA3 3 VAL A 478 ALA A 483 -1 O TYR A 482 N VAL A 448 SHEET 3 AA3 3 GLY A 467 LYS A 470 -1 N GLY A 467 O VAL A 481 SHEET 1 AA4 3 GLN A 457 VAL A 459 0 SHEET 2 AA4 3 ILE A 487 LYS A 491 -1 O ALA A 488 N ILE A 458 SHEET 3 AA4 3 TYR A 532 SER A 533 -1 O TYR A 532 N LYS A 491 SHEET 1 AA5 2 ARG A 501 LEU A 503 0 SHEET 2 AA5 2 THR A 537 LEU A 539 -1 O GLU A 538 N ILE A 502 SHEET 1 AA6 4 ILE A 559 GLU A 560 0 SHEET 2 AA6 4 PRO A 592 VAL A 594 1 O PRO A 592 N ILE A 559 SHEET 3 AA6 4 LEU A 609 ALA A 615 -1 O GLY A 611 N ALA A 593 SHEET 4 AA6 4 CYS A 571 GLU A 575 -1 N VAL A 574 O ILE A 612 LINK SG CYS A 131 SG G47 W 8 1555 1555 2.01 LINK O3' DC W 7 P G47 W 8 1555 1555 1.61 LINK O3' G47 W 8 P DA W 9 1555 1555 1.61 CRYST1 78.723 78.723 403.824 90.00 90.00 90.00 P 41 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 0.012703 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012703 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002476 0.00000