HEADER DNA BINDING PROTEIN/DNA 31-JUL-07 2QSG TITLE CRYSTAL STRUCTURE OF RAD4-RAD23 BOUND TO A UV-DAMAGED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: NATIVE STRAND OF THE CPD-MISMATCH DNA; COMPND 3 CHAIN: W; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DAMAGED STRAND OF THE CPD-MISMATCH DNA; COMPND 7 CHAIN: Y; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: MODIFIED RESIDUES LABELED NN ARE NOT VISIBLE, SEE COMPND 10 REMARK 400; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA REPAIR PROTEIN RAD4; COMPND 13 CHAIN: A; COMPND 14 SYNONYM: RAD4; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: UV EXCISION REPAIR PROTEIN RAD23; COMPND 18 CHAIN: X; COMPND 19 SYNONYM: RAD23; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 7 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 8 ORGANISM_TAXID: 4932; SOURCE 9 GENE: RAD4; SOURCE 10 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 11 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 13 EXPRESSION_SYSTEM_CELL_LINE: HI5; SOURCE 14 EXPRESSION_SYSTEM_ORGAN: EGGS; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 16 EXPRESSION_SYSTEM_VECTOR: PFASTBAC DUAL; SOURCE 17 MOL_ID: 4; SOURCE 18 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 19 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 20 ORGANISM_TAXID: 4932; SOURCE 21 GENE: RAD23; SOURCE 22 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 23 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 24 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 25 EXPRESSION_SYSTEM_CELL_LINE: HI5; SOURCE 26 EXPRESSION_SYSTEM_ORGAN: EGGS; SOURCE 27 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 28 EXPRESSION_SYSTEM_VECTOR: PFASTBAC DUAL KEYWDS ALPHA-BETA STRUCTURE, BETA HAIRPIN, TRANSGLUTAMINASE FOLD, DNA-DAMAGE KEYWDS 2 RECOGNITION, DNA REPAIR, DNA BINDING PROTEIN, NUCLEOTIDE EXCISION KEYWDS 3 REPAIR, XERODERMA PIGMENTOSUM, DNA BINDING, PROTEIN-DNA COMPLEX, KEYWDS 4 CYCLOBUTANEPYRIMIDINE CPD DIMER, ULTRAVIOLET UV DAMAGE, MISMATCH KEYWDS 5 DNA, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.-H.MIN,N.P.PAVLETICH REVDAT 4 21-FEB-24 2QSG 1 SEQADV SEQRES REVDAT 3 24-FEB-09 2QSG 1 VERSN REVDAT 2 20-NOV-07 2QSG 1 JRNL REVDAT 1 02-OCT-07 2QSG 0 JRNL AUTH J.-H.MIN,N.P.PAVLETICH JRNL TITL RECOGNITION OF DNA DAMAGE BY THE RAD4 NUCLEOTIDE EXCISION JRNL TITL 2 REPAIR PROTEIN JRNL REF NATURE V. 449 570 2007 JRNL REFN ISSN 0028-0836 JRNL PMID 17882165 JRNL DOI 10.1038/NATURE06155 REMARK 2 REMARK 2 RESOLUTION. 3.10 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 23084 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) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1170 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) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1485 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.2950 REMARK 3 BIN FREE R VALUE SET COUNT : 73 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4548 REMARK 3 NUCLEIC ACID ATOMS : 932 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.74000 REMARK 3 B22 (A**2) : 1.74000 REMARK 3 B33 (A**2) : -3.48000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.446 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.302 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 37.801 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.919 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.898 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5686 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7855 ; 1.241 ; 2.174 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 553 ; 5.321 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 216 ;34.596 ;23.056 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 891 ;20.824 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 43 ;18.548 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 858 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3934 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2614 ; 0.215 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3754 ; 0.312 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 164 ; 0.143 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL 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): 50 ; 0.179 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.133 ; 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): 2826 ; 0.759 ; 1.250 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4502 ; 1.309 ; 1.750 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3534 ; 1.291 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3353 ; 2.091 ; 3.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2QSG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1000043997. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : NULL 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 : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97922 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23795 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM BIS-TRIS PROPANE, 100MM SODIUM REMARK 280 CHLORIDE, 6% (V/V) ISOPROPANOL, 14 MM CALCIUM CHLORIDE AND 5 MM REMARK 280 DITHIOTHREITOL, PH 6.8, HANGING-DROP VAPOR DIFFUSION, REMARK 280 TEMPERATURE 277K, VAPOR DIFFUSION, HANGING DROP 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 201.98000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.82200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.82200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 100.99000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.82200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.82200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 302.97000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.82200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.82200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 100.99000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.82200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.82200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 302.97000 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 201.98000 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 APPLY THE FOLLOWING TO CHAINS: W, Y, A, X 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 400 REMARK 400 COMPOUND REMARK 400 THE DAMAGED RESIDUES, LABELED NN, FORM CIS-SYN REMARK 400 CYCLOBUTANE PYRIMIDINE DIMER AND ARE NOT VISIBLE REMARK 400 IN ELECTRON DENSITY 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 N Y 9 REMARK 465 N Y 10 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 LYS 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 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 GLU A 525 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 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 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 DT Y 11 P OP1 OP2 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 DG W 3 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA W 4 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC W 5 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA W 9 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC W 10 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT W 12 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 DG W 18 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 DC W 19 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 DT W 20 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC W 22 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DC W 22 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DC W 22 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DA Y 1 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DT Y 2 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT Y 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG Y 7 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT Y 11 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG Y 12 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 DG Y 13 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES REMARK 500 DT Y 15 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT Y 18 C1' - O4' - C4' ANGL. DEV. = -6.0 DEGREES REMARK 500 DT Y 18 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG Y 21 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT Y 22 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC Y 23 O4' - C1' - N1 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 ASN A 130 43.85 -77.64 REMARK 500 ASN A 163 1.80 -60.91 REMARK 500 LEU A 191 87.55 -151.73 REMARK 500 ASN A 222 83.82 -152.97 REMARK 500 GLN A 287 77.09 -115.46 REMARK 500 ASN A 304 28.88 48.11 REMARK 500 TRP A 316 -153.96 -148.07 REMARK 500 ASN A 334 -72.75 -82.92 REMARK 500 ARG A 361 -25.45 -159.62 REMARK 500 CYS A 372 110.18 -176.62 REMARK 500 TRP A 382 58.75 -118.88 REMARK 500 LYS A 442 -78.60 -72.01 REMARK 500 ASN A 443 47.55 -104.22 REMARK 500 ASP A 528 99.68 -66.48 REMARK 500 ASN A 554 -167.93 -74.40 REMARK 500 ASN A 570 15.43 -141.91 REMARK 500 GLU A 600 -155.90 168.91 REMARK 500 ARG A 601 -166.78 68.38 REMARK 500 THR A 604 -179.72 87.77 REMARK 500 ASN X 272 48.77 -141.49 REMARK 500 ALA X 308 10.77 53.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QSF RELATED DB: PDB REMARK 900 RELATED ID: 2QSH RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 DNA PLASMID SEQUENCING DATA CONFIRM THE REPORTED REMARK 999 SEQUENCE OF CHAIN A DBREF 2QSG A 101 632 UNP P14736 RAD4_YEAST 101 632 DBREF 2QSG X 230 398 UNP P32628 RAD23_YEAST 230 398 DBREF 2QSG W 1 24 PDB 2QSG 2QSG 1 24 DBREF 2QSG Y 1 24 PDB 2QSG 2QSG 1 24 SEQADV 2QSG MET A 100 UNP P14736 INITIATING METHIONINE SEQADV 2QSG GLU A 223 UNP P14736 VAL 223 SEE REMARK 999 SEQADV 2QSG LEU A 225 UNP P14736 ILE 225 SEE REMARK 999 SEQADV 2QSG GLY X 228 UNP P32628 EXPRESSION TAG SEQADV 2QSG SER X 229 UNP P32628 EXPRESSION TAG SEQRES 1 W 24 DT DT DG DA DC DT DC DA DA DC DA DT DC SEQRES 2 W 24 DC DT DT DT DG DC DT DA DC DA DA SEQRES 1 Y 24 DA DT DT DG DT DA DG DC N N DT DG DG SEQRES 2 Y 24 DA DT DG DT DT DG DA DG DT DC DA SEQRES 1 A 533 MET GLY ASN GLU VAL ALA GLY VAL GLU ASP ILE SER VAL SEQRES 2 A 533 GLU ILE LYS PRO SER SER LYS ARG ASN SER ASP ALA ARG SEQRES 3 A 533 ARG THR SER ARG ASN VAL CYS SER ASN GLU GLU ARG LYS SEQRES 4 A 533 ARG ARG LYS TYR PHE HIS MET LEU TYR LEU VAL CYS LEU SEQRES 5 A 533 MET VAL HIS GLY PHE ILE ARG ASN GLU TRP ILE ASN SER SEQRES 6 A 533 LYS ARG LEU SER ARG LYS LEU SER ASN LEU VAL PRO GLU SEQRES 7 A 533 LYS VAL PHE GLU LEU LEU HIS PRO GLN LYS ASP GLU GLU SEQRES 8 A 533 LEU PRO LEU ARG SER THR ARG LYS LEU LEU ASP GLY LEU SEQRES 9 A 533 LYS LYS CYS MET GLU LEU TRP GLN LYS HIS TRP LYS ILE SEQRES 10 A 533 THR LYS LYS TYR ASP ASN GLU GLY LEU TYR MET ARG THR SEQRES 11 A 533 TRP LYS GLU ILE GLU MET SER ALA ASN ASN LYS ARG LYS SEQRES 12 A 533 PHE LYS THR LEU LYS ARG SER ASP PHE LEU ARG ALA VAL SEQRES 13 A 533 SER LYS GLY HIS GLY ASP PRO ASP ILE SER VAL GLN GLY SEQRES 14 A 533 PHE VAL ALA MET LEU ARG ALA CYS ASN VAL ASN ALA ARG SEQRES 15 A 533 LEU ILE MET SER CYS GLN PRO PRO ASP PHE THR ASN MET SEQRES 16 A 533 LYS ILE ASP THR SER LEU ASN GLY ASN ASN ALA TYR LYS SEQRES 17 A 533 ASP MET VAL LYS TYR PRO ILE PHE TRP CYS GLU VAL TRP SEQRES 18 A 533 ASP LYS PHE SER LYS LYS TRP ILE THR VAL ASP PRO VAL SEQRES 19 A 533 ASN LEU LYS THR ILE GLU GLN VAL ARG LEU HIS SER LYS SEQRES 20 A 533 LEU ALA PRO LYS GLY VAL ALA CYS CYS GLU ARG ASN MET SEQRES 21 A 533 LEU ARG TYR VAL ILE ALA TYR ASP ARG LYS TYR GLY CYS SEQRES 22 A 533 ARG ASP VAL THR ARG ARG TYR ALA GLN TRP MET ASN SER SEQRES 23 A 533 LYS VAL ARG LYS ARG ARG ILE THR LYS ASP ASP PHE GLY SEQRES 24 A 533 GLU LYS TRP PHE ARG LYS VAL ILE THR ALA LEU HIS HIS SEQRES 25 A 533 ARG LYS ARG THR LYS ILE ASP ASP TYR GLU ASP GLN TYR SEQRES 26 A 533 PHE PHE GLN ARG ASP GLU SER GLU GLY ILE PRO ASP SER SEQRES 27 A 533 VAL GLN ASP LEU LYS ASN HIS PRO TYR TYR VAL LEU GLU SEQRES 28 A 533 GLN ASP ILE LYS GLN THR GLN ILE VAL LYS PRO GLY CYS SEQRES 29 A 533 LYS GLU CYS GLY TYR LEU LYS VAL HIS GLY LYS VAL GLY SEQRES 30 A 533 LYS VAL LEU LYS VAL TYR ALA LYS ARG ASP ILE ALA ASP SEQRES 31 A 533 LEU LYS SER ALA ARG GLN TRP TYR MET ASN GLY ARG ILE SEQRES 32 A 533 LEU LYS THR GLY SER ARG CYS LYS LYS VAL ILE LYS ARG SEQRES 33 A 533 THR VAL GLY ARG PRO LYS GLY GLU ALA GLU GLU GLU ASP SEQRES 34 A 533 GLU ARG LEU TYR SER PHE GLU ASP THR GLU LEU TYR ILE SEQRES 35 A 533 PRO PRO LEU ALA SER ALA SER GLY GLU ILE THR LYS ASN SEQRES 36 A 533 THR PHE GLY ASN ILE GLU VAL PHE ALA PRO THR MET ILE SEQRES 37 A 533 PRO GLY ASN CYS CYS LEU VAL GLU ASN PRO VAL ALA ILE SEQRES 38 A 533 LYS ALA ALA ARG PHE LEU GLY VAL GLU PHE ALA PRO ALA SEQRES 39 A 533 VAL THR SER PHE LYS PHE GLU ARG GLY SER THR VAL LYS SEQRES 40 A 533 PRO VAL LEU SER GLY ILE VAL VAL ALA LYS TRP LEU ARG SEQRES 41 A 533 GLU ALA 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 HELIX 1 1 ASP A 123 ARG A 129 1 7 HELIX 2 2 SER A 133 ASN A 163 1 31 HELIX 3 3 SER A 164 ASN A 173 1 10 HELIX 4 4 PRO A 176 HIS A 184 1 9 HELIX 5 5 PRO A 192 TRP A 214 1 23 HELIX 6 6 THR A 229 ASN A 239 1 11 HELIX 7 7 LYS A 247 GLY A 258 1 12 HELIX 8 8 ASP A 261 ALA A 275 1 15 HELIX 9 9 ASN A 304 VAL A 310 1 7 HELIX 10 10 ALA A 353 ARG A 357 5 5 HELIX 11 11 VAL A 375 ALA A 380 1 6 HELIX 12 12 VAL A 387 ARG A 391 5 5 HELIX 13 13 ASP A 395 HIS A 410 1 16 HELIX 14 14 THR A 415 GLY A 433 1 19 HELIX 15 15 SER A 437 LYS A 442 5 6 HELIX 16 16 GLN A 451 ILE A 453 5 3 HELIX 17 17 ALA A 493 MET A 498 1 6 HELIX 18 18 SER A 533 GLU A 535 5 3 HELIX 19 19 ALA A 563 ILE A 567 5 5 HELIX 20 20 VAL A 578 LEU A 586 1 9 HELIX 21 21 LEU A 618 GLY A 628 1 11 HELIX 22 22 ILE A 629 ILE A 632 5 4 HELIX 23 23 THR X 258 ASN X 272 1 15 HELIX 24 24 ALA X 275 TYR X 287 1 13 HELIX 25 25 GLN X 289 ASN X 297 1 9 HELIX 26 26 ASN X 297 GLU X 307 1 11 SHEET 1 A 2 ILE A 216 THR A 217 0 SHEET 2 A 2 HIS A 259 GLY A 260 1 O GLY A 260 N ILE A 216 SHEET 1 B 6 THR A 337 GLU A 339 0 SHEET 2 B 6 LYS A 326 ASP A 331 -1 N ASP A 331 O THR A 337 SHEET 3 B 6 PHE A 315 ASP A 321 -1 N VAL A 319 O ILE A 328 SHEET 4 B 6 ALA A 280 SER A 285 -1 N ARG A 281 O GLU A 318 SHEET 5 B 6 VAL A 363 TYR A 366 -1 O ILE A 364 N MET A 284 SHEET 6 B 6 ARG A 373 ASP A 374 -1 O ARG A 373 N ALA A 365 SHEET 1 C 3 TYR A 447 LEU A 449 0 SHEET 2 C 3 VAL A 478 ALA A 483 -1 O TYR A 482 N VAL A 448 SHEET 3 C 3 GLY A 467 LYS A 470 -1 N GLY A 467 O VAL A 481 SHEET 1 D 2 GLN A 457 VAL A 459 0 SHEET 2 D 2 ILE A 487 ASP A 489 -1 O ALA A 488 N ILE A 458 SHEET 1 E 3 LYS A 491 SER A 492 0 SHEET 2 E 3 ASP A 528 TYR A 532 -1 O TYR A 532 N LYS A 491 SHEET 3 E 3 LYS A 511 LYS A 514 -1 N ILE A 513 O GLU A 529 SHEET 1 F 2 ARG A 501 LEU A 503 0 SHEET 2 F 2 THR A 537 LEU A 539 -1 O GLU A 538 N ILE A 502 SHEET 1 G 4 ILE A 559 GLU A 560 0 SHEET 2 G 4 ALA A 591 VAL A 594 1 O PRO A 592 N ILE A 559 SHEET 3 G 4 LEU A 609 ALA A 615 -1 O GLY A 611 N ALA A 593 SHEET 4 G 4 CYS A 571 GLU A 575 -1 N VAL A 574 O ILE A 612 SHEET 1 H 2 LYS A 598 PHE A 599 0 SHEET 2 H 2 VAL A 605 LYS A 606 -1 O LYS A 606 N LYS A 598 CRYST1 79.644 79.644 403.960 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 0.012556 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012556 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002475 0.00000