HEADER DNA BINDING PROTEIN/DNA 25-SEP-19 6UG1 TITLE SEQUENCE IMPACT IN DNA DUPLEX OPENING BY THE RAD4/XPC NUCLEOTIDE TITLE 2 EXCISION REPAIR COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA REPAIR PROTEIN RAD4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 129-632; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: UV EXCISION REPAIR PROTEIN RAD23; COMPND 8 CHAIN: X; COMPND 9 FRAGMENT: UNP RESIDUES 256-311; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'- COMPND 13 D(*AP*TP*TP*GP*TP*AP*GP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A)-3'); COMPND 14 CHAIN: Y; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*(G47) COMPND 18 P*AP*CP*AP*TP*CP*CP*CP*CP*TP*AP*CP*AP*A)-3'); COMPND 19 CHAIN: W; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 3 S288C); SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 559292; SOURCE 6 STRAIN: ATCC 204508 / S288C; SOURCE 7 ATCC: 204508; SOURCE 8 GENE: RAD4, YER162C; SOURCE 9 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 10 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 14 S288C); SOURCE 15 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 16 ORGANISM_TAXID: 559292; SOURCE 17 STRAIN: ATCC 204508 / S288C; SOURCE 18 GENE: RAD23, YEL037C, SYGP-ORF29; SOURCE 19 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 20 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 22 MOL_ID: 3; SOURCE 23 SYNTHETIC: YES; SOURCE 24 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 25 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 26 ORGANISM_TAXID: 4932; SOURCE 27 MOL_ID: 4; SOURCE 28 SYNTHETIC: YES; SOURCE 29 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 30 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 31 ORGANISM_TAXID: 4932 KEYWDS DNA DAMAGE RECOGNITION, DNA REPAIR, BETA-HAIRPIN MOTIF, XERODERMA KEYWDS 2 PIGMENTOSUM, XPC, RAD4, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.PAUL,J.-H.MIN REVDAT 2 08-SEP-21 6UG1 1 JRNL REVDAT 1 31-MAR-21 6UG1 0 JRNL AUTH D.PAUL,H.MU,A.TAVAKOLI,Q.DAI,S.CHAKRABORTY,C.HE,A.ANSARI, JRNL AUTH 2 S.BROYDE,J.H.MIN JRNL TITL IMPACT OF DNA SEQUENCES ON DNA 'OPENING' BY THE RAD4/XPC JRNL TITL 2 NUCLEOTIDE EXCISION REPAIR COMPLEX. JRNL REF DNA REPAIR (AMST) V. 107 03194 2021 JRNL REFN ISSN 1568-7856 JRNL PMID 34428697 JRNL DOI 10.1016/J.DNAREP.2021.103194 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH X.CHEN,Y.VELMURUGU,G.ZHENG,B.PARK,Y.SHIM,Y.KIM,L.LIU, REMARK 1 AUTH 2 B.VAN HOUTEN,C.HE,A.ANSARI,J.H.MIN REMARK 1 TITL KINETIC GATING MECHANISM OF DNA DAMAGE RECOGNITION BY REMARK 1 TITL 2 RAD4/XPC. REMARK 1 REF NAT COMMUN V. 6 5849 2015 REMARK 1 REFN ESSN 2041-1723 REMARK 1 PMID 25562780 REMARK 1 DOI 10.1038/NCOMMS6849 REMARK 2 REMARK 2 RESOLUTION. 2.83 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.7 REMARK 3 NUMBER OF REFLECTIONS : 17958 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 886 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 39.4000 - 5.1439 0.99 3235 162 0.1677 0.2132 REMARK 3 2 5.1439 - 4.0843 0.98 3124 186 0.1886 0.2073 REMARK 3 3 4.0843 - 3.5684 0.51 1672 77 0.2962 0.3750 REMARK 3 4 3.5684 - 3.2423 0.96 3117 158 0.2778 0.3647 REMARK 3 5 3.2423 - 3.0100 0.99 3197 170 0.2883 0.3832 REMARK 3 6 3.0100 - 2.8400 0.84 2727 133 0.3151 0.3623 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.490 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 84.18 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 : 0.019 5425 REMARK 3 ANGLE : 2.113 7479 REMARK 3 CHIRALITY : 0.106 815 REMARK 3 PLANARITY : 0.017 798 REMARK 3 DIHEDRAL : 18.353 3146 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 6UG1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1000244540. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-16 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-D 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 : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18202 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 91.2 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 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 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM BTP-HCL, 150 MM SODIUM CHLORIDE, REMARK 280 12% ISOPROPANOL, 100 MM CALCIUM CHLORIDE, PH 6.8, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z 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 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: 7690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, X, Y, W 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 302 REMARK 465 ASN A 303 REMARK 465 ASN A 304 REMARK 465 THR A 505 REMARK 465 LYS A 514 REMARK 465 ARG A 515 REMARK 465 THR A 516 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 GLU A 525 REMARK 465 GLU A 526 REMARK 465 ASP A 527 REMARK 465 ALA A 545 REMARK 465 SER A 546 REMARK 465 PHE A 599 REMARK 465 GLU A 600 REMARK 465 ARG A 601 REMARK 465 GLY A 602 REMARK 465 SER A 603 REMARK 465 THR A 604 REMARK 465 VAL A 605 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 ILE A 559 H VAL A 594 1.54 REMARK 500 N1 DA Y 19 H3 DT W 6 1.55 REMARK 500 O ALA A 591 H VAL A 613 1.55 REMARK 500 OD1 ASP A 290 HG1 THR A 292 1.55 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 HE22 GLN A 186 O3' DC W 22 1545 1.50 REMARK 500 NE2 GLN A 186 O3' DC W 22 1545 2.08 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 TYR A 147 CB TYR A 147 CG -0.098 REMARK 500 VAL A 405 CB VAL A 405 CG2 -0.152 REMARK 500 DG Y 3 O3' DG Y 3 C3' -0.084 REMARK 500 DG Y 8 O3' DG Y 8 C3' -0.040 REMARK 500 DG Y 10 O3' DG Y 10 C3' 0.104 REMARK 500 DG Y 12 O3' DG Y 12 C3' -0.047 REMARK 500 DT Y 16 O3' DT Y 16 C3' 0.091 REMARK 500 DA Y 19 O3' DA Y 19 C3' -0.049 REMARK 500 DT W 2 O3' DT W 2 C3' -0.041 REMARK 500 DA W 9 O3' DA W 9 C3' -0.078 REMARK 500 DC W 13 O3' DC W 13 C3' -0.064 REMARK 500 DC W 19 O3' DC W 19 C3' -0.055 REMARK 500 DC W 22 C1' DC W 22 N1 0.093 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 MET A 152 CG - SD - CE ANGL. DEV. = 11.9 DEGREES REMARK 500 ARG A 169 CG - CD - NE ANGL. DEV. = -12.7 DEGREES REMARK 500 MET A 294 CG - SD - CE ANGL. DEV. = 10.8 DEGREES REMARK 500 ASP A 367 CB - CG - OD1 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 373 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 390 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 391 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 CYS A 466 CA - CB - SG ANGL. DEV. = 9.9 DEGREES REMARK 500 ARG A 584 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 584 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG X 291 CG - CD - NE ANGL. DEV. = 14.0 DEGREES REMARK 500 DG Y 3 O4' - C1' - N9 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT Y 4 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 DA Y 5 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC Y 7 C3' - O3' - P ANGL. DEV. = 8.0 DEGREES REMARK 500 DG Y 8 O3' - P - OP1 ANGL. DEV. = 8.0 DEGREES REMARK 500 DG Y 8 O5' - P - OP1 ANGL. DEV. = -7.5 DEGREES REMARK 500 DG Y 10 O4' - C1' - N9 ANGL. DEV. = -10.8 DEGREES REMARK 500 DC Y 11 O5' - P - OP1 ANGL. DEV. = -10.5 DEGREES REMARK 500 DA Y 13 O5' - P - OP1 ANGL. DEV. = -10.2 DEGREES REMARK 500 DG Y 18 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA Y 19 O5' - P - OP2 ANGL. DEV. = -6.5 DEGREES REMARK 500 DA Y 23 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DT W 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG W 3 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 DC W 5 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT W 6 O4' - C1' - N1 ANGL. DEV. = -5.5 DEGREES REMARK 500 DA W 9 O3' - P - OP1 ANGL. DEV. = 8.7 DEGREES REMARK 500 DA W 9 O4' - C1' - N9 ANGL. DEV. = -7.1 DEGREES REMARK 500 DC W 10 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 DA W 11 O5' - P - OP2 ANGL. DEV. = -6.7 DEGREES REMARK 500 DA W 11 C5' - C4' - C3' ANGL. DEV. = 11.2 DEGREES REMARK 500 DA W 11 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT W 12 O3' - P - OP2 ANGL. DEV. = 7.4 DEGREES REMARK 500 DT W 12 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 DC W 13 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG W 16 O5' - P - OP2 ANGL. DEV. = -7.1 DEGREES REMARK 500 DG W 16 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG W 18 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC W 22 O4' - C1' - N1 ANGL. DEV. = 3.2 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 222 -139.61 50.22 REMARK 500 ARG A 241 -148.05 52.65 REMARK 500 LEU A 246 -66.84 -107.47 REMARK 500 LYS A 247 -176.23 54.18 REMARK 500 GLN A 287 74.27 -115.65 REMARK 500 ASP A 297 -62.23 -94.31 REMARK 500 TRP A 316 -166.76 -163.59 REMARK 500 ASN A 334 -77.87 -82.26 REMARK 500 ARG A 342 -81.71 -109.90 REMARK 500 ARG A 361 -49.35 -136.07 REMARK 500 SER A 385 -76.42 -100.46 REMARK 500 SER A 507 -157.39 -98.49 REMARK 500 ALA A 563 142.24 -172.20 REMARK 500 ASN A 576 131.84 -173.58 REMARK 500 VAL A 588 -108.75 87.92 REMARK 500 GLU A 589 79.60 161.14 REMARK 500 PHE A 590 -162.98 -107.43 REMARK 500 SER A 596 175.26 175.78 REMARK 500 THR X 258 -177.14 -66.73 REMARK 500 GLU X 307 52.71 -93.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU X 307 ALA X 308 146.80 REMARK 500 REMARK 500 REMARK: NULL DBREF 6UG1 A 129 632 UNP P14736 RAD4_YEAST 129 632 DBREF 6UG1 X 256 311 UNP P32628 RAD23_YEAST 256 311 DBREF 6UG1 Y 3 23 PDB 6UG1 6UG1 3 23 DBREF 6UG1 W 2 22 PDB 6UG1 6UG1 2 22 SEQADV 6UG1 CYS A 131 UNP P14736 VAL 131 CONFLICT SEQADV 6UG1 SER A 132 UNP P14736 CYS 132 CONFLICT SEQADV 6UG1 GLU A 223 UNP P14736 VAL 223 CONFLICT SEQADV 6UG1 ARG A 427 UNP P14736 GLN 427 CONFLICT SEQADV 6UG1 ASP A 527 UNP P14736 GLU 527 CONFLICT SEQADV 6UG1 ALA A 528 UNP P14736 ASP 528 CONFLICT SEQADV 6UG1 ALA X 255 UNP P32628 EXPRESSION TAG SEQRES 1 A 504 ARG ASN CYS SER SER ASN GLU GLU ARG LYS ARG ARG LYS SEQRES 2 A 504 TYR PHE HIS MET LEU TYR LEU VAL CYS LEU MET VAL HIS SEQRES 3 A 504 GLY PHE ILE ARG ASN GLU TRP ILE ASN SER LYS ARG LEU SEQRES 4 A 504 SER ARG LYS LEU SER ASN LEU VAL PRO GLU LYS VAL PHE SEQRES 5 A 504 GLU LEU LEU HIS PRO GLN LYS ASP GLU GLU LEU PRO LEU SEQRES 6 A 504 ARG SER THR ARG LYS LEU LEU ASP GLY LEU LYS LYS CYS SEQRES 7 A 504 MET GLU LEU TRP GLN LYS HIS TRP LYS ILE THR LYS LYS SEQRES 8 A 504 TYR ASP ASN GLU GLY LEU TYR MET ARG THR TRP LYS GLU SEQRES 9 A 504 ILE GLU MET SER ALA ASN ASN LYS ARG LYS PHE LYS THR SEQRES 10 A 504 LEU LYS ARG SER ASP PHE LEU ARG ALA VAL SER LYS GLY SEQRES 11 A 504 HIS GLY ASP PRO ASP ILE SER VAL GLN GLY PHE VAL ALA SEQRES 12 A 504 MET LEU ARG ALA CYS ASN VAL ASN ALA ARG LEU ILE MET SEQRES 13 A 504 SER CYS GLN PRO PRO ASP PHE THR ASN MET LYS ILE ASP SEQRES 14 A 504 THR SER LEU ASN GLY ASN ASN ALA TYR LYS ASP MET VAL SEQRES 15 A 504 LYS TYR PRO ILE PHE TRP CYS GLU VAL TRP ASP LYS PHE SEQRES 16 A 504 SER LYS LYS TRP ILE THR VAL ASP PRO VAL ASN LEU LYS SEQRES 17 A 504 THR ILE GLU GLN VAL ARG LEU HIS SER LYS LEU ALA PRO SEQRES 18 A 504 LYS GLY VAL ALA CYS CYS GLU ARG ASN MET LEU ARG TYR SEQRES 19 A 504 VAL ILE ALA TYR ASP ARG LYS TYR GLY CYS ARG ASP VAL SEQRES 20 A 504 THR ARG ARG TYR ALA GLN TRP MET ASN SER LYS VAL ARG SEQRES 21 A 504 LYS ARG ARG ILE THR LYS ASP ASP PHE GLY GLU LYS TRP SEQRES 22 A 504 PHE ARG LYS VAL ILE THR ALA LEU HIS HIS ARG LYS ARG SEQRES 23 A 504 THR LYS ILE ASP ASP TYR GLU ASP GLN TYR PHE PHE ARG SEQRES 24 A 504 ARG ASP GLU SER GLU GLY ILE PRO ASP SER VAL GLN ASP SEQRES 25 A 504 LEU LYS ASN HIS PRO TYR TYR VAL LEU GLU GLN ASP ILE SEQRES 26 A 504 LYS GLN THR GLN ILE VAL LYS PRO GLY CYS LYS GLU CYS SEQRES 27 A 504 GLY TYR LEU LYS VAL HIS GLY LYS VAL GLY LYS VAL LEU SEQRES 28 A 504 LYS VAL TYR ALA LYS ARG ASP ILE ALA ASP LEU LYS SER SEQRES 29 A 504 ALA ARG GLN TRP TYR MET ASN GLY ARG ILE LEU LYS THR SEQRES 30 A 504 GLY SER ARG CYS LYS LYS VAL ILE LYS ARG THR VAL GLY SEQRES 31 A 504 ARG PRO LYS GLY GLU ALA GLU GLU ASP ALA GLU ARG LEU SEQRES 32 A 504 TYR SER PHE GLU ASP THR GLU LEU TYR ILE PRO PRO LEU SEQRES 33 A 504 ALA SER ALA SER GLY GLU ILE THR LYS ASN THR PHE GLY SEQRES 34 A 504 ASN ILE GLU VAL PHE ALA PRO THR MET ILE PRO GLY ASN SEQRES 35 A 504 CYS CYS LEU VAL GLU ASN PRO VAL ALA ILE LYS ALA ALA SEQRES 36 A 504 ARG PHE LEU GLY VAL GLU PHE ALA PRO ALA VAL THR SER SEQRES 37 A 504 PHE LYS PHE GLU ARG GLY SER THR VAL LYS PRO VAL LEU SEQRES 38 A 504 SER GLY ILE VAL VAL ALA LYS TRP LEU ARG GLU ALA ILE SEQRES 39 A 504 GLU THR ALA ILE ASP GLY ILE GLU PHE ILE SEQRES 1 X 57 ALA GLY LEU THR VAL GLU ASP LEU LEU SER LEU ARG GLN SEQRES 2 X 57 VAL VAL SER GLY ASN PRO GLU ALA LEU ALA PRO LEU LEU SEQRES 3 X 57 GLU ASN ILE SER ALA ARG TYR PRO GLN LEU ARG GLU HIS SEQRES 4 X 57 ILE MET ALA ASN PRO GLU VAL PHE VAL SER MET LEU LEU SEQRES 5 X 57 GLU ALA VAL GLY ASP SEQRES 1 Y 21 DG DT DA DG DC DG DC DG DC DG DA DT DG SEQRES 2 Y 21 DT DC DG DA DG DT DC DA SEQRES 1 W 21 DT DG DA DC DT DC G47 DA DC DA DT DC DG SEQRES 2 W 21 DC DG DC DG DC DT DA DC HET G47 W 8 39 HETNAM G47 N2-ETHANETHIOL-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 4 G47 C12 H18 N5 O7 P S HELIX 1 AA1 SER A 133 ASN A 163 1 31 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 ASN A 239 1 11 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 TYR A 306 VAL A 310 1 5 HELIX 9 AA9 ALA A 353 ARG A 357 5 5 HELIX 10 AB1 VAL A 375 ALA A 380 1 6 HELIX 11 AB2 LYS A 386 LYS A 394 5 9 HELIX 12 AB3 ASP A 395 HIS A 410 1 16 HELIX 13 AB4 THR A 415 SER A 431 1 17 HELIX 14 AB5 VAL A 438 LYS A 442 5 5 HELIX 15 AB6 GLN A 451 ILE A 453 5 3 HELIX 16 AB7 ALA A 493 MET A 498 1 6 HELIX 17 AB8 ALA A 563 ILE A 567 5 5 HELIX 18 AB9 VAL A 578 LEU A 586 1 9 HELIX 19 AC1 LEU A 618 GLY A 628 1 11 HELIX 20 AC2 ILE A 629 ILE A 632 5 4 HELIX 21 AC3 THR X 258 ASN X 272 1 15 HELIX 22 AC4 ALA X 275 TYR X 287 1 13 HELIX 23 AC5 GLN X 289 ASN X 297 1 9 HELIX 24 AC6 ASN X 297 GLU X 307 1 11 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 TYR A 366 N LEU A 282 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 4 GLN A 457 VAL A 459 0 SHEET 2 AA4 4 ILE A 487 SER A 492 -1 O ALA A 488 N ILE A 458 SHEET 3 AA4 4 ARG A 530 SER A 533 -1 O TYR A 532 N LYS A 491 SHEET 4 AA4 4 LYS A 511 VAL A 512 -1 N LYS A 511 O LEU A 531 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 VAL A 594 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 1.60 LINK O3' G47 W 8 P DA W 9 1555 1555 1.60 CRYST1 53.244 59.571 78.240 105.51 97.88 107.14 P 1 1 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 0.018781 0.005794 0.004742 0.00000 SCALE2 0.000000 0.017567 0.006041 0.00000 SCALE3 0.000000 0.000000 0.013645 0.00000