PDB Short entry for 4Q0W HEADER HYDROLASE/DNA 02-APR-14 4Q0W TITLE HE CATALYTIC CORE OF RAD2 IN COMPLEX WITH DNA SUBSTRATE (COMPLEX II) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA REPAIR PROTEIN RAD2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RAD2; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(*TP*TP*TP*GP*AP*TP*CP*CP*GP*TP*CP*CP*AP*CP*CP*TP*TP*T)-3'); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'- COMPND 14 D(*TP*TP*AP*GP*GP*TP*GP*GP*AP*CP*GP*GP*AP*TP*CP*AP*TP*T)-3'); COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: RAD2, YGR258C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) ROSSETA; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PET; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS BA ROSSMANN-LIKE, DNA REPAIR, TFIIH, NUCLEUS, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.MIETUS,E.NOWAK,M.JACIUK,P.KUSTOSZ,M.NOWOTNY REVDAT 7 20-SEP-23 4Q0W 1 REMARK LINK REVDAT 6 22-NOV-17 4Q0W 1 REMARK REVDAT 5 09-AUG-17 4Q0W 1 SOURCE REMARK REVDAT 4 29-OCT-14 4Q0W 1 AUTHOR REVDAT 3 01-OCT-14 4Q0W 1 JRNL REVDAT 2 17-SEP-14 4Q0W 1 TITLE REVDAT 1 27-AUG-14 4Q0W 0 JRNL AUTH M.MIETUS,E.NOWAK,M.JACIUK,P.KUSTOSZ,J.STUDNICKA,M.NOWOTNY JRNL TITL CRYSTAL STRUCTURE OF THE CATALYTIC CORE OF RAD2: INSIGHTS JRNL TITL 2 INTO THE MECHANISM OF SUBSTRATE BINDING. JRNL REF NUCLEIC ACIDS RES. V. 42 10762 2014 JRNL REFN ISSN 0305-1048 JRNL PMID 25120270 JRNL DOI 10.1093/NAR/GKU729 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 62159 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 3152 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 30.3891 - 5.9578 1.00 2750 148 0.1897 0.2206 REMARK 3 2 5.9578 - 4.7346 1.00 2650 146 0.1675 0.2033 REMARK 3 3 4.7346 - 4.1378 1.00 2634 129 0.1349 0.1720 REMARK 3 4 4.1378 - 3.7603 1.00 2585 148 0.1495 0.1793 REMARK 3 5 3.7603 - 3.4912 1.00 2543 158 0.1744 0.2348 REMARK 3 6 3.4912 - 3.2856 1.00 2603 137 0.1885 0.2385 REMARK 3 7 3.2856 - 3.1212 1.00 2582 130 0.1951 0.2358 REMARK 3 8 3.1212 - 2.9855 1.00 2558 137 0.2054 0.2441 REMARK 3 9 2.9855 - 2.8706 1.00 2535 159 0.2009 0.2709 REMARK 3 10 2.8706 - 2.7716 1.00 2566 126 0.1990 0.2450 REMARK 3 11 2.7716 - 2.6850 1.00 2575 136 0.2024 0.2448 REMARK 3 12 2.6850 - 2.6083 1.00 2553 134 0.1904 0.2552 REMARK 3 13 2.6083 - 2.5397 1.00 2546 137 0.1978 0.2681 REMARK 3 14 2.5397 - 2.4777 1.00 2540 129 0.1965 0.2286 REMARK 3 15 2.4777 - 2.4214 1.00 2574 132 0.1939 0.2731 REMARK 3 16 2.4214 - 2.3699 1.00 2538 127 0.1955 0.2430 REMARK 3 17 2.3699 - 2.3225 1.00 2530 120 0.2004 0.2602 REMARK 3 18 2.3225 - 2.2787 1.00 2536 151 0.2112 0.2850 REMARK 3 19 2.2787 - 2.2380 1.00 2528 130 0.2196 0.2618 REMARK 3 20 2.2380 - 2.2001 1.00 2534 133 0.2299 0.2894 REMARK 3 21 2.2001 - 2.1646 1.00 2515 138 0.2207 0.2909 REMARK 3 22 2.1646 - 2.1313 0.99 2513 124 0.2188 0.2683 REMARK 3 23 2.1313 - 2.1000 0.99 2519 143 0.2298 0.3094 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 5772 REMARK 3 ANGLE : 1.053 7946 REMARK 3 CHIRALITY : 0.064 876 REMARK 3 PLANARITY : 0.004 921 REMARK 3 DIHEDRAL : 17.744 2183 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 4Q0W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000085464. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.89440 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62159 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.140 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.08800 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) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.83100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4Q0R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9% (W/V) PEG 20000, 20% (V/V) PEG MME REMARK 280 550, 0.2 M D-GLUCOSE, 0.2 M D-MANNOSE, 0.2 M D-GALACTOSE, 0.2 M REMARK 280 L-FRUCTOSE, 0.2 M D-XYLOSE, 0.2 M N-ACETYL-D-GLUCOSAMINE, AND REMARK 280 0.1 M MOPS/HEPES-NA, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-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 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 63.32050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.40650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 63.32050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.40650 REMARK 290 SMTRY3 4 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: 5530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 GLU A 46 REMARK 465 GLY A 47 REMARK 465 SER A 721 REMARK 465 ALA A 722 REMARK 465 LYS A 723 REMARK 465 SER A 724 REMARK 465 THR A 725 REMARK 465 ALA A 726 REMARK 465 ARG A 727 REMARK 465 LYS A 728 REMARK 465 LEU A 729 REMARK 465 LEU A 730 REMARK 465 ALA A 731 REMARK 465 ASN A 732 REMARK 465 THR A 733 REMARK 465 THR A 734 REMARK 465 LEU A 735 REMARK 465 SER A 736 REMARK 465 THR A 737 REMARK 465 SER A 738 REMARK 465 ALA A 739 REMARK 465 GLU A 740 REMARK 465 ARG A 741 REMARK 465 ASN A 742 REMARK 465 VAL A 743 REMARK 465 ALA A 744 REMARK 465 GLU A 745 REMARK 465 ASN A 746 REMARK 465 ALA A 747 REMARK 465 PHE A 748 REMARK 465 VAL A 749 REMARK 465 GLU A 750 REMARK 465 ASP A 751 REMARK 465 GLU A 752 REMARK 465 LEU A 753 REMARK 465 PHE A 754 REMARK 465 GLU A 755 REMARK 465 GLN A 756 REMARK 465 GLN A 757 REMARK 465 MET A 758 REMARK 465 LYS A 759 REMARK 465 ASP A 760 REMARK 465 LYS A 761 REMARK 465 ARG A 762 REMARK 465 ASP A 763 REMARK 465 SER A 764 REMARK 465 ARG A 984 REMARK 465 ASP A 985 REMARK 465 VAL A 986 REMARK 465 LYS B 40 REMARK 465 ALA B 41 REMARK 465 VAL B 42 REMARK 465 ARG B 43 REMARK 465 ASP B 44 REMARK 465 GLN B 45 REMARK 465 GLU B 46 REMARK 465 GLY B 47 REMARK 465 ASN B 48 REMARK 465 ALA B 49 REMARK 465 ARG B 714 REMARK 465 ARG B 715 REMARK 465 GLN B 716 REMARK 465 GLY B 717 REMARK 465 LYS B 718 REMARK 465 ARG B 719 REMARK 465 GLU B 720 REMARK 465 SER B 721 REMARK 465 ALA B 722 REMARK 465 LYS B 723 REMARK 465 SER B 724 REMARK 465 THR B 725 REMARK 465 ALA B 726 REMARK 465 ARG B 727 REMARK 465 LYS B 728 REMARK 465 LEU B 729 REMARK 465 LEU B 730 REMARK 465 ALA B 731 REMARK 465 ASN B 732 REMARK 465 THR B 733 REMARK 465 THR B 734 REMARK 465 LEU B 735 REMARK 465 SER B 736 REMARK 465 THR B 737 REMARK 465 SER B 738 REMARK 465 ALA B 739 REMARK 465 GLU B 740 REMARK 465 ARG B 741 REMARK 465 ASN B 742 REMARK 465 VAL B 743 REMARK 465 ALA B 744 REMARK 465 GLU B 745 REMARK 465 ASN B 746 REMARK 465 ALA B 747 REMARK 465 PHE B 748 REMARK 465 VAL B 749 REMARK 465 GLU B 750 REMARK 465 ASP B 751 REMARK 465 GLU B 752 REMARK 465 LEU B 753 REMARK 465 PHE B 754 REMARK 465 GLU B 755 REMARK 465 GLN B 756 REMARK 465 GLN B 757 REMARK 465 MET B 758 REMARK 465 LYS B 759 REMARK 465 ASP B 760 REMARK 465 PHE B 899 REMARK 465 ASP B 900 REMARK 465 LYS B 901 REMARK 465 ARG B 902 REMARK 465 LYS B 903 REMARK 465 GLN B 904 REMARK 465 VAL B 986 REMARK 465 DT C -1 REMARK 465 DT C 0 REMARK 465 DT D 0 REMARK 465 DT D 16 REMARK 465 DT D 17 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 VAL A 42 CG1 CG2 REMARK 470 ASN A 48 CG OD1 ND2 REMARK 470 LYS A 51 CG CD CE NZ REMARK 470 ARG A 60 NE CZ NH1 NH2 REMARK 470 GLU A 766 CG CD OE1 OE2 REMARK 470 LYS A 773 CD CE NZ REMARK 470 GLN A 802 CG CD OE1 NE2 REMARK 470 LYS A 823 CE NZ REMARK 470 GLU A 841 OE1 OE2 REMARK 470 LYS A 852 NZ REMARK 470 LYS A 901 CG CD CE NZ REMARK 470 ARG A 902 CZ NH1 NH2 REMARK 470 GLU A 905 CG CD OE1 OE2 REMARK 470 LYS A 912 CG CD CE NZ REMARK 470 VAL A 951 CG1 CG2 REMARK 470 GLU A 973 CG CD OE1 OE2 REMARK 470 VAL B 50 CG1 CG2 REMARK 470 LYS B 51 CG CD CE NZ REMARK 470 ARG B 60 CZ NH1 NH2 REMARK 470 VAL B 82 CG1 CG2 REMARK 470 ARG B 91 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 92 CG CD CE NZ REMARK 470 LYS B 761 CG CD CE NZ REMARK 470 LYS B 773 NZ REMARK 470 GLN B 802 CG CD OE1 NE2 REMARK 470 ASN B 833 CG OD1 ND2 REMARK 470 LYS B 870 CG CD CE NZ REMARK 470 LYS B 888 CG CD CE NZ REMARK 470 GLU B 905 CG CD OE1 OE2 REMARK 470 THR B 906 OG1 CG2 REMARK 470 LYS B 909 CG CD CE NZ REMARK 470 LYS B 912 CG CD CE NZ REMARK 470 GLU B 922 CG CD OE1 OE2 REMARK 470 ILE B 924 CG1 CD1 REMARK 470 ARG B 940 CZ NH1 NH2 REMARK 470 GLU B 973 CD OE1 OE2 REMARK 470 ARG B 984 CG CD NE CZ NH1 NH2 REMARK 470 DT C 1 OP1 OP2 REMARK 470 DT C 16 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DT C 16 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT C 16 C7 C6 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 OE1 GLU A 792 OH TYR A 865 2.07 REMARK 500 OE1 GLU B 792 OH TYR B 865 2.12 REMARK 500 NH1 ARG B 15 OD1 ASP B 839 2.17 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 DG C 7 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT C 15 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 DA D 2 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 ASP A 24 -2.90 71.52 REMARK 500 ASP A 44 -111.59 -92.13 REMARK 500 MET A 791 -107.48 -130.86 REMARK 500 ASP A 926 -157.98 -109.43 REMARK 500 ASP B 24 -3.26 72.73 REMARK 500 LYS B 92 44.26 -98.29 REMARK 500 MET B 791 -110.86 -133.56 REMARK 500 THR B 866 143.27 -171.47 REMARK 500 ASN B 908 -179.88 -65.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 794 OE2 REMARK 620 2 ASP A 815 OD2 106.9 REMARK 620 3 ASP A 864 OD2 168.9 80.1 REMARK 620 4 HOH A1144 O 95.3 141.3 83.7 REMARK 620 5 HOH A1267 O 135.6 86.7 52.0 56.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A1002 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 869 O REMARK 620 2 MET A 872 O 85.6 REMARK 620 3 HOH A1109 O 148.2 76.5 REMARK 620 4 HOH A1130 O 100.1 124.8 70.6 REMARK 620 5 HOH A1198 O 96.4 171.2 105.4 63.4 REMARK 620 6 DC D 9 OP2 114.5 81.9 89.0 138.4 89.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 794 OE1 REMARK 620 2 ASP B 813 OD2 80.2 REMARK 620 3 ASP B 815 OD2 97.2 104.2 REMARK 620 4 HOH B1296 O 155.5 75.9 83.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B1002 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU B 869 O REMARK 620 2 MET B 872 O 91.9 REMARK 620 3 HOH B1209 O 174.2 85.7 REMARK 620 4 HOH B1297 O 99.2 147.8 80.2 REMARK 620 5 HOH C 118 O 89.7 151.5 95.0 59.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 1002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Q0R RELATED DB: PDB REMARK 900 RELATED ID: 4Q0Z RELATED DB: PDB REMARK 900 RELATED ID: 4Q10 RELATED DB: PDB DBREF 4Q0W A 2 731 UNP P07276 RAD2_YEAST 2 111 DBREF 4Q0W A 732 986 UNP P07276 RAD2_YEAST 732 986 DBREF 4Q0W B 2 731 UNP P07276 RAD2_YEAST 2 111 DBREF 4Q0W B 732 986 UNP P07276 RAD2_YEAST 732 986 DBREF 4Q0W C -1 16 PDB 4Q0W 4Q0W -1 16 DBREF 4Q0W D 0 17 PDB 4Q0W 4Q0W 0 17 SEQRES 1 A 365 GLY VAL HIS SER PHE TRP ASP ILE ALA GLY PRO THR ALA SEQRES 2 A 365 ARG PRO VAL ARG LEU GLU SER LEU GLU ASP LYS ARG MET SEQRES 3 A 365 ALA VAL ASP ALA SER ILE TRP ILE TYR GLN PHE LEU LYS SEQRES 4 A 365 ALA VAL ARG ASP GLN GLU GLY ASN ALA VAL LYS ASN SER SEQRES 5 A 365 HIS ILE THR GLY PHE PHE ARG ARG ILE CYS LYS LEU LEU SEQRES 6 A 365 TYR PHE GLY ILE ARG PRO VAL PHE VAL PHE ASP GLY GLY SEQRES 7 A 365 VAL PRO VAL LEU LYS ARG GLU THR ILE ARG GLN ARG LYS SEQRES 8 A 365 GLU ARG ARG GLN GLY LYS ARG GLU SER ALA LYS SER THR SEQRES 9 A 365 ALA ARG LYS LEU LEU ALA ASN THR THR LEU SER THR SER SEQRES 10 A 365 ALA GLU ARG ASN VAL ALA GLU ASN ALA PHE VAL GLU ASP SEQRES 11 A 365 GLU LEU PHE GLU GLN GLN MET LYS ASP LYS ARG ASP SER SEQRES 12 A 365 ASP GLU VAL THR MET ASP MET ILE LYS GLU VAL GLN GLU SEQRES 13 A 365 LEU LEU SER ARG PHE GLY ILE PRO TYR ILE THR ALA PRO SEQRES 14 A 365 MET GLU ALA GLU ALA GLN CYS ALA GLU LEU LEU GLN LEU SEQRES 15 A 365 ASN LEU VAL ASP GLY ILE ILE THR ASP ASP SER ASP VAL SEQRES 16 A 365 PHE LEU PHE GLY GLY THR LYS ILE TYR LYS ASN MET PHE SEQRES 17 A 365 HIS GLU LYS ASN TYR VAL GLU PHE TYR ASP ALA GLU SER SEQRES 18 A 365 ILE LEU LYS LEU LEU GLY LEU ASP ARG LYS ASN MET ILE SEQRES 19 A 365 GLU LEU ALA GLN LEU LEU GLY SER ASP TYR THR ASN GLY SEQRES 20 A 365 LEU LYS GLY MET GLY PRO VAL SER SER ILE GLU VAL ILE SEQRES 21 A 365 ALA GLU PHE GLY ASN LEU LYS ASN PHE LYS ASP TRP TYR SEQRES 22 A 365 ASN ASN GLY GLN PHE ASP LYS ARG LYS GLN GLU THR GLU SEQRES 23 A 365 ASN LYS PHE GLU LYS ASP LEU ARG LYS LYS LEU VAL ASN SEQRES 24 A 365 ASN GLU ILE ILE LEU ASP ASP ASP PHE PRO SER VAL MET SEQRES 25 A 365 VAL TYR ASP ALA TYR MET ARG PRO GLU VAL ASP HIS ASP SEQRES 26 A 365 THR THR PRO PHE VAL TRP GLY VAL PRO ASP LEU ASP MET SEQRES 27 A 365 LEU ARG SER PHE MET LYS THR GLN LEU GLY TRP PRO HIS SEQRES 28 A 365 GLU LYS SER ASP GLU ILE LEU ILE PRO LEU ILE ARG ASP SEQRES 29 A 365 VAL SEQRES 1 B 365 GLY VAL HIS SER PHE TRP ASP ILE ALA GLY PRO THR ALA SEQRES 2 B 365 ARG PRO VAL ARG LEU GLU SER LEU GLU ASP LYS ARG MET SEQRES 3 B 365 ALA VAL ASP ALA SER ILE TRP ILE TYR GLN PHE LEU LYS SEQRES 4 B 365 ALA VAL ARG ASP GLN GLU GLY ASN ALA VAL LYS ASN SER SEQRES 5 B 365 HIS ILE THR GLY PHE PHE ARG ARG ILE CYS LYS LEU LEU SEQRES 6 B 365 TYR PHE GLY ILE ARG PRO VAL PHE VAL PHE ASP GLY GLY SEQRES 7 B 365 VAL PRO VAL LEU LYS ARG GLU THR ILE ARG GLN ARG LYS SEQRES 8 B 365 GLU ARG ARG GLN GLY LYS ARG GLU SER ALA LYS SER THR SEQRES 9 B 365 ALA ARG LYS LEU LEU ALA ASN THR THR LEU SER THR SER SEQRES 10 B 365 ALA GLU ARG ASN VAL ALA GLU ASN ALA PHE VAL GLU ASP SEQRES 11 B 365 GLU LEU PHE GLU GLN GLN MET LYS ASP LYS ARG ASP SER SEQRES 12 B 365 ASP GLU VAL THR MET ASP MET ILE LYS GLU VAL GLN GLU SEQRES 13 B 365 LEU LEU SER ARG PHE GLY ILE PRO TYR ILE THR ALA PRO SEQRES 14 B 365 MET GLU ALA GLU ALA GLN CYS ALA GLU LEU LEU GLN LEU SEQRES 15 B 365 ASN LEU VAL ASP GLY ILE ILE THR ASP ASP SER ASP VAL SEQRES 16 B 365 PHE LEU PHE GLY GLY THR LYS ILE TYR LYS ASN MET PHE SEQRES 17 B 365 HIS GLU LYS ASN TYR VAL GLU PHE TYR ASP ALA GLU SER SEQRES 18 B 365 ILE LEU LYS LEU LEU GLY LEU ASP ARG LYS ASN MET ILE SEQRES 19 B 365 GLU LEU ALA GLN LEU LEU GLY SER ASP TYR THR ASN GLY SEQRES 20 B 365 LEU LYS GLY MET GLY PRO VAL SER SER ILE GLU VAL ILE SEQRES 21 B 365 ALA GLU PHE GLY ASN LEU LYS ASN PHE LYS ASP TRP TYR SEQRES 22 B 365 ASN ASN GLY GLN PHE ASP LYS ARG LYS GLN GLU THR GLU SEQRES 23 B 365 ASN LYS PHE GLU LYS ASP LEU ARG LYS LYS LEU VAL ASN SEQRES 24 B 365 ASN GLU ILE ILE LEU ASP ASP ASP PHE PRO SER VAL MET SEQRES 25 B 365 VAL TYR ASP ALA TYR MET ARG PRO GLU VAL ASP HIS ASP SEQRES 26 B 365 THR THR PRO PHE VAL TRP GLY VAL PRO ASP LEU ASP MET SEQRES 27 B 365 LEU ARG SER PHE MET LYS THR GLN LEU GLY TRP PRO HIS SEQRES 28 B 365 GLU LYS SER ASP GLU ILE LEU ILE PRO LEU ILE ARG ASP SEQRES 29 B 365 VAL SEQRES 1 C 18 DT DT DT DG DA DT DC DC DG DT DC DC DA SEQRES 2 C 18 DC DC DT DT DT SEQRES 1 D 18 DT DT DA DG DG DT DG DG DA DC DG DG DA SEQRES 2 D 18 DT DC DA DT DT HET CA A1001 1 HET K A1002 1 HET CA B1001 1 HET K B1002 1 HETNAM CA CALCIUM ION HETNAM K POTASSIUM ION FORMUL 5 CA 2(CA 2+) FORMUL 6 K 2(K 1+) FORMUL 9 HOH *567(H2 O) HELIX 1 1 SER A 5 GLY A 11 1 7 HELIX 2 2 PRO A 12 ALA A 14 5 3 HELIX 3 3 GLU A 20 GLU A 23 5 4 HELIX 4 4 ILE A 33 VAL A 42 1 10 HELIX 5 5 ASN A 52 PHE A 68 1 17 HELIX 6 6 PRO A 81 GLY A 97 1 17 HELIX 7 7 THR A 768 PHE A 782 1 15 HELIX 8 8 GLU A 792 LEU A 803 1 12 HELIX 9 9 SER A 814 PHE A 819 1 6 HELIX 10 10 ALA A 840 GLY A 848 1 9 HELIX 11 11 ASP A 850 GLY A 862 1 13 HELIX 12 12 GLY A 873 GLY A 885 1 13 HELIX 13 13 ASN A 886 ASP A 900 1 15 HELIX 14 14 LYS A 901 GLU A 905 5 5 HELIX 15 15 ASN A 908 ASN A 921 1 14 HELIX 16 16 SER A 931 ARG A 940 1 10 HELIX 17 17 ASP A 956 GLY A 969 1 14 HELIX 18 18 PRO A 971 ILE A 983 1 13 HELIX 19 19 SER B 5 GLY B 11 1 7 HELIX 20 20 PRO B 12 ALA B 14 5 3 HELIX 21 21 GLU B 20 GLU B 23 5 4 HELIX 22 22 ILE B 33 PHE B 38 1 6 HELIX 23 23 ASN B 52 PHE B 68 1 17 HELIX 24 24 PRO B 81 GLN B 90 1 10 HELIX 25 25 ASP B 763 PHE B 782 1 20 HELIX 26 26 GLU B 792 LEU B 803 1 12 HELIX 27 27 SER B 814 PHE B 819 1 6 HELIX 28 28 ASP B 839 GLY B 848 1 10 HELIX 29 29 ASP B 850 GLY B 862 1 13 HELIX 30 30 GLY B 873 GLY B 885 1 13 HELIX 31 31 ASN B 886 GLN B 898 1 13 HELIX 32 32 ASN B 908 ASN B 921 1 14 HELIX 33 33 SER B 931 ARG B 940 1 10 HELIX 34 34 ASP B 956 GLY B 969 1 14 HELIX 35 35 PRO B 971 ILE B 980 1 10 HELIX 36 36 PRO B 981 ILE B 983 5 3 SHEET 1 A 7 ARG A 15 ARG A 18 0 SHEET 2 A 7 TYR A 834 ASP A 839 -1 O VAL A 835 N VAL A 17 SHEET 3 A 7 LYS A 823 LYS A 826 -1 N LYS A 826 O GLU A 836 SHEET 4 A 7 GLY A 808 ILE A 810 1 N ILE A 809 O TYR A 825 SHEET 5 A 7 ARG A 26 ASP A 30 1 N ALA A 28 O ILE A 810 SHEET 6 A 7 ARG A 71 PHE A 76 1 O VAL A 73 N VAL A 29 SHEET 7 A 7 TYR A 786 THR A 788 1 O ILE A 787 N PHE A 76 SHEET 1 B 7 ARG B 15 ARG B 18 0 SHEET 2 B 7 TYR B 834 TYR B 838 -1 O VAL B 835 N VAL B 17 SHEET 3 B 7 ILE B 824 LYS B 826 -1 N ILE B 824 O TYR B 838 SHEET 4 B 7 GLY B 808 ILE B 810 1 N ILE B 809 O TYR B 825 SHEET 5 B 7 ARG B 26 ASP B 30 1 N ALA B 28 O ILE B 810 SHEET 6 B 7 ARG B 71 PHE B 76 1 O VAL B 73 N VAL B 29 SHEET 7 B 7 TYR B 786 THR B 788 1 O ILE B 787 N PHE B 74 LINK OE2 GLU A 794 CA CA A1001 1555 1555 2.22 LINK OD2 ASP A 815 CA CA A1001 1555 1555 2.49 LINK OD2 ASP A 864 CA CA A1001 1555 1555 3.18 LINK O LEU A 869 K K A1002 1555 1555 2.96 LINK O MET A 872 K K A1002 1555 1555 3.11 LINK CA CA A1001 O HOH A1144 1555 1555 2.37 LINK CA CA A1001 O HOH A1267 1555 1555 2.47 LINK K K A1002 O HOH A1109 1555 1555 2.63 LINK K K A1002 O HOH A1130 1555 1555 2.59 LINK K K A1002 O HOH A1198 1555 1555 2.57 LINK K K A1002 OP2 DC D 9 1555 1555 2.97 LINK OE1 GLU B 794 CA CA B1001 1555 1555 2.58 LINK OD2 ASP B 813 CA CA B1001 1555 1555 2.50 LINK OD2 ASP B 815 CA CA B1001 1555 1555 2.47 LINK O LEU B 869 K K B1002 1555 1555 2.80 LINK O MET B 872 K K B1002 1555 1555 2.78 LINK CA CA B1001 O HOH B1296 1555 1555 2.47 LINK K K B1002 O HOH B1209 1555 1555 2.58 LINK K K B1002 O HOH B1297 1555 1555 2.63 LINK K K B1002 O HOH C 118 1555 1555 2.86 CISPEP 1 PHE A 929 PRO A 930 0 -3.75 CISPEP 2 PHE B 929 PRO B 930 0 -1.32 SITE 1 AC1 7 GLU A 792 GLU A 794 ASP A 813 ASP A 815 SITE 2 AC1 7 ASP A 864 HOH A1144 HOH A1267 SITE 1 AC2 6 LEU A 869 MET A 872 HOH A1109 HOH A1130 SITE 2 AC2 6 HOH A1198 DC D 9 SITE 1 AC3 5 GLU B 794 ASP B 813 ASP B 815 ASP B 864 SITE 2 AC3 5 HOH B1296 SITE 1 AC4 6 LEU B 860 LEU B 869 MET B 872 HOH B1209 SITE 2 AC4 6 HOH B1297 HOH C 118 CRYST1 126.641 76.813 108.192 90.00 90.00 90.00 P 21 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 0.007896 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013019 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009243 0.00000