HEADER ISOMERASE/DNA 29-JAN-98 1A35 TITLE HUMAN TOPOISOMERASE I/DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*TP*AP*GP*AP*AP*AP*AP*AP*(BRU)P*(BRU) COMPND 4 P*TP*TP*T)-3'); COMPND 5 CHAIN: C; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(*AP*AP*AP*AP*AP*TP*+UP*+UP*+UP*+UP*CP*+UP*AP*AP*GP*TP*CP*TP*TP*TP*+ COMPND 10 UP*T)-3'); COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: PROTEIN (DNA TOPOISOMERASE I); COMPND 15 CHAIN: A; COMPND 16 FRAGMENT: CORE DOMAIN AND C-TERMINAL DOMAIN; COMPND 17 EC: 5.99.1.2; COMPND 18 ENGINEERED: YES; COMPND 19 MUTATION: 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: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 CELLULAR_LOCATION: NUCLEUS; SOURCE 10 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 11 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 13 EXPRESSION_SYSTEM_VECTOR: BACULOVIRUS KEYWDS TOPOISOMERASE I/DNA), DNA, TOPOISOMERASE I, ISOMERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.R.REDINBO,L.STEWART,P.KUHN,J.J.CHAMPOUX,W.G.HOL REVDAT 5 03-APR-24 1A35 1 REMARK REVDAT 4 07-FEB-24 1A35 1 REMARK REVDAT 3 03-NOV-21 1A35 1 SEQADV LINK REVDAT 2 24-FEB-09 1A35 1 VERSN REVDAT 1 28-AUG-98 1A35 0 JRNL AUTH M.R.REDINBO,L.STEWART,P.KUHN,J.J.CHAMPOUX,W.G.HOL JRNL TITL CRYSTAL STRUCTURES OF HUMAN TOPOISOMERASE I IN COVALENT AND JRNL TITL 2 NONCOVALENT COMPLEXES WITH DNA. JRNL REF SCIENCE V. 279 1504 1998 JRNL REFN ISSN 0036-8075 JRNL PMID 9488644 JRNL DOI 10.1126/SCIENCE.279.5356.1504 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.0 REMARK 3 NUMBER OF REFLECTIONS : 20807 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 SET) : 0.209 REMARK 3 FREE R VALUE : 0.308 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1467 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 55.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1261 REMARK 3 BIN R VALUE (WORKING SET) : 0.3150 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 81 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3778 REMARK 3 NUCLEIC ACID ATOMS : 896 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 273 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) : -2.35000 REMARK 3 B22 (A**2) : 4.70600 REMARK 3 B33 (A**2) : -2.35000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.75300 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.470 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.460 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM_NDBX.DNA REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOP_NDBX.DNA REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1A35 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000170333. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUN-96 REMARK 200 TEMPERATURE (KELVIN) : 100.00 REMARK 200 PH : 7.70 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18834 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.9 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.26900 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: RIGID BODY REFINEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: RECONSTITUTED HUMAN TOPOISOMERASE I COVALENT REMARK 200 COMPLEX WITH 22 BASE PAIR DUPLEX DNA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.70, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 295.00K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 33.15000 REMARK 290 SMTRY3 2 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 RESIDUES 215-635 OF CHAIN A COMPRISE THE CORE DOMAIN OF REMARK 400 THE MOLECULE. RESIDUES 715-765 OF CHAIN A COMPRISE THE REMARK 400 C-TERMINAL DOMAIN. 1-22 OF CHAIN C COMPRISE THE SCISSILE REMARK 400 STRAND OF THE DNA, 101-122 OF CHAIN D THE INTACT DNA REMARK 400 STRAND. REMARK 400 REMARK 400 NOTE THAT THE LINKER DOMAIN (636-714) IS NOT REMARK 400 PRESENT IN THE CONSTRUCT OF THIS RECONSTITUTED ENZYME. REMARK 400 THE RECONSTITUTED ENZYME IS MADE UP OF RESIDUES 175-659 OF REMARK 400 THE CORE (EXPRESSED IN BACULOVIRUS) AND RESIDUES 713-765 OF REMARK 400 THE C-TERMINAL DOMAIN (EXPRESSED IN E. COLI). REMARK 400 REMARK 400 CHAIN A RESIDUES 175-214 AND 636-659 OF THE CORE REMARK 400 AND 713-719 OF THE C-TERMINAL DOMAIN ARE DISORDERED AND NOT REMARK 400 PRESENT IN THE STRUCTURE. REMARK 400 REMARK 400 TER REMARK 400 ALA 635 A IS THE TERMINAL RESIDUE OF THE CORE DOMAIN. REMARK 400 PHE 765 A IS THE TERMINAL RESIDUE OF THE C-TERMINAL DOMAIN. REMARK 400 REMARK 400 THY 22 C IS THE 3' TERMINAL NUCLEOTIDE OF THE SCISSILE REMARK 400 STRAND OF THE DNA DUPLEX. REMARK 400 REMARK 400 THY 122 D IS THE 3' TERMINAL NUCLEOTIDE OF THE INTACT REMARK 400 STRAND OF THE DNA DUPLEX. 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 LYS A 175 REMARK 465 PRO A 176 REMARK 465 LYS A 177 REMARK 465 ASN A 178 REMARK 465 LYS A 179 REMARK 465 ASP A 180 REMARK 465 LYS A 181 REMARK 465 ASP A 182 REMARK 465 LYS A 183 REMARK 465 LYS A 184 REMARK 465 VAL A 185 REMARK 465 PRO A 186 REMARK 465 GLU A 187 REMARK 465 PRO A 188 REMARK 465 ASP A 189 REMARK 465 ASN A 190 REMARK 465 LYS A 191 REMARK 465 LYS A 192 REMARK 465 LYS A 193 REMARK 465 LYS A 194 REMARK 465 PRO A 195 REMARK 465 LYS A 196 REMARK 465 LYS A 197 REMARK 465 GLU A 198 REMARK 465 GLU A 199 REMARK 465 GLU A 200 REMARK 465 GLN A 201 REMARK 465 LYS A 202 REMARK 465 TRP A 203 REMARK 465 LYS A 204 REMARK 465 TRP A 205 REMARK 465 TRP A 206 REMARK 465 GLU A 207 REMARK 465 GLU A 208 REMARK 465 GLU A 209 REMARK 465 ARG A 210 REMARK 465 TYR A 211 REMARK 465 PRO A 212 REMARK 465 GLU A 213 REMARK 465 GLY A 214 REMARK 465 PRO A 636 REMARK 465 PRO A 637 REMARK 465 LYS A 638 REMARK 465 THR A 639 REMARK 465 PHE A 640 REMARK 465 GLU A 641 REMARK 465 LYS A 642 REMARK 465 SER A 643 REMARK 465 MET A 644 REMARK 465 MET A 645 REMARK 465 ASN A 646 REMARK 465 LEU A 647 REMARK 465 GLN A 648 REMARK 465 THR A 649 REMARK 465 LYS A 650 REMARK 465 ILE A 651 REMARK 465 ASP A 652 REMARK 465 ALA A 653 REMARK 465 LYS A 654 REMARK 465 LYS A 655 REMARK 465 GLU A 656 REMARK 465 GLN A 657 REMARK 465 LEU A 658 REMARK 465 ALA A 659 REMARK 465 ASP A 660 REMARK 465 ALA A 661 REMARK 465 ARG A 662 REMARK 465 ARG A 663 REMARK 465 ASP A 664 REMARK 465 LEU A 665 REMARK 465 LYS A 666 REMARK 465 SER A 667 REMARK 465 ALA A 668 REMARK 465 LYS A 669 REMARK 465 ALA A 670 REMARK 465 ASP A 671 REMARK 465 ALA A 672 REMARK 465 LYS A 673 REMARK 465 VAL A 674 REMARK 465 MET A 675 REMARK 465 LYS A 676 REMARK 465 ASP A 677 REMARK 465 ALA A 678 REMARK 465 LYS A 679 REMARK 465 THR A 680 REMARK 465 LYS A 681 REMARK 465 LYS A 682 REMARK 465 VAL A 683 REMARK 465 VAL A 684 REMARK 465 GLU A 685 REMARK 465 SER A 686 REMARK 465 LYS A 687 REMARK 465 LYS A 688 REMARK 465 LYS A 689 REMARK 465 ALA A 690 REMARK 465 VAL A 691 REMARK 465 GLN A 692 REMARK 465 ARG A 693 REMARK 465 LEU A 694 REMARK 465 GLU A 695 REMARK 465 GLU A 696 REMARK 465 GLN A 697 REMARK 465 LEU A 698 REMARK 465 MET A 699 REMARK 465 LYS A 700 REMARK 465 LEU A 701 REMARK 465 GLU A 702 REMARK 465 VAL A 703 REMARK 465 GLN A 704 REMARK 465 ALA A 705 REMARK 465 THR A 706 REMARK 465 ASP A 707 REMARK 465 ARG A 708 REMARK 465 GLU A 709 REMARK 465 GLU A 710 REMARK 465 ASN A 711 REMARK 465 LYS A 712 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 GLU A 267 CG CD OE1 OE2 REMARK 470 LYS A 276 CG CD CE NZ REMARK 470 GLU A 289 CG CD OE1 OE2 REMARK 470 GLU A 322 CG CD OE1 OE2 REMARK 470 GLU A 323 CG CD OE1 OE2 REMARK 470 GLU A 332 CG CD OE1 OE2 REMARK 470 LYS A 336 CG CD CE NZ REMARK 470 GLU A 337 CG CD OE1 OE2 REMARK 470 ASN A 345 CG OD1 ND2 REMARK 470 LYS A 347 CG CD CE NZ REMARK 470 LYS A 388 CG CD CE NZ REMARK 470 GLU A 463 CG CD OE1 OE2 REMARK 470 LYS A 466 CG CD CE NZ REMARK 470 GLU A 469 CG CD OE1 OE2 REMARK 470 LYS A 484 CG CD CE NZ REMARK 470 GLU A 495 CG CD OE1 OE2 REMARK 470 GLU A 497 CG CD OE1 OE2 REMARK 470 GLU A 517 CG CD OE1 OE2 REMARK 470 ASP A 519 CG OD1 OD2 REMARK 470 GLN A 521 CG CD OE1 NE2 REMARK 470 GLU A 522 CG CD OE1 OE2 REMARK 470 LYS A 545 CG CD CE NZ REMARK 470 ARG A 546 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 556 CG CD OE1 OE2 REMARK 470 ARG A 567 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 579 CG OD1 OD2 REMARK 470 GLU A 582 CG CD OE1 OE2 REMARK 470 ASP A 609 CG OD1 OD2 REMARK 470 GLU A 610 CG CD OE1 OE2 REMARK 470 ARG A 621 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 624 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 634 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 713 CG CD OE1 NE2 REMARK 470 GLU A 741 CG CD OE1 OE2 REMARK 470 LYS A 742 CG CD CE NZ REMARK 470 LYS A 746 CG CD CE NZ REMARK 470 ASP A 760 CG OD1 OD2 REMARK 470 GLU A 761 CG CD OE1 OE2 REMARK 470 ASP A 762 CG OD1 OD2 REMARK 470 GLU A 764 CG CD OE1 OE2 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 DC C 8 O4' - C1' - N1 ANGL. DEV. = 2.2 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 LYS A 284 -8.24 -55.57 REMARK 500 ILE A 294 85.52 -69.90 REMARK 500 ALA A 315 6.91 -69.04 REMARK 500 GLN A 318 50.01 -107.71 REMARK 500 ASP A 344 -127.98 52.97 REMARK 500 ALA A 351 -82.80 -70.47 REMARK 500 ARG A 362 72.01 -111.48 REMARK 500 GLU A 495 100.14 -49.97 REMARK 500 TYR A 523 59.23 72.88 REMARK 500 ASN A 539 148.00 -173.86 REMARK 500 LYS A 545 -55.74 -28.87 REMARK 500 PHE A 565 58.06 -95.06 REMARK 500 ASN A 631 45.25 73.30 REMARK 500 ILE A 714 102.06 -56.62 REMARK 500 ILE A 756 1.93 -65.65 REMARK 500 GLU A 761 3.21 -53.39 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 DC C 8 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1A35 A 175 765 UNP P11387 TOP1_HUMAN 175 765 DBREF 1A35 C 1 22 PDB 1A35 1A35 1 22 DBREF 1A35 D 101 122 PDB 1A35 1A35 101 122 SEQADV 1A35 PHE A 723 UNP P11387 TYR 723 ENGINEERED MUTATION SEQRES 1 C 22 DA DA DA DA DA DG DA DC DT DT DA DG DA SEQRES 2 C 22 DA DA DA DA BRU BRU DT DT DT SEQRES 1 D 22 DA DA DA DA DA DT BRU BRU BRU BRU DC BRU DA SEQRES 2 D 22 DA DG DT DC DT DT DT BRU DT SEQRES 1 A 591 LYS PRO LYS ASN LYS ASP LYS ASP LYS LYS VAL PRO GLU SEQRES 2 A 591 PRO ASP ASN LYS LYS LYS LYS PRO LYS LYS GLU GLU GLU SEQRES 3 A 591 GLN LYS TRP LYS TRP TRP GLU GLU GLU ARG TYR PRO GLU SEQRES 4 A 591 GLY ILE LYS TRP LYS PHE LEU GLU HIS LYS GLY PRO VAL SEQRES 5 A 591 PHE ALA PRO PRO TYR GLU PRO LEU PRO GLU ASN VAL LYS SEQRES 6 A 591 PHE TYR TYR ASP GLY LYS VAL MET LYS LEU SER PRO LYS SEQRES 7 A 591 ALA GLU GLU VAL ALA THR PHE PHE ALA LYS MET LEU ASP SEQRES 8 A 591 HIS GLU TYR THR THR LYS GLU ILE PHE ARG LYS ASN PHE SEQRES 9 A 591 PHE LYS ASP TRP ARG LYS GLU MET THR ASN GLU GLU LYS SEQRES 10 A 591 ASN ILE ILE THR ASN LEU SER LYS CYS ASP PHE THR GLN SEQRES 11 A 591 MET SER GLN TYR PHE LYS ALA GLN THR GLU ALA ARG LYS SEQRES 12 A 591 GLN MET SER LYS GLU GLU LYS LEU LYS ILE LYS GLU GLU SEQRES 13 A 591 ASN GLU LYS LEU LEU LYS GLU TYR GLY PHE CYS ILE MET SEQRES 14 A 591 ASP ASN HIS LYS GLU ARG ILE ALA ASN PHE LYS ILE GLU SEQRES 15 A 591 PRO PRO GLY LEU PHE ARG GLY ARG GLY ASN HIS PRO LYS SEQRES 16 A 591 MET GLY MET LEU LYS ARG ARG ILE MET PRO GLU ASP ILE SEQRES 17 A 591 ILE ILE ASN CYS SER LYS ASP ALA LYS VAL PRO SER PRO SEQRES 18 A 591 PRO PRO GLY HIS LYS TRP LYS GLU VAL ARG HIS ASP ASN SEQRES 19 A 591 LYS VAL THR TRP LEU VAL SER TRP THR GLU ASN ILE GLN SEQRES 20 A 591 GLY SER ILE LYS TYR ILE MET LEU ASN PRO SER SER ARG SEQRES 21 A 591 ILE LYS GLY GLU LYS ASP TRP GLN LYS TYR GLU THR ALA SEQRES 22 A 591 ARG ARG LEU LYS LYS CYS VAL ASP LYS ILE ARG ASN GLN SEQRES 23 A 591 TYR ARG GLU ASP TRP LYS SER LYS GLU MET LYS VAL ARG SEQRES 24 A 591 GLN ARG ALA VAL ALA LEU TYR PHE ILE ASP LYS LEU ALA SEQRES 25 A 591 LEU ARG ALA GLY ASN GLU LYS GLU GLU GLY GLU THR ALA SEQRES 26 A 591 ASP THR VAL GLY CYS CYS SER LEU ARG VAL GLU HIS ILE SEQRES 27 A 591 ASN LEU HIS PRO GLU LEU ASP GLY GLN GLU TYR VAL VAL SEQRES 28 A 591 GLU PHE ASP PHE LEU GLY LYS ASP SER ILE ARG TYR TYR SEQRES 29 A 591 ASN LYS VAL PRO VAL GLU LYS ARG VAL PHE LYS ASN LEU SEQRES 30 A 591 GLN LEU PHE MET GLU ASN LYS GLN PRO GLU ASP ASP LEU SEQRES 31 A 591 PHE ASP ARG LEU ASN THR GLY ILE LEU ASN LYS HIS LEU SEQRES 32 A 591 GLN ASP LEU MET GLU GLY LEU THR ALA LYS VAL PHE ARG SEQRES 33 A 591 THR TYR ASN ALA SER ILE THR LEU GLN GLN GLN LEU LYS SEQRES 34 A 591 GLU LEU THR ALA PRO ASP GLU ASN ILE PRO ALA LYS ILE SEQRES 35 A 591 LEU SER TYR ASN ARG ALA ASN ARG ALA VAL ALA ILE LEU SEQRES 36 A 591 CYS ASN HIS GLN ARG ALA PRO PRO LYS THR PHE GLU LYS SEQRES 37 A 591 SER MET MET ASN LEU GLN THR LYS ILE ASP ALA LYS LYS SEQRES 38 A 591 GLU GLN LEU ALA ASP ALA ARG ARG ASP LEU LYS SER ALA SEQRES 39 A 591 LYS ALA ASP ALA LYS VAL MET LYS ASP ALA LYS THR LYS SEQRES 40 A 591 LYS VAL VAL GLU SER LYS LYS LYS ALA VAL GLN ARG LEU SEQRES 41 A 591 GLU GLU GLN LEU MET LYS LEU GLU VAL GLN ALA THR ASP SEQRES 42 A 591 ARG GLU GLU ASN LYS GLN ILE ALA LEU GLY THR SER LYS SEQRES 43 A 591 LEU ASN PHE LEU ASP PRO ARG ILE THR VAL ALA TRP CYS SEQRES 44 A 591 LYS LYS TRP GLY VAL PRO ILE GLU LYS ILE TYR ASN LYS SEQRES 45 A 591 THR GLN ARG GLU LYS PHE ALA TRP ALA ILE ASP MET ALA SEQRES 46 A 591 ASP GLU ASP TYR GLU PHE MODRES 1A35 BRU C 18 DU MODRES 1A35 BRU C 19 DU MODRES 1A35 BRU D 107 DU MODRES 1A35 BRU D 108 DU MODRES 1A35 BRU D 109 DU MODRES 1A35 BRU D 110 DU MODRES 1A35 BRU D 112 DU MODRES 1A35 BRU D 121 DU HET BRU C 18 20 HET BRU C 19 20 HET BRU D 107 20 HET BRU D 108 20 HET BRU D 109 20 HET BRU D 110 20 HET BRU D 112 20 HET BRU D 121 20 HETNAM BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE FORMUL 1 BRU 8(C9 H12 BR N2 O8 P) FORMUL 4 HOH *273(H2 O) HELIX 1 1 PRO A 251 MET A 263 1 13 HELIX 2 2 GLU A 267 THR A 269 5 3 HELIX 3 3 GLU A 272 GLU A 285 1 14 HELIX 4 4 GLU A 290 ILE A 293 1 4 HELIX 5 5 THR A 303 LYS A 317 1 15 HELIX 6 6 LYS A 321 TYR A 338 1 18 HELIX 7 7 PRO A 379 ASP A 381 5 3 HELIX 8 8 ARG A 434 ASP A 464 1 31 HELIX 9 9 VAL A 472 LEU A 485 1 14 HELIX 10 10 VAL A 509 HIS A 511 5 3 HELIX 11 11 LYS A 532 SER A 534 5 3 HELIX 12 12 LYS A 545 MET A 555 1 11 HELIX 13 13 THR A 570 LEU A 580 1 11 HELIX 14 14 ALA A 586 GLU A 604 1 19 HELIX 15 15 ILE A 612 LEU A 629 1 18 HELIX 16 16 PRO A 726 LYS A 735 1 10 HELIX 17 17 ILE A 740 LYS A 742 5 3 HELIX 18 18 LYS A 746 MET A 758 1 13 SHEET 1 A 3 LEU A 220 HIS A 222 0 SHEET 2 A 3 PHE A 340 MET A 343 -1 O ILE A 342 N GLU A 221 SHEET 3 A 3 HIS A 346 ARG A 349 -1 O HIS A 346 N MET A 343 SHEET 1 B 3 LYS A 245 VAL A 246 0 SHEET 2 B 3 TYR A 241 TYR A 242 -1 N TYR A 242 O LYS A 245 SHEET 3 B 3 CYS A 300 ASP A 301 -1 N ASP A 301 O TYR A 241 SHEET 1 C 2 GLY A 359 LEU A 360 0 SHEET 2 C 2 LEU A 373 LYS A 374 -1 N LYS A 374 O GLY A 359 SHEET 1 D 4 GLU A 403 ARG A 405 0 SHEET 2 D 4 ILE A 383 ASN A 385 1 O ILE A 384 N ARG A 405 SHEET 3 D 4 VAL A 414 THR A 417 -1 O SER A 415 N ILE A 383 SHEET 4 D 4 ILE A 424 ILE A 427 -1 N LYS A 425 O TRP A 416 SHEET 1 E 3 ILE A 512 LEU A 518 0 SHEET 2 E 3 GLN A 521 LEU A 530 -1 O GLN A 521 N LEU A 518 SHEET 3 E 3 ARG A 536 PRO A 542 -1 N TYR A 537 O PHE A 529 LINK O3' DA C 17 P BRU C 18 1555 1555 1.60 LINK O3' BRU C 18 P BRU C 19 1555 1555 1.60 LINK O3' BRU C 19 P DT C 20 1555 1555 1.59 LINK O3' DT D 106 P BRU D 107 1555 1555 1.62 LINK O3' BRU D 107 P BRU D 108 1555 1555 1.60 LINK O3' BRU D 108 P BRU D 109 1555 1555 1.59 LINK O3' BRU D 109 P BRU D 110 1555 1555 1.61 LINK O3' BRU D 110 P DC D 111 1555 1555 1.62 LINK O3' DC D 111 P BRU D 112 1555 1555 1.62 LINK O3' BRU D 112 P DA D 113 1555 1555 1.60 LINK O3' DT D 120 P BRU D 121 1555 1555 1.61 LINK O3' BRU D 121 P DT D 122 1555 1555 1.61 CRYST1 71.800 66.300 71.800 90.00 98.40 90.00 P 1 21 1 2 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 0.013928 0.000000 0.002057 0.00000 SCALE2 0.000000 0.015083 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014079 0.00000