HEADER SIGNALING PROTEIN 07-MAY-19 6RMM TITLE CRYSTAL STRUCTURE OF TOPBP1 BRCT4,5 IN COMPLEX WITH A 53BP1 TITLE 2 PHOSPHOPEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA TOPOISOMERASE 2-BINDING PROTEIN 1; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: DNA TOPOISOMERASE II-BETA-BINDING PROTEIN 1,TOPBP1,DNA COMPND 5 TOPOISOMERASE II-BINDING PROTEIN 1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 53BP1; COMPND 9 CHAIN: P, R; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TOPBP1, KIAA0259; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS BRCT DOMAIN PHOSPHOPEPTIDE RECOGNITION, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.DAY,A.W.OLIVER,L.H.PEARL REVDAT 3 24-JAN-24 6RMM 1 REMARK REVDAT 2 21-AUG-19 6RMM 1 REMARK REVDAT 1 12-JUN-19 6RMM 0 JRNL AUTH N.BIGOT,M.DAY,R.A.BALDOCK,F.Z.WATTS,A.W.OLIVER,L.H.PEARL JRNL TITL PHOSPHORYLATION-MEDIATED INTERACTIONS WITH TOPBP1 COUPLE JRNL TITL 2 53BP1 AND 9-1-1 TO CONTROL THE G1 DNA DAMAGE CHECKPOINT. JRNL REF ELIFE V. 8 2019 JRNL REFN ESSN 2050-084X JRNL PMID 31135337 JRNL DOI 10.7554/ELIFE.44353 REMARK 2 REMARK 2 RESOLUTION. 3.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20813 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1047 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 67.4173 - 6.7509 1.00 3046 158 0.1627 0.1580 REMARK 3 2 6.7509 - 5.3591 1.00 2864 152 0.2278 0.2715 REMARK 3 3 5.3591 - 4.6819 1.00 2811 143 0.2238 0.2559 REMARK 3 4 4.6819 - 4.2539 1.00 2766 161 0.2585 0.2864 REMARK 3 5 4.2539 - 3.9490 1.00 2757 156 0.2804 0.2981 REMARK 3 6 3.9490 - 3.7162 1.00 2762 135 0.3156 0.2927 REMARK 3 7 3.7162 - 3.5301 1.00 2760 142 0.3336 0.3334 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.990 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 : 0.023 6196 REMARK 3 ANGLE : 2.444 8404 REMARK 3 CHIRALITY : 0.124 986 REMARK 3 PLANARITY : 0.020 1062 REMARK 3 DIHEDRAL : 3.966 3726 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 6RMM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1292102157. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20816 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.530 REMARK 200 RESOLUTION RANGE LOW (A) : 67.405 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 70.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: PHASER REMARK 200 STARTING MODEL: 3UEN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% W/V PEG 4000, 20% V/V GLYCEROL REMARK 280 0.02 M OF EACH CARBOXYLIC ACID 0.1 M MOPS/HEPES-NA PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 287.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 202.01333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 101.00667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 151.51000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 50.50333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 252.51667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 202.01333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 101.00667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 50.50333 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 151.51000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 252.51667 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, P, R 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 HIS C 546 REMARK 465 SER C 547 REMARK 465 THR C 548 REMARK 465 GLU C 549 REMARK 465 GLU C 550 REMARK 465 GLY C 551 REMARK 465 HIS D 546 REMARK 465 SER D 547 REMARK 465 THR D 548 REMARK 465 GLU D 549 REMARK 465 GLU D 550 REMARK 465 GLY D 551 REMARK 465 SER P 359 REMARK 465 ALA P 369 REMARK 465 PHE P 370 REMARK 465 ARG P 371 REMARK 465 SER P 372 REMARK 465 THR P 373 REMARK 465 SER R 359 REMARK 465 ALA R 369 REMARK 465 PHE R 370 REMARK 465 ARG R 371 REMARK 465 SER R 372 REMARK 465 THR R 373 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 OH TYR A 705 OE1 GLU A 739 2.11 REMARK 500 OH TYR B 705 OE1 GLU B 739 2.11 REMARK 500 OE1 GLN B 676 OH TYR B 678 2.12 REMARK 500 OE1 GLN A 676 OH TYR A 678 2.12 REMARK 500 NE2 GLN C 676 O PHE C 690 2.19 REMARK 500 NE2 GLN D 676 O PHE D 690 2.19 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 NH1 ARG A 726 O GLY C 608 12544 2.18 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 SER A 547 CA SER A 547 CB 0.101 REMARK 500 SER A 547 CB SER A 547 OG 0.083 REMARK 500 GLU A 549 CG GLU A 549 CD 0.091 REMARK 500 VAL A 595 CB VAL A 595 CG1 -0.127 REMARK 500 TRP A 711 CB TRP A 711 CG -0.127 REMARK 500 SER B 547 CA SER B 547 CB 0.101 REMARK 500 SER B 547 CB SER B 547 OG 0.084 REMARK 500 GLU B 549 CG GLU B 549 CD 0.091 REMARK 500 VAL B 595 CB VAL B 595 CG1 -0.127 REMARK 500 TRP B 711 CB TRP B 711 CG -0.127 REMARK 500 GLU C 662 CB GLU C 662 CG 0.130 REMARK 500 GLU C 662 CG GLU C 662 CD 0.190 REMARK 500 GLU D 662 CB GLU D 662 CG 0.130 REMARK 500 GLU D 662 CG GLU D 662 CD 0.190 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 THR A 548 N - CA - C ANGL. DEV. = 18.4 DEGREES REMARK 500 LEU A 561 CA - CB - CG ANGL. DEV. = 14.1 DEGREES REMARK 500 LEU A 599 CB - CG - CD1 ANGL. DEV. = -11.9 DEGREES REMARK 500 LEU A 633 CB - CG - CD2 ANGL. DEV. = -14.7 DEGREES REMARK 500 MET A 689 CG - SD - CE ANGL. DEV. = 10.4 DEGREES REMARK 500 LEU A 713 CB - CG - CD2 ANGL. DEV. = -11.3 DEGREES REMARK 500 THR B 548 N - CA - C ANGL. DEV. = 18.4 DEGREES REMARK 500 LEU B 561 CA - CB - CG ANGL. DEV. = 14.1 DEGREES REMARK 500 LEU B 599 CB - CG - CD1 ANGL. DEV. = -11.9 DEGREES REMARK 500 LEU B 633 CB - CG - CD2 ANGL. DEV. = -14.8 DEGREES REMARK 500 MET B 689 CG - SD - CE ANGL. DEV. = 10.4 DEGREES REMARK 500 LEU B 713 CB - CG - CD2 ANGL. DEV. = -11.3 DEGREES REMARK 500 SER C 587 C - N - CA ANGL. DEV. = 16.8 DEGREES REMARK 500 LEU C 633 CB - CG - CD2 ANGL. DEV. = -11.7 DEGREES REMARK 500 TYR C 678 CA - CB - CG ANGL. DEV. = 12.0 DEGREES REMARK 500 ARG C 700 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 LEU C 722 CB - CG - CD2 ANGL. DEV. = -12.0 DEGREES REMARK 500 ARG C 730 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 SER D 587 C - N - CA ANGL. DEV. = 16.8 DEGREES REMARK 500 LEU D 633 CB - CG - CD2 ANGL. DEV. = -11.7 DEGREES REMARK 500 TYR D 678 CA - CB - CG ANGL. DEV. = 12.0 DEGREES REMARK 500 ARG D 700 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 LEU D 722 CB - CG - CD2 ANGL. DEV. = -12.0 DEGREES REMARK 500 ARG D 730 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 PRO P 365 C - N - CA ANGL. DEV. = 12.2 DEGREES REMARK 500 PRO R 365 C - N - CA ANGL. DEV. = 12.3 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 SER A 547 15.34 170.54 REMARK 500 THR A 548 -57.26 34.72 REMARK 500 GLU A 549 14.21 159.69 REMARK 500 SER B 547 15.42 170.50 REMARK 500 THR B 548 -57.29 34.67 REMARK 500 GLU B 549 14.15 159.65 REMARK 500 LEU C 586 8.18 53.10 REMARK 500 SER C 587 158.91 10.01 REMARK 500 ARG C 588 -103.34 -62.94 REMARK 500 LEU D 586 8.30 53.05 REMARK 500 SER D 587 158.91 9.90 REMARK 500 ARG D 588 -103.32 -62.90 REMARK 500 ASP P 361 27.68 -140.89 REMARK 500 LEU P 362 108.28 -171.51 REMARK 500 PRO P 365 177.77 -35.43 REMARK 500 SEP P 366 41.70 -108.62 REMARK 500 PRO P 367 105.31 -42.82 REMARK 500 ASP R 361 27.69 -140.96 REMARK 500 LEU R 362 108.29 -171.49 REMARK 500 PRO R 365 177.79 -35.42 REMARK 500 SEP R 366 41.73 -108.66 REMARK 500 PRO R 367 105.24 -42.82 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 THR A 548 GLU A 549 -134.13 REMARK 500 THR B 548 GLU B 549 -134.03 REMARK 500 SEP P 366 PRO P 367 -144.89 REMARK 500 SEP R 366 PRO R 367 -144.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLN A 623 12.03 REMARK 500 ASN A 631 -10.58 REMARK 500 GLN B 623 12.01 REMARK 500 ASN B 631 -10.66 REMARK 500 REMARK 500 REMARK: NULL DBREF 6RMM A 548 741 UNP Q92547 TOPB1_HUMAN 548 741 DBREF 6RMM B 548 741 UNP Q92547 TOPB1_HUMAN 548 741 DBREF 6RMM C 548 741 UNP Q92547 TOPB1_HUMAN 548 741 DBREF 6RMM D 548 741 UNP Q92547 TOPB1_HUMAN 548 741 DBREF 6RMM P 359 373 PDB 6RMM 6RMM 359 373 DBREF 6RMM R 359 373 PDB 6RMM 6RMM 359 373 SEQADV 6RMM HIS A 546 UNP Q92547 EXPRESSION TAG SEQADV 6RMM SER A 547 UNP Q92547 EXPRESSION TAG SEQADV 6RMM HIS B 546 UNP Q92547 EXPRESSION TAG SEQADV 6RMM SER B 547 UNP Q92547 EXPRESSION TAG SEQADV 6RMM HIS C 546 UNP Q92547 EXPRESSION TAG SEQADV 6RMM SER C 547 UNP Q92547 EXPRESSION TAG SEQADV 6RMM HIS D 546 UNP Q92547 EXPRESSION TAG SEQADV 6RMM SER D 547 UNP Q92547 EXPRESSION TAG SEQRES 1 A 196 HIS SER THR GLU GLU GLY LEU PHE SER GLN LYS SER PHE SEQRES 2 A 196 LEU VAL LEU GLY PHE SER ASN GLU ASN GLU SER ASN ILE SEQRES 3 A 196 ALA ASN ILE ILE LYS GLU ASN ALA GLY LYS ILE MET SER SEQRES 4 A 196 LEU LEU SER ARG THR VAL ALA ASP TYR ALA VAL VAL PRO SEQRES 5 A 196 LEU LEU GLY CYS GLU VAL GLU ALA THR VAL GLY GLU VAL SEQRES 6 A 196 VAL THR ASN THR TRP LEU VAL THR CYS ILE ASP TYR GLN SEQRES 7 A 196 THR LEU PHE ASP PRO LYS SER ASN PRO LEU PHE THR PRO SEQRES 8 A 196 VAL PRO VAL MET THR GLY MET THR PRO LEU GLU ASP CYS SEQRES 9 A 196 VAL ILE SER PHE SER GLN CYS ALA GLY ALA GLU LYS GLU SEQRES 10 A 196 SER LEU THR PHE LEU ALA ASN LEU LEU GLY ALA SER VAL SEQRES 11 A 196 GLN GLU TYR PHE VAL ARG LYS SER ASN ALA LYS LYS GLY SEQRES 12 A 196 MET PHE ALA SER THR HIS LEU ILE LEU LYS GLU ARG GLY SEQRES 13 A 196 GLY SER LYS TYR GLU ALA ALA LYS LYS TRP ASN LEU PRO SEQRES 14 A 196 ALA VAL THR ILE ALA TRP LEU LEU GLU THR ALA ARG THR SEQRES 15 A 196 GLY LYS ARG ALA ASP GLU SER HIS PHE LEU ILE GLU ASN SEQRES 16 A 196 SER SEQRES 1 B 196 HIS SER THR GLU GLU GLY LEU PHE SER GLN LYS SER PHE SEQRES 2 B 196 LEU VAL LEU GLY PHE SER ASN GLU ASN GLU SER ASN ILE SEQRES 3 B 196 ALA ASN ILE ILE LYS GLU ASN ALA GLY LYS ILE MET SER SEQRES 4 B 196 LEU LEU SER ARG THR VAL ALA ASP TYR ALA VAL VAL PRO SEQRES 5 B 196 LEU LEU GLY CYS GLU VAL GLU ALA THR VAL GLY GLU VAL SEQRES 6 B 196 VAL THR ASN THR TRP LEU VAL THR CYS ILE ASP TYR GLN SEQRES 7 B 196 THR LEU PHE ASP PRO LYS SER ASN PRO LEU PHE THR PRO SEQRES 8 B 196 VAL PRO VAL MET THR GLY MET THR PRO LEU GLU ASP CYS SEQRES 9 B 196 VAL ILE SER PHE SER GLN CYS ALA GLY ALA GLU LYS GLU SEQRES 10 B 196 SER LEU THR PHE LEU ALA ASN LEU LEU GLY ALA SER VAL SEQRES 11 B 196 GLN GLU TYR PHE VAL ARG LYS SER ASN ALA LYS LYS GLY SEQRES 12 B 196 MET PHE ALA SER THR HIS LEU ILE LEU LYS GLU ARG GLY SEQRES 13 B 196 GLY SER LYS TYR GLU ALA ALA LYS LYS TRP ASN LEU PRO SEQRES 14 B 196 ALA VAL THR ILE ALA TRP LEU LEU GLU THR ALA ARG THR SEQRES 15 B 196 GLY LYS ARG ALA ASP GLU SER HIS PHE LEU ILE GLU ASN SEQRES 16 B 196 SER SEQRES 1 C 196 HIS SER THR GLU GLU GLY LEU PHE SER GLN LYS SER PHE SEQRES 2 C 196 LEU VAL LEU GLY PHE SER ASN GLU ASN GLU SER ASN ILE SEQRES 3 C 196 ALA ASN ILE ILE LYS GLU ASN ALA GLY LYS ILE MET SER SEQRES 4 C 196 LEU LEU SER ARG THR VAL ALA ASP TYR ALA VAL VAL PRO SEQRES 5 C 196 LEU LEU GLY CYS GLU VAL GLU ALA THR VAL GLY GLU VAL SEQRES 6 C 196 VAL THR ASN THR TRP LEU VAL THR CYS ILE ASP TYR GLN SEQRES 7 C 196 THR LEU PHE ASP PRO LYS SER ASN PRO LEU PHE THR PRO SEQRES 8 C 196 VAL PRO VAL MET THR GLY MET THR PRO LEU GLU ASP CYS SEQRES 9 C 196 VAL ILE SER PHE SER GLN CYS ALA GLY ALA GLU LYS GLU SEQRES 10 C 196 SER LEU THR PHE LEU ALA ASN LEU LEU GLY ALA SER VAL SEQRES 11 C 196 GLN GLU TYR PHE VAL ARG LYS SER ASN ALA LYS LYS GLY SEQRES 12 C 196 MET PHE ALA SER THR HIS LEU ILE LEU LYS GLU ARG GLY SEQRES 13 C 196 GLY SER LYS TYR GLU ALA ALA LYS LYS TRP ASN LEU PRO SEQRES 14 C 196 ALA VAL THR ILE ALA TRP LEU LEU GLU THR ALA ARG THR SEQRES 15 C 196 GLY LYS ARG ALA ASP GLU SER HIS PHE LEU ILE GLU ASN SEQRES 16 C 196 SER SEQRES 1 D 196 HIS SER THR GLU GLU GLY LEU PHE SER GLN LYS SER PHE SEQRES 2 D 196 LEU VAL LEU GLY PHE SER ASN GLU ASN GLU SER ASN ILE SEQRES 3 D 196 ALA ASN ILE ILE LYS GLU ASN ALA GLY LYS ILE MET SER SEQRES 4 D 196 LEU LEU SER ARG THR VAL ALA ASP TYR ALA VAL VAL PRO SEQRES 5 D 196 LEU LEU GLY CYS GLU VAL GLU ALA THR VAL GLY GLU VAL SEQRES 6 D 196 VAL THR ASN THR TRP LEU VAL THR CYS ILE ASP TYR GLN SEQRES 7 D 196 THR LEU PHE ASP PRO LYS SER ASN PRO LEU PHE THR PRO SEQRES 8 D 196 VAL PRO VAL MET THR GLY MET THR PRO LEU GLU ASP CYS SEQRES 9 D 196 VAL ILE SER PHE SER GLN CYS ALA GLY ALA GLU LYS GLU SEQRES 10 D 196 SER LEU THR PHE LEU ALA ASN LEU LEU GLY ALA SER VAL SEQRES 11 D 196 GLN GLU TYR PHE VAL ARG LYS SER ASN ALA LYS LYS GLY SEQRES 12 D 196 MET PHE ALA SER THR HIS LEU ILE LEU LYS GLU ARG GLY SEQRES 13 D 196 GLY SER LYS TYR GLU ALA ALA LYS LYS TRP ASN LEU PRO SEQRES 14 D 196 ALA VAL THR ILE ALA TRP LEU LEU GLU THR ALA ARG THR SEQRES 15 D 196 GLY LYS ARG ALA ASP GLU SER HIS PHE LEU ILE GLU ASN SEQRES 16 D 196 SER SEQRES 1 P 15 SER SER ASP LEU VAL ALA PRO SEP PRO ASP ALA PHE ARG SEQRES 2 P 15 SER THR SEQRES 1 R 15 SER SER ASP LEU VAL ALA PRO SEP PRO ASP ALA PHE ARG SEQRES 2 R 15 SER THR HET SEP P 366 10 HET SEP R 366 10 HETNAM SEP PHOSPHOSERINE HETSYN SEP PHOSPHONOSERINE FORMUL 5 SEP 2(C3 H8 N O6 P) HELIX 1 AA1 SER A 564 ASN A 578 1 15 HELIX 2 AA2 ASN A 613 GLN A 623 1 11 HELIX 3 AA3 ALA A 657 LEU A 671 1 15 HELIX 4 AA4 GLY A 702 TRP A 711 1 10 HELIX 5 AA5 ILE A 718 GLY A 728 1 11 HELIX 6 AA6 ASP A 732 LEU A 737 5 6 HELIX 7 AA7 SER B 564 ASN B 578 1 15 HELIX 8 AA8 ASN B 613 GLN B 623 1 11 HELIX 9 AA9 ALA B 657 LEU B 671 1 15 HELIX 10 AB1 GLY B 702 TRP B 711 1 10 HELIX 11 AB2 ILE B 718 GLY B 728 1 11 HELIX 12 AB3 ASP B 732 LEU B 737 5 6 HELIX 13 AB4 SER C 564 ASN C 578 1 15 HELIX 14 AB5 ASN C 613 TYR C 622 1 10 HELIX 15 AB6 ASP C 627 THR C 635 5 9 HELIX 16 AB7 ALA C 657 LEU C 671 1 15 HELIX 17 AB8 GLY C 702 ASN C 712 1 11 HELIX 18 AB9 ILE C 718 GLY C 728 1 11 HELIX 19 AC1 ASP C 732 SER C 741 5 10 HELIX 20 AC2 SER D 564 ASN D 578 1 15 HELIX 21 AC3 ASN D 613 TYR D 622 1 10 HELIX 22 AC4 ASP D 627 THR D 635 5 9 HELIX 23 AC5 ALA D 657 LEU D 671 1 15 HELIX 24 AC6 GLY D 702 ASN D 712 1 11 HELIX 25 AC7 ILE D 718 GLY D 728 1 11 HELIX 26 AC8 ASP D 732 SER D 741 5 10 SHEET 1 AA1 4 LYS A 581 ILE A 582 0 SHEET 2 AA1 4 SER A 557 VAL A 560 1 N PHE A 558 O LYS A 581 SHEET 3 AA1 4 ALA A 591 VAL A 596 1 O VAL A 595 N LEU A 559 SHEET 4 AA1 4 VAL A 607 THR A 612 1 O VAL A 611 N ALA A 594 SHEET 1 AA2 4 SER A 674 VAL A 675 0 SHEET 2 AA2 4 VAL A 650 PHE A 653 1 N ILE A 651 O SER A 674 SHEET 3 AA2 4 HIS A 694 LEU A 697 1 O HIS A 694 N SER A 652 SHEET 4 AA2 4 ALA A 715 THR A 717 1 O VAL A 716 N LEU A 697 SHEET 1 AA3 4 LYS B 581 ILE B 582 0 SHEET 2 AA3 4 SER B 557 VAL B 560 1 N PHE B 558 O LYS B 581 SHEET 3 AA3 4 ALA B 591 VAL B 596 1 O VAL B 595 N LEU B 559 SHEET 4 AA3 4 VAL B 607 THR B 612 1 O VAL B 611 N ALA B 594 SHEET 1 AA4 4 SER B 674 VAL B 675 0 SHEET 2 AA4 4 VAL B 650 PHE B 653 1 N ILE B 651 O SER B 674 SHEET 3 AA4 4 HIS B 694 LEU B 697 1 O HIS B 694 N SER B 652 SHEET 4 AA4 4 ALA B 715 THR B 717 1 O VAL B 716 N LEU B 697 SHEET 1 AA5 4 LYS C 581 ILE C 582 0 SHEET 2 AA5 4 SER C 557 VAL C 560 1 N PHE C 558 O LYS C 581 SHEET 3 AA5 4 TYR C 593 VAL C 596 1 O VAL C 595 N LEU C 559 SHEET 4 AA5 4 VAL C 610 THR C 612 1 O VAL C 611 N ALA C 594 SHEET 1 AA6 4 SER C 674 VAL C 675 0 SHEET 2 AA6 4 VAL C 650 PHE C 653 1 N ILE C 651 O SER C 674 SHEET 3 AA6 4 HIS C 694 LEU C 697 1 O ILE C 696 N SER C 652 SHEET 4 AA6 4 ALA C 715 THR C 717 1 O VAL C 716 N LEU C 695 SHEET 1 AA7 2 PHE C 679 VAL C 680 0 SHEET 2 AA7 2 LEU R 362 VAL R 363 -1 O VAL R 363 N PHE C 679 SHEET 1 AA8 4 LYS D 581 ILE D 582 0 SHEET 2 AA8 4 SER D 557 VAL D 560 1 N PHE D 558 O LYS D 581 SHEET 3 AA8 4 TYR D 593 VAL D 596 1 O VAL D 595 N LEU D 559 SHEET 4 AA8 4 VAL D 610 THR D 612 1 O VAL D 611 N ALA D 594 SHEET 1 AA9 4 SER D 674 VAL D 675 0 SHEET 2 AA9 4 VAL D 650 PHE D 653 1 N ILE D 651 O SER D 674 SHEET 3 AA9 4 HIS D 694 LEU D 697 1 O ILE D 696 N SER D 652 SHEET 4 AA9 4 ALA D 715 THR D 717 1 O VAL D 716 N LEU D 695 SHEET 1 AB1 2 PHE D 679 VAL D 680 0 SHEET 2 AB1 2 LEU P 362 VAL P 363 -1 O VAL P 363 N PHE D 679 LINK NZ LYS C 704 O2P SEP R 366 1555 1555 1.30 LINK NZ LYS D 704 O1P SEP P 366 1555 1555 1.34 LINK C PRO P 365 N SEP P 366 1555 1555 1.33 LINK C SEP P 366 N PRO P 367 1555 1555 1.37 LINK C PRO R 365 N SEP R 366 1555 1555 1.33 LINK C SEP R 366 N PRO R 367 1555 1555 1.37 CRYST1 134.810 134.810 303.020 90.00 90.00 120.00 P 65 2 2 48 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 0.007418 0.004283 0.000000 0.00000 SCALE2 0.000000 0.008565 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003300 0.00000