PDB Short entry for 6BOR HEADER DNA BINDING PROTEIN/DNA 20-NOV-17 6BOR TITLE HUMAN APE1 SUBSTRATE COMPLEX WITH AN G/G MISMATCH ADJACENT THE THF COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: APEX NUCLEASE,APEN,APURINIC-APYRIMIDINIC ENDONUCLEASE 1,APE- COMPND 5 1,REF-1,REDOX FACTOR-1; COMPND 6 EC: 3.1.-.-,4.2.99.18; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 21-MER DNA; COMPND 11 CHAIN: P; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 21-MER DNA; COMPND 15 CHAIN: V; COMPND 16 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: APEX1, APE, APE1, APEX, APX, HAP1, REF1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS HYDROLASE LYASE / DNA, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.D.FREUDENTHAL,A.M.WHITAKER,M.S.FAIRLAMB REVDAT 4 04-OCT-23 6BOR 1 REMARK REVDAT 3 18-DEC-19 6BOR 1 REMARK REVDAT 2 20-FEB-19 6BOR 1 REMARK REVDAT 1 15-AUG-18 6BOR 0 JRNL AUTH M.S.FAIRLAMB,A.M.WHITAKER,B.D.FREUDENTHAL JRNL TITL APURINIC/APYRIMIDINIC (AP) ENDONUCLEASE 1 PROCESSING OF AP JRNL TITL 2 SITES WITH 5' MISMATCHES. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 74 760 2018 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 30082511 JRNL DOI 10.1107/S2059798318003340 REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.7 REMARK 3 NUMBER OF REFLECTIONS : 115113 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.150 REMARK 3 FREE R VALUE TEST SET COUNT : 3621 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 24.8128 - 5.4326 0.98 4711 154 0.1414 0.1530 REMARK 3 2 5.4326 - 4.3194 0.99 4718 155 0.1288 0.1501 REMARK 3 3 4.3194 - 3.7756 0.98 4703 150 0.1350 0.1735 REMARK 3 4 3.7756 - 3.4313 0.98 4677 154 0.1468 0.1892 REMARK 3 5 3.4313 - 3.1859 0.98 4683 154 0.1516 0.1666 REMARK 3 6 3.1859 - 2.9984 0.98 4668 149 0.1741 0.1945 REMARK 3 7 2.9984 - 2.8485 0.97 4649 150 0.1833 0.2193 REMARK 3 8 2.8485 - 2.7247 0.97 4659 150 0.1727 0.2094 REMARK 3 9 2.7247 - 2.6199 0.96 4562 149 0.1740 0.2460 REMARK 3 10 2.6199 - 2.5296 0.96 4664 150 0.1770 0.2235 REMARK 3 11 2.5296 - 2.4506 0.95 4499 149 0.1748 0.2564 REMARK 3 12 2.4506 - 2.3806 0.94 4531 144 0.1860 0.2619 REMARK 3 13 2.3806 - 2.3179 0.93 4332 138 0.1806 0.2533 REMARK 3 14 2.3179 - 2.2614 0.91 4464 147 0.1890 0.2380 REMARK 3 15 2.2614 - 2.2101 0.90 4228 136 0.1820 0.2347 REMARK 3 16 2.2101 - 2.1630 0.89 4299 139 0.1938 0.2804 REMARK 3 17 2.1630 - 2.1198 0.88 4138 139 0.1939 0.2506 REMARK 3 18 2.1198 - 2.0798 0.87 4118 130 0.2040 0.2974 REMARK 3 19 2.0798 - 2.0427 0.83 4009 133 0.2096 0.2509 REMARK 3 20 2.0427 - 2.0081 0.83 3937 122 0.2103 0.2305 REMARK 3 21 2.0081 - 1.9757 0.82 4030 127 0.2136 0.2465 REMARK 3 22 1.9757 - 1.9453 0.81 3817 124 0.2186 0.2849 REMARK 3 23 1.9453 - 1.9167 0.79 3751 126 0.2225 0.2639 REMARK 3 24 1.9167 - 1.8897 0.77 3720 126 0.2398 0.2677 REMARK 3 25 1.8897 - 1.8642 0.76 3581 120 0.2698 0.2830 REMARK 3 26 1.8642 - 1.8400 0.70 3344 106 0.2929 0.3092 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.24 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 : 0.015 5398 REMARK 3 ANGLE : 1.448 7502 REMARK 3 CHIRALITY : 0.082 809 REMARK 3 PLANARITY : 0.009 820 REMARK 3 DIHEDRAL : 19.181 3079 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 6BOR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1000231121. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 115113 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.50500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 5DFF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 7% PEG 20K, 100MM SODIUM CITRATE, 15% REMARK 280 GLYCEROL, 5MM CACL2, PH 5.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K 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, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P, V 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 MET A 1 REMARK 465 PRO A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 GLY A 5 REMARK 465 LYS A 6 REMARK 465 LYS A 7 REMARK 465 GLY A 8 REMARK 465 ALA A 9 REMARK 465 VAL A 10 REMARK 465 ALA A 11 REMARK 465 GLU A 12 REMARK 465 ASP A 13 REMARK 465 GLY A 14 REMARK 465 ASP A 15 REMARK 465 GLU A 16 REMARK 465 LEU A 17 REMARK 465 ARG A 18 REMARK 465 THR A 19 REMARK 465 GLU A 20 REMARK 465 PRO A 21 REMARK 465 GLU A 22 REMARK 465 ALA A 23 REMARK 465 LYS A 24 REMARK 465 LYS A 25 REMARK 465 SER A 26 REMARK 465 LYS A 27 REMARK 465 THR A 28 REMARK 465 ALA A 29 REMARK 465 ALA A 30 REMARK 465 LYS A 31 REMARK 465 LYS A 32 REMARK 465 ASN A 33 REMARK 465 ASP A 34 REMARK 465 LYS A 35 REMARK 465 GLU A 36 REMARK 465 ALA A 37 REMARK 465 ALA A 38 REMARK 465 GLY A 39 REMARK 465 GLU A 40 REMARK 465 GLY A 41 REMARK 465 PRO A 42 REMARK 465 MET B 1 REMARK 465 PRO B 2 REMARK 465 LYS B 3 REMARK 465 ARG B 4 REMARK 465 GLY B 5 REMARK 465 LYS B 6 REMARK 465 LYS B 7 REMARK 465 GLY B 8 REMARK 465 ALA B 9 REMARK 465 VAL B 10 REMARK 465 ALA B 11 REMARK 465 GLU B 12 REMARK 465 ASP B 13 REMARK 465 GLY B 14 REMARK 465 ASP B 15 REMARK 465 GLU B 16 REMARK 465 LEU B 17 REMARK 465 ARG B 18 REMARK 465 THR B 19 REMARK 465 GLU B 20 REMARK 465 PRO B 21 REMARK 465 GLU B 22 REMARK 465 ALA B 23 REMARK 465 LYS B 24 REMARK 465 LYS B 25 REMARK 465 SER B 26 REMARK 465 LYS B 27 REMARK 465 THR B 28 REMARK 465 ALA B 29 REMARK 465 ALA B 30 REMARK 465 LYS B 31 REMARK 465 LYS B 32 REMARK 465 ASN B 33 REMARK 465 ASP B 34 REMARK 465 LYS B 35 REMARK 465 GLU B 36 REMARK 465 ALA B 37 REMARK 465 ALA B 38 REMARK 465 GLY B 39 REMARK 465 GLU B 40 REMARK 465 GLY B 41 REMARK 465 PRO B 42 REMARK 465 SER B 123 REMARK 465 ASP B 124 REMARK 465 LYS B 125 REMARK 465 GLU B 126 REMARK 465 GLY B 127 REMARK 465 GLU B 149 REMARK 465 GLU B 150 REMARK 465 HIS B 151 REMARK 465 ASP B 152 REMARK 465 GLN B 153 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 ASP A 124 CG OD1 OD2 REMARK 470 LYS A 125 CG CD CE NZ REMARK 470 GLU A 126 CG CD OE1 OE2 REMARK 470 ARG A 177 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 224 CG CD CE NZ REMARK 470 TYR B 128 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 224 CG CD CE NZ 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 DC P 12 O3' DC P 12 C3' -0.042 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 P 4 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG V 1 O4' - C1' - N9 ANGL. DEV. = 2.8 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 125 58.56 -92.54 REMARK 500 SER A 129 -140.87 46.43 REMARK 500 SER A 129 -138.74 42.31 REMARK 500 ASP A 148 35.50 -141.37 REMARK 500 PHE A 232 25.61 -141.56 REMARK 500 GLU B 110 37.16 -96.84 REMARK 500 SER B 129 -149.46 -126.20 REMARK 500 ASN B 222 64.26 -118.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 767 DISTANCE = 6.65 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6BOQ RELATED DB: PDB REMARK 900 RELATED ID: 6BOS RELATED DB: PDB REMARK 900 RELATED ID: 6BOT RELATED DB: PDB REMARK 900 RELATED ID: 6BOU RELATED DB: PDB REMARK 900 RELATED ID: 6BOV RELATED DB: PDB REMARK 900 RELATED ID: 6BOW RELATED DB: PDB DBREF 6BOR A 1 318 UNP P27695 APEX1_HUMAN 1 318 DBREF 6BOR B 1 318 UNP P27695 APEX1_HUMAN 1 318 DBREF 6BOR P 1 21 PDB 6BOR 6BOR 1 21 DBREF 6BOR V 1 21 PDB 6BOR 6BOR 1 21 SEQADV 6BOR GLN A 96 UNP P27695 GLU 96 ENGINEERED MUTATION SEQADV 6BOR ASN A 210 UNP P27695 ASP 210 ENGINEERED MUTATION SEQADV 6BOR GLN B 96 UNP P27695 GLU 96 ENGINEERED MUTATION SEQADV 6BOR ASN B 210 UNP P27695 ASP 210 ENGINEERED MUTATION SEQRES 1 A 318 MET PRO LYS ARG GLY LYS LYS GLY ALA VAL ALA GLU ASP SEQRES 2 A 318 GLY ASP GLU LEU ARG THR GLU PRO GLU ALA LYS LYS SER SEQRES 3 A 318 LYS THR ALA ALA LYS LYS ASN ASP LYS GLU ALA ALA GLY SEQRES 4 A 318 GLU GLY PRO ALA LEU TYR GLU ASP PRO PRO ASP GLN LYS SEQRES 5 A 318 THR SER PRO SER GLY LYS PRO ALA THR LEU LYS ILE CYS SEQRES 6 A 318 SER TRP ASN VAL ASP GLY LEU ARG ALA TRP ILE LYS LYS SEQRES 7 A 318 LYS GLY LEU ASP TRP VAL LYS GLU GLU ALA PRO ASP ILE SEQRES 8 A 318 LEU CYS LEU GLN GLN THR LYS CYS SER GLU ASN LYS LEU SEQRES 9 A 318 PRO ALA GLU LEU GLN GLU LEU PRO GLY LEU SER HIS GLN SEQRES 10 A 318 TYR TRP SER ALA PRO SER ASP LYS GLU GLY TYR SER GLY SEQRES 11 A 318 VAL GLY LEU LEU SER ARG GLN CYS PRO LEU LYS VAL SER SEQRES 12 A 318 TYR GLY ILE GLY ASP GLU GLU HIS ASP GLN GLU GLY ARG SEQRES 13 A 318 VAL ILE VAL ALA GLU PHE ASP SER PHE VAL LEU VAL THR SEQRES 14 A 318 ALA TYR VAL PRO ASN ALA GLY ARG GLY LEU VAL ARG LEU SEQRES 15 A 318 GLU TYR ARG GLN ARG TRP ASP GLU ALA PHE ARG LYS PHE SEQRES 16 A 318 LEU LYS GLY LEU ALA SER ARG LYS PRO LEU VAL LEU CYS SEQRES 17 A 318 GLY ASN LEU ASN VAL ALA HIS GLU GLU ILE ASP LEU ARG SEQRES 18 A 318 ASN PRO LYS GLY ASN LYS LYS ASN ALA GLY PHE THR PRO SEQRES 19 A 318 GLN GLU ARG GLN GLY PHE GLY GLU LEU LEU GLN ALA VAL SEQRES 20 A 318 PRO LEU ALA ASP SER PHE ARG HIS LEU TYR PRO ASN THR SEQRES 21 A 318 PRO TYR ALA TYR THR PHE TRP THR TYR MET MET ASN ALA SEQRES 22 A 318 ARG SER LYS ASN VAL GLY TRP ARG LEU ASP TYR PHE LEU SEQRES 23 A 318 LEU SER HIS SER LEU LEU PRO ALA LEU CYS ASP SER LYS SEQRES 24 A 318 ILE ARG SER LYS ALA LEU GLY SER ASP HIS CYS PRO ILE SEQRES 25 A 318 THR LEU TYR LEU ALA LEU SEQRES 1 B 318 MET PRO LYS ARG GLY LYS LYS GLY ALA VAL ALA GLU ASP SEQRES 2 B 318 GLY ASP GLU LEU ARG THR GLU PRO GLU ALA LYS LYS SER SEQRES 3 B 318 LYS THR ALA ALA LYS LYS ASN ASP LYS GLU ALA ALA GLY SEQRES 4 B 318 GLU GLY PRO ALA LEU TYR GLU ASP PRO PRO ASP GLN LYS SEQRES 5 B 318 THR SER PRO SER GLY LYS PRO ALA THR LEU LYS ILE CYS SEQRES 6 B 318 SER TRP ASN VAL ASP GLY LEU ARG ALA TRP ILE LYS LYS SEQRES 7 B 318 LYS GLY LEU ASP TRP VAL LYS GLU GLU ALA PRO ASP ILE SEQRES 8 B 318 LEU CYS LEU GLN GLN THR LYS CYS SER GLU ASN LYS LEU SEQRES 9 B 318 PRO ALA GLU LEU GLN GLU LEU PRO GLY LEU SER HIS GLN SEQRES 10 B 318 TYR TRP SER ALA PRO SER ASP LYS GLU GLY TYR SER GLY SEQRES 11 B 318 VAL GLY LEU LEU SER ARG GLN CYS PRO LEU LYS VAL SER SEQRES 12 B 318 TYR GLY ILE GLY ASP GLU GLU HIS ASP GLN GLU GLY ARG SEQRES 13 B 318 VAL ILE VAL ALA GLU PHE ASP SER PHE VAL LEU VAL THR SEQRES 14 B 318 ALA TYR VAL PRO ASN ALA GLY ARG GLY LEU VAL ARG LEU SEQRES 15 B 318 GLU TYR ARG GLN ARG TRP ASP GLU ALA PHE ARG LYS PHE SEQRES 16 B 318 LEU LYS GLY LEU ALA SER ARG LYS PRO LEU VAL LEU CYS SEQRES 17 B 318 GLY ASN LEU ASN VAL ALA HIS GLU GLU ILE ASP LEU ARG SEQRES 18 B 318 ASN PRO LYS GLY ASN LYS LYS ASN ALA GLY PHE THR PRO SEQRES 19 B 318 GLN GLU ARG GLN GLY PHE GLY GLU LEU LEU GLN ALA VAL SEQRES 20 B 318 PRO LEU ALA ASP SER PHE ARG HIS LEU TYR PRO ASN THR SEQRES 21 B 318 PRO TYR ALA TYR THR PHE TRP THR TYR MET MET ASN ALA SEQRES 22 B 318 ARG SER LYS ASN VAL GLY TRP ARG LEU ASP TYR PHE LEU SEQRES 23 B 318 LEU SER HIS SER LEU LEU PRO ALA LEU CYS ASP SER LYS SEQRES 24 B 318 ILE ARG SER LYS ALA LEU GLY SER ASP HIS CYS PRO ILE SEQRES 25 B 318 THR LEU TYR LEU ALA LEU SEQRES 1 P 21 DG DC DT DG DA DT DG DC DG DG 3DR DC DG SEQRES 2 P 21 DA DC DG DG DA DT DC DC SEQRES 1 V 21 DG DG DA DT DC DC DG DT DC DG DA DG DC SEQRES 2 V 21 DG DC DA DT DC DA DG DC HET 3DR P 11 11 HET EDO A 401 4 HET EDO A 402 4 HET EDO A 403 4 HET CL A 404 1 HET EDO B 401 4 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETSYN 3DR ABASIC DIDEOXYRIBOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 3DR C5 H11 O6 P FORMUL 5 EDO 4(C2 H6 O2) FORMUL 8 CL CL 1- FORMUL 10 HOH *564(H2 O) HELIX 1 AA1 GLY A 71 LYS A 78 1 8 HELIX 2 AA2 LYS A 79 ALA A 88 1 10 HELIX 3 AA3 SER A 100 LEU A 104 5 5 HELIX 4 AA4 PRO A 105 LEU A 111 5 7 HELIX 5 AA5 GLY A 176 VAL A 180 5 5 HELIX 6 AA6 ARG A 181 SER A 201 1 21 HELIX 7 AA7 GLU A 216 LEU A 220 5 5 HELIX 8 AA8 PRO A 223 LYS A 227 5 5 HELIX 9 AA9 THR A 233 VAL A 247 1 15 HELIX 10 AB1 SER A 252 TYR A 257 1 6 HELIX 11 AB2 TYR A 269 ASN A 277 5 9 HELIX 12 AB3 HIS A 289 PRO A 293 5 5 HELIX 13 AB4 GLY B 71 LYS B 78 1 8 HELIX 14 AB5 LYS B 79 ALA B 88 1 10 HELIX 15 AB6 SER B 100 LEU B 104 5 5 HELIX 16 AB7 PRO B 105 SER B 115 5 11 HELIX 17 AB8 GLY B 176 VAL B 180 5 5 HELIX 18 AB9 ARG B 181 SER B 201 1 21 HELIX 19 AC1 GLU B 216 LEU B 220 5 5 HELIX 20 AC2 PRO B 223 LYS B 227 5 5 HELIX 21 AC3 THR B 233 VAL B 247 1 15 HELIX 22 AC4 SER B 252 TYR B 257 1 6 HELIX 23 AC5 TYR B 269 ALA B 273 5 5 HELIX 24 AC6 HIS B 289 PRO B 293 5 5 SHEET 1 AA1 6 HIS A 116 SER A 120 0 SHEET 2 AA1 6 VAL A 131 SER A 135 -1 O LEU A 133 N TYR A 118 SHEET 3 AA1 6 ILE A 91 GLN A 95 -1 N LEU A 92 O LEU A 134 SHEET 4 AA1 6 LEU A 62 ASN A 68 1 N CYS A 65 O CYS A 93 SHEET 5 AA1 6 ILE A 312 LEU A 316 -1 O LEU A 314 N ILE A 64 SHEET 6 AA1 6 LEU A 295 ILE A 300 -1 N LYS A 299 O THR A 313 SHEET 1 AA2 6 LYS A 141 TYR A 144 0 SHEET 2 AA2 6 VAL A 157 GLU A 161 -1 O VAL A 159 N SER A 143 SHEET 3 AA2 6 VAL A 166 TYR A 171 -1 O LEU A 167 N ALA A 160 SHEET 4 AA2 6 LEU A 205 ASN A 210 1 O CYS A 208 N VAL A 168 SHEET 5 AA2 6 ASP A 283 LEU A 287 -1 O LEU A 286 N LEU A 207 SHEET 6 AA2 6 ALA A 250 ASP A 251 -1 N ALA A 250 O LEU A 287 SHEET 1 AA3 6 HIS B 116 SER B 120 0 SHEET 2 AA3 6 VAL B 131 SER B 135 -1 O LEU B 133 N TYR B 118 SHEET 3 AA3 6 ILE B 91 GLN B 95 -1 N LEU B 92 O LEU B 134 SHEET 4 AA3 6 LEU B 62 ASN B 68 1 N CYS B 65 O ILE B 91 SHEET 5 AA3 6 ILE B 312 LEU B 316 -1 O LEU B 314 N ILE B 64 SHEET 6 AA3 6 LEU B 295 ILE B 300 -1 N LYS B 299 O THR B 313 SHEET 1 AA4 6 LYS B 141 TYR B 144 0 SHEET 2 AA4 6 VAL B 157 GLU B 161 -1 O GLU B 161 N LYS B 141 SHEET 3 AA4 6 VAL B 166 TYR B 171 -1 O LEU B 167 N ALA B 160 SHEET 4 AA4 6 LEU B 205 ASN B 210 1 O VAL B 206 N VAL B 168 SHEET 5 AA4 6 ASP B 283 LEU B 287 -1 O LEU B 286 N LEU B 207 SHEET 6 AA4 6 ALA B 250 ASP B 251 -1 N ALA B 250 O LEU B 287 LINK O3' DG P 10 P 3DR P 11 1555 1555 1.59 LINK O3' 3DR P 11 P DC P 12 1555 1555 1.59 CISPEP 1 VAL A 247 PRO A 248 0 -6.27 CISPEP 2 VAL B 247 PRO B 248 0 -6.23 SITE 1 AC1 4 ASP A 189 PHE A 192 PHE A 240 HOH A 552 SITE 1 AC2 8 LYS A 63 GLU A 86 GLU A 87 GLY A 178 SITE 2 AC2 8 LEU A 179 HOH A 517 HOH A 541 HOH A 655 SITE 1 AC3 7 LEU A 44 TYR A 45 ASN A 277 HOH A 509 SITE 2 AC3 7 HOH A 548 HOH A 612 HOH A 641 SITE 1 AC4 4 GLN A 96 SER A 129 TYR A 171 DG P 10 SITE 1 AC5 6 ASP B 189 PHE B 192 GLY B 239 PHE B 240 SITE 2 AC5 6 HOH B 534 HOH B 618 CRYST1 44.408 60.204 73.014 82.94 80.29 89.10 P 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 0.022518 -0.000353 -0.003838 0.00000 SCALE2 0.000000 0.016612 -0.002043 0.00000 SCALE3 0.000000 0.000000 0.014000 0.00000