HEADER DNA BINDING PROTEIN/DNA 20-NOV-17 6BOV TITLE HUMAN APE1 SUBSTRATE COMPLEX WITH AN A/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 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.D.FREUDENTHAL,A.M.WHITAKER,M.S.FAIRLAMB REVDAT 4 04-OCT-23 6BOV 1 REMARK REVDAT 3 18-DEC-19 6BOV 1 REMARK REVDAT 2 20-FEB-19 6BOV 1 REMARK REVDAT 1 15-AUG-18 6BOV 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. 1.98 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 98881 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.870 REMARK 3 FREE R VALUE TEST SET COUNT : 3825 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 24.7730 - 5.8978 0.98 3635 149 0.1671 0.1913 REMARK 3 2 5.8978 - 4.6917 0.99 3660 148 0.1625 0.1659 REMARK 3 3 4.6917 - 4.1017 0.99 3651 146 0.1542 0.1563 REMARK 3 4 4.1017 - 3.7280 0.99 3647 147 0.1790 0.2102 REMARK 3 5 3.7280 - 3.4616 0.99 3682 147 0.1862 0.2177 REMARK 3 6 3.4616 - 3.2580 0.98 3695 148 0.1957 0.2602 REMARK 3 7 3.2580 - 3.0951 0.98 3593 144 0.2185 0.3075 REMARK 3 8 3.0951 - 2.9606 0.97 3594 145 0.2281 0.2172 REMARK 3 9 2.9606 - 2.8468 0.97 3567 144 0.2453 0.2879 REMARK 3 10 2.8468 - 2.7487 0.96 3591 144 0.2363 0.2859 REMARK 3 11 2.7487 - 2.6629 0.96 3603 145 0.2516 0.3410 REMARK 3 12 2.6629 - 2.5868 0.96 3508 144 0.2511 0.3082 REMARK 3 13 2.5868 - 2.5188 0.96 3516 143 0.2534 0.2853 REMARK 3 14 2.5188 - 2.4574 0.96 3527 142 0.2529 0.2660 REMARK 3 15 2.4574 - 2.4016 0.95 3604 142 0.2535 0.3543 REMARK 3 16 2.4016 - 2.3505 0.95 3455 140 0.2718 0.3488 REMARK 3 17 2.3505 - 2.3035 0.94 3492 141 0.2741 0.3218 REMARK 3 18 2.3035 - 2.2601 0.94 3572 146 0.2636 0.2858 REMARK 3 19 2.2601 - 2.2198 0.94 3334 134 0.2608 0.3048 REMARK 3 20 2.2198 - 2.1821 0.94 3554 144 0.2671 0.3209 REMARK 3 21 2.1821 - 2.1470 0.93 3470 133 0.2656 0.3092 REMARK 3 22 2.1470 - 2.1140 0.93 3353 133 0.2651 0.2985 REMARK 3 23 2.1140 - 2.0829 0.92 3461 140 0.2776 0.2943 REMARK 3 24 2.0829 - 2.0536 0.92 3409 135 0.2740 0.2892 REMARK 3 25 2.0536 - 2.0258 0.92 3440 138 0.2803 0.3343 REMARK 3 26 2.0258 - 1.9995 0.91 3331 132 0.3030 0.2866 REMARK 3 27 1.9995 - 1.9745 0.82 3112 131 0.3157 0.3805 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.04 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 : 0.011 5381 REMARK 3 ANGLE : 1.176 7468 REMARK 3 CHIRALITY : 0.059 806 REMARK 3 PLANARITY : 0.007 811 REMARK 3 DIHEDRAL : 19.183 3063 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 6BOV 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_1000231174. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-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 : 98881 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.975 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.47300 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: NULL REMARK 200 STARTING MODEL: 5DFF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 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: 4920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 ASP A 148 REMARK 465 GLU A 149 REMARK 465 GLU A 150 REMARK 465 HIS A 151 REMARK 465 ASP A 152 REMARK 465 GLN A 153 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 LYS B 125 REMARK 465 GLU B 126 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 TYR A 128 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 154 CG CD OE1 OE2 REMARK 470 ARG A 202 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 51 CD OE1 NE2 REMARK 470 LYS B 79 CG CD CE NZ REMARK 470 ASP B 124 CG OD1 OD2 REMARK 470 TYR B 128 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG B 202 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 272 CG OD1 ND2 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' -0.039 REMARK 500 DC V 9 O3' DC V 9 C3' -0.038 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 CYS B 310 CA - CB - SG ANGL. DEV. = 8.1 DEGREES REMARK 500 DG P 4 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC P 12 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG V 1 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC V 15 O4' - C1' - N1 ANGL. DEV. = 2.4 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 129 -147.21 59.50 REMARK 500 SER A 129 -142.63 51.34 REMARK 500 ARG A 202 -79.39 -109.07 REMARK 500 ASN A 222 63.72 -117.70 REMARK 500 PHE A 232 31.85 -144.21 REMARK 500 TYR A 262 17.30 59.63 REMARK 500 LEU B 114 49.37 -144.25 REMARK 500 SER B 129 -149.70 -128.10 REMARK 500 LEU B 199 -58.71 -120.42 REMARK 500 ALA B 200 -18.97 -48.15 REMARK 500 ARG B 202 -79.24 -112.90 REMARK 500 ASN B 222 67.63 -115.59 REMARK 500 ASN B 272 41.95 35.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PEG B 401 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 401 DBREF 6BOV A 1 318 UNP P27695 APEX1_HUMAN 1 318 DBREF 6BOV B 1 318 UNP P27695 APEX1_HUMAN 1 318 DBREF 6BOV P 1 21 PDB 6BOV 6BOV 1 21 DBREF 6BOV V 1 21 PDB 6BOV 6BOV 1 21 SEQADV 6BOV GLN A 96 UNP P27695 GLU 96 ENGINEERED MUTATION SEQADV 6BOV ALA A 138 UNP P27695 CYS 138 ENGINEERED MUTATION SEQADV 6BOV ASN A 210 UNP P27695 ASP 210 ENGINEERED MUTATION SEQADV 6BOV GLN B 96 UNP P27695 GLU 96 ENGINEERED MUTATION SEQADV 6BOV ALA B 138 UNP P27695 CYS 138 ENGINEERED MUTATION SEQADV 6BOV 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 ALA 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 ALA 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 DA DC SEQRES 2 V 21 DG DC DA DT DC DA DG DC HET 3DR P 11 11 HET PEG B 401 5 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 3 3DR C5 H11 O6 P FORMUL 5 PEG C4 H10 O3 FORMUL 6 HOH *281(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 SER A 115 5 11 HELIX 5 AA5 GLY A 176 VAL A 180 5 5 HELIX 6 AA6 ARG A 181 GLY A 198 1 18 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 HIS A 289 PRO A 293 5 5 HELIX 12 AB3 GLY B 71 LYS B 78 1 8 HELIX 13 AB4 LYS B 79 ALA B 88 1 10 HELIX 14 AB5 SER B 100 LEU B 104 5 5 HELIX 15 AB6 PRO B 105 LEU B 111 5 7 HELIX 16 AB7 GLY B 176 VAL B 180 5 5 HELIX 17 AB8 ARG B 181 SER B 201 1 21 HELIX 18 AB9 GLU B 216 LEU B 220 5 5 HELIX 19 AC1 ASN B 222 LYS B 227 1 6 HELIX 20 AC2 THR B 233 VAL B 247 1 15 HELIX 21 AC3 SER B 252 TYR B 257 1 6 HELIX 22 AC4 ASN B 272 ASN B 277 1 6 HELIX 23 AC5 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 VAL A 131 N SER A 120 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 TRP A 67 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 SER B 135 N HIS B 116 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 CYS B 93 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 1.58 LINK O3' 3DR P 11 P DC P 12 1555 1555 1.59 CISPEP 1 VAL A 247 PRO A 248 0 -7.21 CISPEP 2 VAL B 247 PRO B 248 0 -16.41 SITE 1 AC1 4 TYR A 144 HIS B 116 GLN B 117 TYR B 118 CRYST1 44.358 60.371 73.343 83.56 78.43 88.30 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 0.022544 -0.000671 -0.004570 0.00000 SCALE2 0.000000 0.016572 -0.001808 0.00000 SCALE3 0.000000 0.000000 0.014000 0.00000