PDB Short entry for 5WN3 HEADER HYDROLASE, LYASE/DNA 31-JUL-17 5WN3 TITLE APE1 F266A EXONUCLEASE SUBSTRATE COMPLEX WITH A C/T MISMATCH COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'); COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DV3))-3'); COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'- COMPND 11 D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)- COMPND 12 3'); COMPND 13 CHAIN: E; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE; COMPND 17 CHAIN: A, B; COMPND 18 SYNONYM: APEX1, APEX NUCLEASE,APEN,APURINIC-APYRIMIDINIC ENDONUCLEASE COMPND 19 1, APE-1, REF-1, REDOX FACTOR-1; COMPND 20 EC: 3.1.-.-, 4.2.99.18; COMPND 21 ENGINEERED: YES; COMPND 22 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 4; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 GENE: APEX1, APE, APE1, APEX, APX, HAP1, REF1; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21 (DE3); SOURCE 19 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HYDROLASE, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.D.FREUDENTHAL,A.M.WHITAKER REVDAT 4 04-OCT-23 5WN3 1 LINK REVDAT 3 27-NOV-19 5WN3 1 REMARK REVDAT 2 20-FEB-19 5WN3 1 REMARK REVDAT 1 28-FEB-18 5WN3 0 JRNL AUTH A.M.WHITAKER,T.S.FLYNN,B.D.FREUDENTHAL JRNL TITL MOLECULAR SNAPSHOTS OF APE1 PROOFREADING MISMATCHES AND JRNL TITL 2 REMOVING DNA DAMAGE. JRNL REF NAT COMMUN V. 9 399 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 29374164 JRNL DOI 10.1038/S41467-017-02175-Y REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 53376 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1975 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 24.7635 - 4.7880 1.00 3844 141 0.1698 0.2035 REMARK 3 2 4.7880 - 3.8049 0.99 3740 139 0.1595 0.1949 REMARK 3 3 3.8049 - 3.3252 1.00 3763 152 0.1725 0.2303 REMARK 3 4 3.3252 - 3.0217 0.98 3659 143 0.2155 0.2289 REMARK 3 5 3.0217 - 2.8055 0.96 3579 134 0.2528 0.3160 REMARK 3 6 2.8055 - 2.6403 0.97 3623 138 0.2615 0.3706 REMARK 3 7 2.6403 - 2.5082 0.98 3677 143 0.2660 0.3389 REMARK 3 8 2.5082 - 2.3991 0.99 3675 138 0.2628 0.3288 REMARK 3 9 2.3991 - 2.3068 0.99 3666 141 0.2819 0.3796 REMARK 3 10 2.3068 - 2.2273 0.99 3707 137 0.2913 0.3293 REMARK 3 11 2.2273 - 2.1577 1.00 3664 154 0.2529 0.3484 REMARK 3 12 2.1577 - 2.0960 1.00 3725 141 0.2523 0.2952 REMARK 3 13 2.0960 - 2.0409 0.99 3693 137 0.2689 0.3053 REMARK 3 14 2.0409 - 1.9911 0.91 3386 137 0.2998 0.3384 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.79 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 5583 REMARK 3 ANGLE : 1.298 7761 REMARK 3 CHIRALITY : 0.067 827 REMARK 3 PLANARITY : 0.007 842 REMARK 3 DIHEDRAL : 21.559 3200 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 5WN3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1000228922. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-17 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 : 53955 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.89200 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: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 5DFF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 7% PEG20000, 100 MM SODIUM CITRATE, REMARK 280 15% GLYCEROL, 5 MM CALCIUM CHLORIDE, PH 5.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K 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 32.77250 REMARK 290 SMTRY3 2 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, E, 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 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: 840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 ALA B 43 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 B 110 CG CD OE1 OE2 REMARK 470 ASP B 124 CG OD1 OD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG C 6 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC D 8 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 DG E 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT E 8 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC E 9 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DC E 21 O4' - C1' - N1 ANGL. DEV. = 2.5 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 -146.29 53.90 REMARK 500 LYS A 141 141.45 -170.94 REMARK 500 GLU B 110 53.25 -100.22 REMARK 500 LEU B 111 85.04 -152.61 REMARK 500 ASP B 124 49.36 -150.87 REMARK 500 LYS B 125 99.26 -162.96 REMARK 500 SER B 129 -143.34 53.62 REMARK 500 MET B 271 17.48 57.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 66 OG REMARK 620 2 GLN A 95 OE1 80.0 REMARK 620 3 ASP A 283 OD1 158.2 107.4 REMARK 620 4 HOH A 560 O 131.8 110.0 66.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 403 DBREF 5WN3 C 1 11 PDB 5WN3 5WN3 1 11 DBREF 5WN3 D 1 10 PDB 5WN3 5WN3 1 10 DBREF 5WN3 E 1 21 PDB 5WN3 5WN3 1 21 DBREF 5WN3 A 43 318 UNP P27695 APEX1_HUMAN 43 318 DBREF 5WN3 B 43 318 UNP P27695 APEX1_HUMAN 43 318 SEQADV 5WN3 ALA A 138 UNP P27695 CYS 138 ENGINEERED MUTATION SEQADV 5WN3 ALA A 266 UNP P27695 PHE 266 ENGINEERED MUTATION SEQADV 5WN3 ALA B 138 UNP P27695 CYS 138 ENGINEERED MUTATION SEQADV 5WN3 ALA B 266 UNP P27695 PHE 266 ENGINEERED MUTATION SEQRES 1 C 11 DT DC DG DA DC DG DG DA DT DC DC SEQRES 1 D 10 DG DC DT DG DA DT DG DC DG C7R SEQRES 1 E 21 DG DG DA DT DC DC DG DT DC DG DA DT DC SEQRES 2 E 21 DG DC DA DT DC DA DG DC SEQRES 1 A 276 ALA LEU TYR GLU ASP PRO PRO ASP GLN LYS THR SER PRO SEQRES 2 A 276 SER GLY LYS PRO ALA THR LEU LYS ILE CYS SER TRP ASN SEQRES 3 A 276 VAL ASP GLY LEU ARG ALA TRP ILE LYS LYS LYS GLY LEU SEQRES 4 A 276 ASP TRP VAL LYS GLU GLU ALA PRO ASP ILE LEU CYS LEU SEQRES 5 A 276 GLN GLU THR LYS CYS SER GLU ASN LYS LEU PRO ALA GLU SEQRES 6 A 276 LEU GLN GLU LEU PRO GLY LEU SER HIS GLN TYR TRP SER SEQRES 7 A 276 ALA PRO SER ASP LYS GLU GLY TYR SER GLY VAL GLY LEU SEQRES 8 A 276 LEU SER ARG GLN ALA PRO LEU LYS VAL SER TYR GLY ILE SEQRES 9 A 276 GLY ASP GLU GLU HIS ASP GLN GLU GLY ARG VAL ILE VAL SEQRES 10 A 276 ALA GLU PHE ASP SER PHE VAL LEU VAL THR ALA TYR VAL SEQRES 11 A 276 PRO ASN ALA GLY ARG GLY LEU VAL ARG LEU GLU TYR ARG SEQRES 12 A 276 GLN ARG TRP ASP GLU ALA PHE ARG LYS PHE LEU LYS GLY SEQRES 13 A 276 LEU ALA SER ARG LYS PRO LEU VAL LEU CYS GLY ASP LEU SEQRES 14 A 276 ASN VAL ALA HIS GLU GLU ILE ASP LEU ARG ASN PRO LYS SEQRES 15 A 276 GLY ASN LYS LYS ASN ALA GLY PHE THR PRO GLN GLU ARG SEQRES 16 A 276 GLN GLY PHE GLY GLU LEU LEU GLN ALA VAL PRO LEU ALA SEQRES 17 A 276 ASP SER PHE ARG HIS LEU TYR PRO ASN THR PRO TYR ALA SEQRES 18 A 276 TYR THR ALA TRP THR TYR MET MET ASN ALA ARG SER LYS SEQRES 19 A 276 ASN VAL GLY TRP ARG LEU ASP TYR PHE LEU LEU SER HIS SEQRES 20 A 276 SER LEU LEU PRO ALA LEU CYS ASP SER LYS ILE ARG SER SEQRES 21 A 276 LYS ALA LEU GLY SER ASP HIS CYS PRO ILE THR LEU TYR SEQRES 22 A 276 LEU ALA LEU SEQRES 1 B 276 ALA LEU TYR GLU ASP PRO PRO ASP GLN LYS THR SER PRO SEQRES 2 B 276 SER GLY LYS PRO ALA THR LEU LYS ILE CYS SER TRP ASN SEQRES 3 B 276 VAL ASP GLY LEU ARG ALA TRP ILE LYS LYS LYS GLY LEU SEQRES 4 B 276 ASP TRP VAL LYS GLU GLU ALA PRO ASP ILE LEU CYS LEU SEQRES 5 B 276 GLN GLU THR LYS CYS SER GLU ASN LYS LEU PRO ALA GLU SEQRES 6 B 276 LEU GLN GLU LEU PRO GLY LEU SER HIS GLN TYR TRP SER SEQRES 7 B 276 ALA PRO SER ASP LYS GLU GLY TYR SER GLY VAL GLY LEU SEQRES 8 B 276 LEU SER ARG GLN ALA PRO LEU LYS VAL SER TYR GLY ILE SEQRES 9 B 276 GLY ASP GLU GLU HIS ASP GLN GLU GLY ARG VAL ILE VAL SEQRES 10 B 276 ALA GLU PHE ASP SER PHE VAL LEU VAL THR ALA TYR VAL SEQRES 11 B 276 PRO ASN ALA GLY ARG GLY LEU VAL ARG LEU GLU TYR ARG SEQRES 12 B 276 GLN ARG TRP ASP GLU ALA PHE ARG LYS PHE LEU LYS GLY SEQRES 13 B 276 LEU ALA SER ARG LYS PRO LEU VAL LEU CYS GLY ASP LEU SEQRES 14 B 276 ASN VAL ALA HIS GLU GLU ILE ASP LEU ARG ASN PRO LYS SEQRES 15 B 276 GLY ASN LYS LYS ASN ALA GLY PHE THR PRO GLN GLU ARG SEQRES 16 B 276 GLN GLY PHE GLY GLU LEU LEU GLN ALA VAL PRO LEU ALA SEQRES 17 B 276 ASP SER PHE ARG HIS LEU TYR PRO ASN THR PRO TYR ALA SEQRES 18 B 276 TYR THR ALA TRP THR TYR MET MET ASN ALA ARG SER LYS SEQRES 19 B 276 ASN VAL GLY TRP ARG LEU ASP TYR PHE LEU LEU SER HIS SEQRES 20 B 276 SER LEU LEU PRO ALA LEU CYS ASP SER LYS ILE ARG SER SEQRES 21 B 276 LYS ALA LEU GLY SER ASP HIS CYS PRO ILE THR LEU TYR SEQRES 22 B 276 LEU ALA LEU HET C7R D 10 38 HET CA D 101 1 HET EDO A 401 4 HET EDO A 402 4 HET NA A 403 1 HET CL A 404 1 HET CL A 405 1 HET EDO B 401 4 HET EDO B 402 4 HET NA B 403 1 HET NA B 404 1 HETNAM C7R 2'-DEOXY-5'-O-THIOPHOSPHONOCYTIDINE HETNAM CA CALCIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETSYN C7R 2'-DEOXY-5'-O-THIOPHOSPHONOCYTIDINE (THIOPHOSPHO HETSYN 2 C7R CONNECTION ISOFORM 1) HETSYN EDO ETHYLENE GLYCOL FORMUL 2 C7R C9 H14 N3 O6 P S FORMUL 6 CA CA 2+ FORMUL 7 EDO 4(C2 H6 O2) FORMUL 9 NA 3(NA 1+) FORMUL 10 CL 2(CL 1-) FORMUL 16 HOH *243(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 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 MET A 271 5 3 HELIX 12 AB3 ASN A 272 ASN A 277 1 6 HELIX 13 AB4 HIS A 289 PRO A 293 5 5 HELIX 14 AB5 GLY B 71 LYS B 78 1 8 HELIX 15 AB6 LYS B 79 ALA B 88 1 10 HELIX 16 AB7 SER B 100 LEU B 104 5 5 HELIX 17 AB8 PRO B 105 GLU B 110 5 6 HELIX 18 AB9 ASP B 148 ASP B 152 5 5 HELIX 19 AC1 GLY B 176 VAL B 180 5 5 HELIX 20 AC2 ARG B 181 SER B 201 1 21 HELIX 21 AC3 GLU B 216 LEU B 220 5 5 HELIX 22 AC4 PRO B 223 LYS B 227 5 5 HELIX 23 AC5 THR B 233 VAL B 247 1 15 HELIX 24 AC6 SER B 252 TYR B 257 1 6 HELIX 25 AC7 TYR B 269 MET B 271 5 3 HELIX 26 AC8 ASN B 272 ASN B 277 1 6 HELIX 27 AC9 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 ILE A 91 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 ASP A 210 1 O VAL A 206 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 VAL B 131 N SER B 120 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 ASP 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'A DG D 9 P AC7R D 10 1555 1555 1.60 LINK O3'B DG D 9 P BC7R D 10 1555 1555 1.60 LINK OP2 DC D 8 CA CA D 101 1555 1555 2.83 LINK OG SER A 66 NA NA A 403 1555 1555 2.87 LINK OE1 GLN A 95 NA NA A 403 1555 1555 2.55 LINK OD1 ASP A 283 NA NA A 403 1555 1555 2.82 LINK NA NA A 403 O HOH A 560 1555 1555 2.94 LINK OE2 GLU B 217 NA NA B 403 1555 1555 2.43 CISPEP 1 VAL A 247 PRO A 248 0 -11.81 CISPEP 2 VAL B 247 PRO B 248 0 -4.70 SITE 1 AC1 2 DG D 7 DC D 8 SITE 1 AC2 4 ALA A 60 THR A 61 ASP A 90 TYR A 315 SITE 1 AC3 5 LEU A 44 TYR A 45 ARG A 274 ASN A 277 SITE 2 AC3 5 HOH A 521 SITE 1 AC4 7 SER A 66 TRP A 67 ASN A 68 GLN A 95 SITE 2 AC4 7 GLY A 209 ASP A 283 HOH A 560 SITE 1 AC5 1 ASP A 163 SITE 1 AC6 5 TYR A 257 PRO A 258 ASN A 259 THR A 260 SITE 2 AC6 5 HOH A 563 SITE 1 AC7 3 TYR B 45 ARG B 274 ASN B 277 SITE 1 AC8 4 ASN B 222 PRO B 223 LYS B 224 GLY B 225 SITE 1 AC9 2 GLU B 217 ARG B 237 CRYST1 71.144 65.545 91.441 90.00 110.08 90.00 P 1 21 1 4 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 0.014056 0.000000 0.005138 0.00000 SCALE2 0.000000 0.015257 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011644 0.00000