HEADER HYDROLASE/DNA 28-MAR-18 6CVS TITLE HUMAN APRATAXIN (APTX) L248M BOUND TO DNA, AMP AND ZN PRODUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: APRATAXIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: APRATAXIN CATALYTIC DOMAIN; COMPND 5 SYNONYM: FORKHEAD-ASSOCIATED DOMAIN HISTIDINE TRIAD-LIKE PROTEIN,FHA- COMPND 6 HIT; COMPND 7 EC: 3.1.11.7,3.1.12.2; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: DNA (5'-D(P*GP*TP*TP*CP*TP*AP*GP*AP*AP*C)-3'); COMPND 12 CHAIN: D, E, G, H; COMPND 13 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: APTX, AXA1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS PROTEIN-DNA COMPLEX, DNA REPAIR, 5'-DNA END PROCESSING, HISTIDINE KEYWDS 2 TRIAD DOMAIN, HIT DOMAIN, ZINC-FINGER, 5'-DNA END RECOGNITION, KEYWDS 3 HYDROLASE, HYDROLASE-DNA-RNA COMPLEX, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.J.SCHELLENBERG,P.S.TUMBALE,R.S.WILLIAMS REVDAT 5 04-OCT-23 6CVS 1 REMARK REVDAT 4 18-DEC-19 6CVS 1 REMARK REVDAT 3 06-NOV-19 6CVS 1 REMARK REVDAT 2 25-JUL-18 6CVS 1 JRNL REVDAT 1 04-JUL-18 6CVS 0 JRNL AUTH P.TUMBALE,M.J.SCHELLENBERG,G.A.MUELLER,E.FAIRWEATHER, JRNL AUTH 2 M.WATSON,J.N.LITTLE,J.KRAHN,I.WADDELL,R.E.LONDON, JRNL AUTH 3 R.S.WILLIAMS JRNL TITL MECHANISM OF APTX NICKED DNA SENSING AND PLEIOTROPIC JRNL TITL 2 INACTIVATION IN NEURODEGENERATIVE DISEASE. JRNL REF EMBO J. V. 37 2018 JRNL REFN ESSN 1460-2075 JRNL PMID 29934293 JRNL DOI 10.15252/EMBJ.201798875 REMARK 2 REMARK 2 RESOLUTION. 2.11 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) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 31247 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1576 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 28.8912 - 4.6867 0.90 2763 130 0.1601 0.1812 REMARK 3 2 4.6867 - 3.7225 0.94 2682 173 0.1364 0.1597 REMARK 3 3 3.7225 - 3.2527 0.95 2710 135 0.1525 0.1571 REMARK 3 4 3.2527 - 2.9556 0.96 2710 137 0.1734 0.2017 REMARK 3 5 2.9556 - 2.7439 0.96 2699 146 0.1938 0.2520 REMARK 3 6 2.7439 - 2.5823 0.97 2712 151 0.2036 0.2558 REMARK 3 7 2.5823 - 2.4530 0.96 2686 148 0.1947 0.2166 REMARK 3 8 2.4530 - 2.3463 0.97 2671 150 0.2148 0.2366 REMARK 3 9 2.3463 - 2.2560 0.97 2693 145 0.2187 0.2528 REMARK 3 10 2.2560 - 2.1782 0.97 2700 132 0.2238 0.2513 REMARK 3 11 2.1782 - 2.1101 0.96 2645 129 0.2359 0.2160 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.22 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 : 0.004 4192 REMARK 3 ANGLE : 0.611 5864 REMARK 3 CHIRALITY : 0.044 634 REMARK 3 PLANARITY : 0.003 576 REMARK 3 DIHEDRAL : 19.011 2356 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 6CVS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1000233359. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31283 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.110 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.58300 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: PHENIX REMARK 200 STARTING MODEL: 4NDF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES, 25% W/V POLYETHYLENE REMARK 280 GLYCOL 4000, VAPOR DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 20.19200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.77950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 58.15800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.77950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.19200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 58.15800 REMARK 290 SMTRY3 4 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: 2530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, E 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, G, H 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 THR A 341 REMARK 465 GLN A 342 REMARK 465 GLY B 161 REMARK 465 SER B 162 REMARK 465 THR B 341 REMARK 465 GLN B 342 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 HZ1 LYS A 179 O HOH A 504 1.52 REMARK 500 HZ3 LYS A 179 O HOH B 503 1.52 REMARK 500 HE21 GLN B 187 O HOH B 510 1.57 REMARK 500 O PRO A 196 HG SER A 270 1.57 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 D 7 O4' - C1' - N9 ANGL. DEV. = 2.9 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 HIS A 258 112.59 81.16 REMARK 500 ALA B 239 41.32 -140.79 REMARK 500 MET B 256 -86.35 -117.29 REMARK 500 HIS B 258 152.10 72.03 REMARK 500 HIS B 339 20.05 -76.98 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 744 DISTANCE = 6.81 ANGSTROMS 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 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 319 SG REMARK 620 2 CYS A 322 SG 118.4 REMARK 620 3 HIS A 335 NE2 104.4 101.6 REMARK 620 4 HIS A 339 NE2 105.9 116.8 108.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 319 SG REMARK 620 2 CYS B 322 SG 126.2 REMARK 620 3 HIS B 335 NE2 99.2 106.7 REMARK 620 4 HIS B 339 NE2 100.2 123.4 93.9 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 AMP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BME A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BME B 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NDH RELATED DB: PDB REMARK 900 4NDH CONTAINS WILDTYPE APTX BOUND TO THE SAME DNA DBREF 6CVS A 165 342 UNP Q7Z2E3 APTX_HUMAN 179 356 DBREF 6CVS B 165 342 UNP Q7Z2E3 APTX_HUMAN 179 356 DBREF 6CVS D 1 10 PDB 6CVS 6CVS 1 10 DBREF 6CVS E 1 10 PDB 6CVS 6CVS 1 10 DBREF 6CVS G 1 10 PDB 6CVS 6CVS 1 10 DBREF 6CVS H 1 10 PDB 6CVS 6CVS 1 10 SEQADV 6CVS GLY A 161 UNP Q7Z2E3 EXPRESSION TAG SEQADV 6CVS SER A 162 UNP Q7Z2E3 EXPRESSION TAG SEQADV 6CVS HIS A 163 UNP Q7Z2E3 EXPRESSION TAG SEQADV 6CVS MET A 164 UNP Q7Z2E3 EXPRESSION TAG SEQADV 6CVS MET A 248 UNP Q7Z2E3 LEU 262 ENGINEERED MUTATION SEQADV 6CVS GLY B 161 UNP Q7Z2E3 EXPRESSION TAG SEQADV 6CVS SER B 162 UNP Q7Z2E3 EXPRESSION TAG SEQADV 6CVS HIS B 163 UNP Q7Z2E3 EXPRESSION TAG SEQADV 6CVS MET B 164 UNP Q7Z2E3 EXPRESSION TAG SEQADV 6CVS MET B 248 UNP Q7Z2E3 LEU 262 ENGINEERED MUTATION SEQRES 1 A 182 GLY SER HIS MET GLY HIS TRP SER GLN GLY LEU LYS ILE SEQRES 2 A 182 SER MET GLN ASP PRO LYS MET GLN VAL TYR LYS ASP GLU SEQRES 3 A 182 GLN VAL VAL VAL ILE LYS ASP LYS TYR PRO LYS ALA ARG SEQRES 4 A 182 TYR HIS TRP LEU VAL LEU PRO TRP THR SER ILE SER SER SEQRES 5 A 182 LEU LYS ALA VAL ALA ARG GLU HIS LEU GLU LEU LEU LYS SEQRES 6 A 182 HIS MET HIS THR VAL GLY GLU LYS VAL ILE VAL ASP PHE SEQRES 7 A 182 ALA GLY SER SER LYS LEU ARG PHE ARG MET GLY TYR HIS SEQRES 8 A 182 ALA ILE PRO SER MET SER HIS VAL HIS LEU HIS VAL ILE SEQRES 9 A 182 SER GLN ASP PHE ASP SER PRO CYS LEU LYS ASN LYS LYS SEQRES 10 A 182 HIS TRP ASN SER PHE ASN THR GLU TYR PHE LEU GLU SER SEQRES 11 A 182 GLN ALA VAL ILE GLU MET VAL GLN GLU ALA GLY ARG VAL SEQRES 12 A 182 THR VAL ARG ASP GLY MET PRO GLU LEU LEU LYS LEU PRO SEQRES 13 A 182 LEU ARG CYS HIS GLU CYS GLN GLN LEU LEU PRO SER ILE SEQRES 14 A 182 PRO GLN LEU LYS GLU HIS LEU ARG LYS HIS TRP THR GLN SEQRES 1 B 182 GLY SER HIS MET GLY HIS TRP SER GLN GLY LEU LYS ILE SEQRES 2 B 182 SER MET GLN ASP PRO LYS MET GLN VAL TYR LYS ASP GLU SEQRES 3 B 182 GLN VAL VAL VAL ILE LYS ASP LYS TYR PRO LYS ALA ARG SEQRES 4 B 182 TYR HIS TRP LEU VAL LEU PRO TRP THR SER ILE SER SER SEQRES 5 B 182 LEU LYS ALA VAL ALA ARG GLU HIS LEU GLU LEU LEU LYS SEQRES 6 B 182 HIS MET HIS THR VAL GLY GLU LYS VAL ILE VAL ASP PHE SEQRES 7 B 182 ALA GLY SER SER LYS LEU ARG PHE ARG MET GLY TYR HIS SEQRES 8 B 182 ALA ILE PRO SER MET SER HIS VAL HIS LEU HIS VAL ILE SEQRES 9 B 182 SER GLN ASP PHE ASP SER PRO CYS LEU LYS ASN LYS LYS SEQRES 10 B 182 HIS TRP ASN SER PHE ASN THR GLU TYR PHE LEU GLU SER SEQRES 11 B 182 GLN ALA VAL ILE GLU MET VAL GLN GLU ALA GLY ARG VAL SEQRES 12 B 182 THR VAL ARG ASP GLY MET PRO GLU LEU LEU LYS LEU PRO SEQRES 13 B 182 LEU ARG CYS HIS GLU CYS GLN GLN LEU LEU PRO SER ILE SEQRES 14 B 182 PRO GLN LEU LYS GLU HIS LEU ARG LYS HIS TRP THR GLN SEQRES 1 D 10 DG DT DT DC DT DA DG DA DA DC SEQRES 1 E 10 DG DT DT DC DT DA DG DA DA DC SEQRES 1 G 10 DG DT DT DC DT DA DG DA DA DC SEQRES 1 H 10 DG DT DT DC DT DA DG DA DA DC HET AMP A 401 29 HET ZN A 402 1 HET BME A 403 9 HET AMP B 401 29 HET ZN B 402 1 HET BME B 403 9 HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM ZN ZINC ION HETNAM BME BETA-MERCAPTOETHANOL FORMUL 7 AMP 2(C10 H14 N5 O7 P) FORMUL 8 ZN 2(ZN 2+) FORMUL 9 BME 2(C2 H6 O S) FORMUL 13 HOH *498(H2 O) HELIX 1 AA1 HIS A 166 SER A 168 5 3 HELIX 2 AA2 GLN A 169 MET A 175 1 7 HELIX 3 AA3 SER A 212 VAL A 216 5 5 HELIX 4 AA4 ALA A 217 GLU A 219 5 3 HELIX 5 AA5 HIS A 220 GLY A 240 1 21 HELIX 6 AA6 SER A 241 LYS A 243 5 3 HELIX 7 AA7 ASN A 275 THR A 284 1 10 HELIX 8 AA8 SER A 290 GLY A 301 1 12 HELIX 9 AA9 GLY A 308 LEU A 313 1 6 HELIX 10 AB1 SER A 328 ARG A 337 1 10 HELIX 11 AB2 LYS A 338 TRP A 340 5 3 HELIX 12 AB3 GLY B 165 SER B 168 5 4 HELIX 13 AB4 GLN B 169 GLN B 176 1 8 HELIX 14 AB5 ASP B 177 LYS B 179 5 3 HELIX 15 AB6 SER B 212 VAL B 216 5 5 HELIX 16 AB7 ALA B 217 GLU B 219 5 3 HELIX 17 AB8 HIS B 220 ALA B 239 1 20 HELIX 18 AB9 ASN B 275 THR B 284 1 10 HELIX 19 AC1 SER B 290 GLY B 301 1 12 HELIX 20 AC2 GLY B 308 LEU B 313 1 6 HELIX 21 AC3 SER B 328 LEU B 336 1 9 SHEET 1 AA1 6 GLN A 181 LYS A 184 0 SHEET 2 AA1 6 VAL A 188 LYS A 192 -1 O VAL A 190 N VAL A 182 SHEET 3 AA1 6 HIS A 201 PRO A 206 -1 O LEU A 205 N VAL A 189 SHEET 4 AA1 6 LEU A 261 SER A 265 -1 O LEU A 261 N VAL A 204 SHEET 5 AA1 6 PHE A 246 HIS A 251 -1 N GLY A 249 O HIS A 262 SHEET 6 AA1 6 PHE A 287 GLU A 289 -1 O LEU A 288 N TYR A 250 SHEET 1 AA2 2 LEU A 317 ARG A 318 0 SHEET 2 AA2 2 LEU A 325 LEU A 326 -1 O LEU A 326 N LEU A 317 SHEET 1 AA3 6 GLN B 181 LYS B 184 0 SHEET 2 AA3 6 VAL B 188 LYS B 192 -1 O VAL B 190 N TYR B 183 SHEET 3 AA3 6 HIS B 201 PRO B 206 -1 O LEU B 205 N VAL B 189 SHEET 4 AA3 6 LEU B 261 SER B 265 -1 O VAL B 263 N TRP B 202 SHEET 5 AA3 6 PHE B 246 HIS B 251 -1 N GLY B 249 O HIS B 262 SHEET 6 AA3 6 PHE B 287 GLU B 289 -1 O LEU B 288 N TYR B 250 LINK SG CYS A 319 ZN ZN A 402 1555 1555 2.33 LINK SG CYS A 322 ZN ZN A 402 1555 1555 2.26 LINK NE2 HIS A 335 ZN ZN A 402 1555 1555 2.03 LINK NE2 HIS A 339 ZN ZN A 402 1555 1555 1.99 LINK SG CYS B 319 ZN ZN B 402 1555 1555 2.32 LINK SG CYS B 322 ZN ZN B 402 1555 1555 2.32 LINK NE2 HIS B 335 ZN ZN B 402 1555 1555 1.98 LINK NE2 HIS B 339 ZN ZN B 402 1555 1555 2.01 SITE 1 AC1 17 LEU A 171 SER A 174 ASP A 193 LYS A 194 SITE 2 AC1 17 TYR A 195 LYS A 197 HIS A 201 LEU A 203 SITE 3 AC1 17 HIS A 251 PRO A 254 SER A 255 MET A 256 SITE 4 AC1 17 HIS A 260 HIS A 262 HOH A 585 HOH A 634 SITE 5 AC1 17 HOH D 105 SITE 1 AC2 4 CYS A 319 CYS A 322 HIS A 335 HIS A 339 SITE 1 AC3 5 TYR A 195 CYS A 272 LYS A 274 DT D 3 SITE 2 AC3 5 HOH D 108 SITE 1 AC4 21 GLY B 170 SER B 174 ILE B 191 LYS B 192 SITE 2 AC4 21 ASP B 193 LYS B 194 TYR B 195 LEU B 203 SITE 3 AC4 21 HIS B 251 SER B 255 MET B 256 HIS B 260 SITE 4 AC4 21 HIS B 262 HOH B 502 HOH B 508 HOH B 544 SITE 5 AC4 21 HOH B 553 HOH B 568 HOH B 589 HOH B 593 SITE 6 AC4 21 DG G 1 SITE 1 AC5 4 CYS B 319 CYS B 322 HIS B 335 HIS B 339 SITE 1 AC6 6 TYR B 195 CYS B 272 LYS B 274 DT G 2 SITE 2 AC6 6 DT G 3 HOH G 101 CRYST1 40.384 116.316 117.559 90.00 90.00 90.00 P 21 21 21 16 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 0.024762 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008597 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008506 0.00000