HEADER LYASE 09-DEC-16 5U6Z TITLE CRYSTAL STRUCTURE OF XENOPUS LAEVIS APEX2 C-TERMINAL ZNF-GRF DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 446-517; COMPND 5 EC: 4.2.99.18; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 4 ORGANISM_TAXID: 8355; SOURCE 5 GENE: APEX2, APEX2-PROV; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GRF ZINC FINGER, 3' AP ENDO/EXONUCLEASE, DNA BINDING, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR B.D.WALLACE,R.S.WILLIAMS REVDAT 3 06-MAR-24 5U6Z 1 REMARK REVDAT 2 25-JAN-17 5U6Z 1 JRNL REVDAT 1 11-JAN-17 5U6Z 0 JRNL AUTH B.D.WALLACE,Z.BERMAN,G.A.MUELLER,Y.LIN,T.CHANG,S.N.ANDRES, JRNL AUTH 2 J.L.WOJTASZEK,E.F.DEROSE,C.D.APPEL,R.E.LONDON,S.YAN, JRNL AUTH 3 R.S.WILLIAMS JRNL TITL APE2 ZF-GRF FACILITATES 3'-5' RESECTION OF DNA DAMAGE JRNL TITL 2 FOLLOWING OXIDATIVE STRESS. JRNL REF PROC. NATL. ACAD. SCI. V. 114 304 2017 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 28028224 JRNL DOI 10.1073/PNAS.1610011114 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.420 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 5562 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.050 REMARK 3 FREE R VALUE TEST SET COUNT : 559 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 45.1729 - 4.1026 1.00 1278 148 0.1847 0.2203 REMARK 3 2 4.1026 - 3.2567 1.00 1290 137 0.1885 0.2457 REMARK 3 3 3.2567 - 2.8451 0.99 1271 138 0.2197 0.3048 REMARK 3 4 2.8451 - 2.5850 0.92 1164 136 0.2345 0.2898 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.12 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 : 0.013 542 REMARK 3 ANGLE : 1.460 738 REMARK 3 CHIRALITY : 0.082 73 REMARK 3 PLANARITY : 0.009 97 REMARK 3 DIHEDRAL : 16.610 200 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 5U6Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1000225422. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-14 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 : 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) : 1.28257 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5570 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 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 (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.31400 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: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8 M (NH4)2SO4, 0.1 M BICINE PH 9.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 45.16600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.16600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 11.55250 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 45.16600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.16600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 11.55250 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 45.16600 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 45.16600 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 11.55250 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 45.16600 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 45.16600 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 11.55250 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 SER A 1 REMARK 465 LYS A 69 REMARK 465 LYS A 70 REMARK 465 ALA A 71 REMARK 465 GLY A 72 REMARK 465 CYS A 73 REMARK 465 GLU A 74 REMARK 465 ASP A 75 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 ASN A 2 CG OD1 ND2 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 O4 SO4 A 102 O HOH A 201 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 OG1 THR A 5 OD1 ASN A 62 7544 1.94 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 PRO A 15 151.22 -49.33 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 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 21 SG REMARK 620 2 HIS A 24 ND1 104.4 REMARK 620 3 CYS A 47 SG 120.5 110.6 REMARK 620 4 CYS A 61 SG 103.2 116.4 102.2 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 ZN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 102 DBREF 5U6Z A 4 75 UNP Q6DDT4 Q6DDT4_XENLA 446 517 SEQADV 5U6Z SER A 1 UNP Q6DDT4 EXPRESSION TAG SEQADV 5U6Z ASN A 2 UNP Q6DDT4 EXPRESSION TAG SEQADV 5U6Z ALA A 3 UNP Q6DDT4 EXPRESSION TAG SEQRES 1 A 75 SER ASN ALA GLN THR ALA PHE TRP LYS SER LEU LEU LYS SEQRES 2 A 75 GLY PRO PRO PRO PRO PRO ASN CYS LYS GLY HIS SER GLU SEQRES 3 A 75 PRO CYS VAL LEU ARG THR VAL LYS LYS ALA GLY PRO ASN SEQRES 4 A 75 CYS GLY ARG GLN PHE TYR VAL CYS ALA ARG PRO GLU GLY SEQRES 5 A 75 HIS SER SER ASN PRO GLN ALA ARG CYS ASN PHE PHE LEU SEQRES 6 A 75 TRP LEU THR LYS LYS ALA GLY CYS GLU ASP HET ZN A 101 1 HET SO4 A 102 5 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 2 ZN ZN 2+ FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *18(H2 O) HELIX 1 AA1 ASN A 2 LEU A 12 1 11 SHEET 1 AA1 3 VAL A 29 THR A 32 0 SHEET 2 AA1 3 GLN A 43 VAL A 46 -1 O PHE A 44 N ARG A 31 SHEET 3 AA1 3 PHE A 64 TRP A 66 -1 O LEU A 65 N TYR A 45 LINK SG CYS A 21 ZN ZN A 101 1555 1555 2.43 LINK ND1 HIS A 24 ZN ZN A 101 1555 1555 2.03 LINK SG CYS A 47 ZN ZN A 101 1555 1555 2.25 LINK SG CYS A 61 ZN ZN A 101 1555 1555 2.36 SITE 1 AC1 4 CYS A 21 HIS A 24 CYS A 47 CYS A 61 SITE 1 AC2 5 ARG A 31 THR A 32 LYS A 34 HOH A 201 SITE 2 AC2 5 HOH A 207 CRYST1 90.332 90.332 23.105 90.00 90.00 90.00 I 4 8 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 0.011070 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011070 0.000000 0.00000 SCALE3 0.000000 0.000000 0.043281 0.00000