HEADER LYASE 28-MAY-14 4QHD TITLE CRYSTAL STRUCTURE OF APO HUMAN APE1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 38-318; COMPND 5 SYNONYM: APEX NUCLEASE, APEN, APURINIC-APYRIMIDINIC ENDONUCLEASE 1, COMPND 6 AP ENDONUCLEASE 1, APE-1, REF-1, REDOX FACTOR-1, DNA-(APURINIC OR COMPND 7 APYRIMIDINIC SITE) LYASE, MITOCHONDRIAL; COMPND 8 EC: 3.1.-.-, 4.2.99.18; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: 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 KEYWDS BETA SANDWICH, ENDONUCLEASE, DNA-BINDING, NUCLEUS, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR H.HE,Q.CHEN,M.M.GEORGIADIS REVDAT 2 28-FEB-24 4QHD 1 REMARK SEQADV REVDAT 1 12-NOV-14 4QHD 0 JRNL AUTH H.HE,Q.CHEN,M.M.GEORGIADIS JRNL TITL HIGH-RESOLUTION CRYSTAL STRUCTURES REVEAL PLASTICITY IN THE JRNL TITL 2 METAL BINDING SITE OF APURINIC/APYRIMIDINIC ENDONUCLEASE I. JRNL REF BIOCHEMISTRY V. 53 6520 2014 JRNL REFN ISSN 0006-2960 JRNL PMID 25251148 JRNL DOI 10.1021/BI500676P REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 35396 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1783 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 32.4783 - 3.8777 0.99 2833 166 0.1642 0.1872 REMARK 3 2 3.8777 - 3.0786 0.98 2693 145 0.1716 0.1882 REMARK 3 3 3.0786 - 2.6897 0.97 2649 143 0.1879 0.2234 REMARK 3 4 2.6897 - 2.4438 0.95 2572 157 0.1916 0.2219 REMARK 3 5 2.4438 - 2.2687 0.98 2614 143 0.1917 0.2272 REMARK 3 6 2.2687 - 2.1350 0.98 2632 136 0.2026 0.3005 REMARK 3 7 2.1350 - 2.0281 0.98 2600 130 0.2131 0.2473 REMARK 3 8 2.0281 - 1.9398 0.97 2596 133 0.2300 0.2968 REMARK 3 9 1.9398 - 1.8651 0.97 2550 137 0.2248 0.2682 REMARK 3 10 1.8651 - 1.8008 0.96 2551 124 0.2396 0.2833 REMARK 3 11 1.8008 - 1.7445 0.94 2489 125 0.2322 0.2980 REMARK 3 12 1.7445 - 1.6946 0.92 2448 128 0.2538 0.2905 REMARK 3 13 1.6946 - 1.6500 0.90 2386 116 0.2802 0.3503 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 : 0.34 REMARK 3 B_SOL : 37.98 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.040 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.32200 REMARK 3 B22 (A**2) : 0.70060 REMARK 3 B33 (A**2) : -0.54210 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.005 2309 REMARK 3 ANGLE : 0.994 3129 REMARK 3 CHIRALITY : 0.066 331 REMARK 3 PLANARITY : 0.004 406 REMARK 3 DIHEDRAL : 17.229 853 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 4QHD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000086056. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : APEX II CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS PLUS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36466 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES, 0.2M SODIUM CHLORIDE, 19% REMARK 280 PEG 3350, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 -X+1/2,Y+1/2,-Z 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 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 -1.000000 0.000000 0.000000 23.31500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 70.56400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.31500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 70.56400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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 GLY A 34 REMARK 465 SER A 35 REMARK 465 HIS A 36 REMARK 465 MET A 37 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 LEU A 108 4.14 -69.15 REMARK 500 ASP A 124 0.40 -65.34 REMARK 500 SER A 129 -142.54 52.55 REMARK 500 ALA A 317 77.75 -102.36 REMARK 500 REMARK 500 REMARK: NULL 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 EDO A 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QH9 RELATED DB: PDB REMARK 900 RELATED ID: 4QHE RELATED DB: PDB DBREF 4QHD A 38 318 UNP P27695 APEX1_HUMAN 38 318 SEQADV 4QHD GLY A 34 UNP P27695 EXPRESSION TAG SEQADV 4QHD SER A 35 UNP P27695 EXPRESSION TAG SEQADV 4QHD HIS A 36 UNP P27695 EXPRESSION TAG SEQADV 4QHD MET A 37 UNP P27695 EXPRESSION TAG SEQADV 4QHD SER A 39 UNP P27695 GLY 39 VARIANT SEQADV 4QHD ALA A 138 UNP P27695 CYS 138 ENGINEERED MUTATION SEQRES 1 A 285 GLY SER HIS MET ALA SER GLU GLY PRO ALA LEU TYR GLU SEQRES 2 A 285 ASP PRO PRO ASP GLN LYS THR SER PRO SER GLY LYS PRO SEQRES 3 A 285 ALA THR LEU LYS ILE CYS SER TRP ASN VAL ASP GLY LEU SEQRES 4 A 285 ARG ALA TRP ILE LYS LYS LYS GLY LEU ASP TRP VAL LYS SEQRES 5 A 285 GLU GLU ALA PRO ASP ILE LEU CYS LEU GLN GLU THR LYS SEQRES 6 A 285 CYS SER GLU ASN LYS LEU PRO ALA GLU LEU GLN GLU LEU SEQRES 7 A 285 PRO GLY LEU SER HIS GLN TYR TRP SER ALA PRO SER ASP SEQRES 8 A 285 LYS GLU GLY TYR SER GLY VAL GLY LEU LEU SER ARG GLN SEQRES 9 A 285 ALA PRO LEU LYS VAL SER TYR GLY ILE GLY ASP GLU GLU SEQRES 10 A 285 HIS ASP GLN GLU GLY ARG VAL ILE VAL ALA GLU PHE ASP SEQRES 11 A 285 SER PHE VAL LEU VAL THR ALA TYR VAL PRO ASN ALA GLY SEQRES 12 A 285 ARG GLY LEU VAL ARG LEU GLU TYR ARG GLN ARG TRP ASP SEQRES 13 A 285 GLU ALA PHE ARG LYS PHE LEU LYS GLY LEU ALA SER ARG SEQRES 14 A 285 LYS PRO LEU VAL LEU CYS GLY ASP LEU ASN VAL ALA HIS SEQRES 15 A 285 GLU GLU ILE ASP LEU ARG ASN PRO LYS GLY ASN LYS LYS SEQRES 16 A 285 ASN ALA GLY PHE THR PRO GLN GLU ARG GLN GLY PHE GLY SEQRES 17 A 285 GLU LEU LEU GLN ALA VAL PRO LEU ALA ASP SER PHE ARG SEQRES 18 A 285 HIS LEU TYR PRO ASN THR PRO TYR ALA TYR THR PHE TRP SEQRES 19 A 285 THR TYR MET MET ASN ALA ARG SER LYS ASN VAL GLY TRP SEQRES 20 A 285 ARG LEU ASP TYR PHE LEU LEU SER HIS SER LEU LEU PRO SEQRES 21 A 285 ALA LEU CYS ASP SER LYS ILE ARG SER LYS ALA LEU GLY SEQRES 22 A 285 SER ASP HIS CYS PRO ILE THR LEU TYR LEU ALA LEU HET EDO A 401 4 HET EDO A 402 4 HET EDO A 403 4 HET EDO A 404 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 4(C2 H6 O2) FORMUL 6 HOH *237(H2 O) HELIX 1 1 GLY A 71 LYS A 78 1 8 HELIX 2 2 LYS A 79 ALA A 88 1 10 HELIX 3 3 PRO A 105 GLU A 110 5 6 HELIX 4 4 LEU A 111 SER A 115 5 5 HELIX 5 5 ASP A 148 ASP A 152 5 5 HELIX 6 6 GLY A 176 VAL A 180 5 5 HELIX 7 7 ARG A 181 SER A 201 1 21 HELIX 8 8 GLU A 216 LEU A 220 5 5 HELIX 9 9 THR A 233 VAL A 247 1 15 HELIX 10 10 SER A 252 TYR A 257 1 6 HELIX 11 11 HIS A 289 PRO A 293 5 5 SHEET 1 A 6 HIS A 116 SER A 120 0 SHEET 2 A 6 VAL A 131 SER A 135 -1 O SER A 135 N HIS A 116 SHEET 3 A 6 ILE A 91 GLN A 95 -1 N LEU A 92 O LEU A 134 SHEET 4 A 6 LEU A 62 ASN A 68 1 N CYS A 65 O CYS A 93 SHEET 5 A 6 ILE A 312 LEU A 316 -1 O LEU A 314 N ILE A 64 SHEET 6 A 6 LEU A 295 ILE A 300 -1 N LYS A 299 O THR A 313 SHEET 1 B 6 LYS A 141 TYR A 144 0 SHEET 2 B 6 VAL A 157 GLU A 161 -1 O GLU A 161 N LYS A 141 SHEET 3 B 6 VAL A 166 TYR A 171 -1 O LEU A 167 N ALA A 160 SHEET 4 B 6 LEU A 205 ASP A 210 1 O VAL A 206 N VAL A 168 SHEET 5 B 6 ASP A 283 LEU A 287 -1 O LEU A 286 N LEU A 207 SHEET 6 B 6 ALA A 250 ASP A 251 -1 N ALA A 250 O LEU A 287 CISPEP 1 VAL A 247 PRO A 248 0 -5.78 SITE 1 AC1 6 ASN A 174 ALA A 230 PHE A 266 TRP A 280 SITE 2 AC1 6 HOH A 610 HOH A 672 SITE 1 AC2 5 SER A 115 HIS A 116 GLN A 117 TYR A 118 SITE 2 AC2 5 HOH A 647 SITE 1 AC3 5 PRO A 248 SER A 288 HIS A 289 SER A 290 SITE 2 AC3 5 HOH A 556 SITE 1 AC4 5 HIS A 215 GLU A 216 ARG A 237 GLN A 238 SITE 2 AC4 5 GLY A 241 CRYST1 46.630 141.128 45.246 90.00 90.00 90.00 P 21 21 2 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 0.021445 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007086 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022101 0.00000