HEADER LYASE 17-OCT-06 2ISI TITLE CRYSTAL STRUCTURE OF APE1 FROM HOMO SAPIENS IN A NEW CRYSTAL FORM TITLE 2 COMPLEXED WITH A LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: AP ENDONUCLEASE 1, APEX NUCLEASE, APEN, REF-1 PROTEIN; COMPND 5 EC: 4.2.99.18; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS APE1, MAGNESIUM, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR R.AGARWAL,M.D.NAIDU REVDAT 3 30-AUG-23 2ISI 1 REMARK LINK REVDAT 2 24-FEB-09 2ISI 1 VERSN REVDAT 1 31-OCT-06 2ISI 0 JRNL AUTH R.AGARWAL,M.D.NAIDU JRNL TITL CRYSTAL STRUCTURE OF HAPE1 IN A NEW CRYSTAL FORM WITH A JRNL TITL 2 BOUND LIGAND: IMPLICATIONS ON CATALYTIC MECHANISM AND ITS JRNL TITL 3 INHIBITION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 67800.380 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 82.9 REMARK 3 NUMBER OF REFLECTIONS : 26206 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.900 REMARK 3 FREE R VALUE TEST SET COUNT : 753 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.93 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 38.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1977 REMARK 3 BIN R VALUE (WORKING SET) : 0.4660 REMARK 3 BIN FREE R VALUE : 0.5680 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 67 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.069 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6560 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 37 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 4.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.61000 REMARK 3 B22 (A**2) : 10.63000 REMARK 3 B33 (A**2) : -9.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 14.30000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.45 REMARK 3 ESD FROM SIGMAA (A) : 0.72 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.50 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.66 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.130 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 30.91 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE MISSING RESIDUES LISTED IN REMARK REMARK 3 465, AND MISSING ATOMS LISTED IN REMARK 470, ARE DUE TO LACK OF REMARK 3 ELECTRON DENSITY. REMARK 4 REMARK 4 2ISI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000039960. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27372 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.760 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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: 1HD7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 70% MPD, PH 7.5, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 83.67350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.19600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 83.67350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 46.19600 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, 3 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 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 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 PRO C 2 REMARK 465 LYS C 3 REMARK 465 ARG C 4 REMARK 465 GLY C 5 REMARK 465 LYS C 6 REMARK 465 LYS C 7 REMARK 465 GLY C 8 REMARK 465 ALA C 9 REMARK 465 VAL C 10 REMARK 465 ALA C 11 REMARK 465 GLU C 12 REMARK 465 ASP C 13 REMARK 465 GLY C 14 REMARK 465 ASP C 15 REMARK 465 GLU C 16 REMARK 465 LEU C 17 REMARK 465 ARG C 18 REMARK 465 THR C 19 REMARK 465 GLU C 20 REMARK 465 PRO C 21 REMARK 465 GLU C 22 REMARK 465 ALA C 23 REMARK 465 LYS C 24 REMARK 465 LYS C 25 REMARK 465 SER C 26 REMARK 465 LYS C 27 REMARK 465 THR C 28 REMARK 465 ALA C 29 REMARK 465 ALA C 30 REMARK 465 LYS C 31 REMARK 465 LYS C 32 REMARK 465 ASN C 33 REMARK 465 ASP C 34 REMARK 465 LYS C 35 REMARK 465 GLU C 36 REMARK 465 ALA C 37 REMARK 465 ALA C 38 REMARK 465 GLY C 39 REMARK 465 GLU C 40 REMARK 465 GLY C 41 REMARK 465 PRO C 42 REMARK 465 SER C 123 REMARK 465 ASP C 124 REMARK 465 LYS C 125 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 B 124 CG OD1 OD2 REMARK 470 LYS B 125 CG CD CE NZ REMARK 470 GLU B 126 CG CD OE1 OE2 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 PRO A 248 C - N - CD ANGL. DEV. = -17.2 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 LYS A 52 40.05 -98.82 REMARK 500 LYS A 103 30.26 -94.88 REMARK 500 GLU A 110 35.09 -90.04 REMARK 500 GLU A 126 149.52 -174.41 REMARK 500 SER A 129 -157.57 52.21 REMARK 500 GLU A 149 -46.83 -9.27 REMARK 500 SER A 201 13.16 -67.88 REMARK 500 ASN A 212 74.17 26.51 REMARK 500 VAL A 213 137.70 179.17 REMARK 500 LYS A 224 -19.34 -47.19 REMARK 500 ASN A 226 6.66 -166.87 REMARK 500 VAL A 247 44.01 -104.22 REMARK 500 PRO A 248 69.24 23.52 REMARK 500 TYR A 257 60.03 -118.60 REMARK 500 CYS A 296 -62.44 -92.75 REMARK 500 ARG A 301 65.66 -64.39 REMARK 500 ASP B 50 99.24 -66.69 REMARK 500 PRO B 55 -7.70 -56.97 REMARK 500 TRP B 67 115.61 -165.89 REMARK 500 LEU B 72 -50.26 63.27 REMARK 500 ALA B 88 78.19 39.17 REMARK 500 CYS B 99 156.79 178.88 REMARK 500 GLN B 109 49.48 -79.37 REMARK 500 GLU B 110 -9.71 -155.52 REMARK 500 PRO B 112 -116.52 -19.35 REMARK 500 PRO B 122 101.31 -48.99 REMARK 500 LYS B 125 55.68 -161.51 REMARK 500 GLU B 126 174.10 -50.00 REMARK 500 SER B 129 -125.02 -163.53 REMARK 500 ASP B 148 82.95 -168.23 REMARK 500 GLU B 149 -35.27 -29.94 REMARK 500 ALA B 175 0.16 -59.83 REMARK 500 ARG B 202 -103.38 -86.69 REMARK 500 ASN B 212 60.88 29.46 REMARK 500 VAL B 213 142.84 -170.86 REMARK 500 HIS B 215 -72.66 -36.91 REMARK 500 PHE B 232 25.04 -140.41 REMARK 500 VAL B 278 76.94 -103.70 REMARK 500 LEU C 44 -168.70 -121.80 REMARK 500 PRO C 49 175.85 -40.23 REMARK 500 ASP C 70 66.71 30.13 REMARK 500 LYS C 103 68.98 -101.35 REMARK 500 GLN C 109 35.04 -69.03 REMARK 500 GLU C 110 -13.39 -143.38 REMARK 500 SER C 115 51.64 -97.23 REMARK 500 HIS C 116 83.60 -155.78 REMARK 500 SER C 129 -149.36 50.54 REMARK 500 ASP C 148 104.42 -163.72 REMARK 500 ASP C 152 30.54 -96.87 REMARK 500 ASP C 163 -83.08 -50.25 REMARK 500 REMARK 500 THIS ENTRY HAS 58 RAMACHANDRAN OUTLIERS. 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 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 70 OD1 REMARK 620 2 GLU A 96 OE1 124.6 REMARK 620 3 GLU A 96 OE2 74.5 54.9 REMARK 620 4 HOH A 414 O 80.9 129.5 105.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 70 OD1 REMARK 620 2 GLU B 96 OE1 85.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 70 OD1 REMARK 620 2 GLU C 96 OE1 79.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HD7 RELATED DB: PDB REMARK 900 THE SAME PROTEIN REMARK 900 RELATED ID: 1E9N RELATED DB: PDB REMARK 900 THE SAME PROTEIN REMARK 900 RELATED ID: 1DEW RELATED DB: PDB REMARK 900 THE SAME PROTEIN REMARK 900 RELATED ID: 1DE9 RELATED DB: PDB REMARK 900 THE SAME PROTEIN REMARK 900 RELATED ID: 1DE8 RELATED DB: PDB REMARK 900 THE SAME PROTEIN DBREF 2ISI A 2 318 UNP P27695 APEX1_HUMAN 1 317 DBREF 2ISI B 2 318 UNP P27695 APEX1_HUMAN 1 317 DBREF 2ISI C 2 318 UNP P27695 APEX1_HUMAN 1 317 SEQRES 1 A 317 PRO LYS ARG GLY LYS LYS GLY ALA VAL ALA GLU ASP GLY SEQRES 2 A 317 ASP GLU LEU ARG THR GLU PRO GLU ALA LYS LYS SER LYS SEQRES 3 A 317 THR ALA ALA LYS LYS ASN ASP LYS GLU ALA ALA GLY GLU SEQRES 4 A 317 GLY PRO ALA LEU TYR GLU ASP PRO PRO ASP GLN LYS THR SEQRES 5 A 317 SER PRO SER GLY LYS PRO ALA THR LEU LYS ILE CYS SER SEQRES 6 A 317 TRP ASN VAL ASP GLY LEU ARG ALA TRP ILE LYS LYS LYS SEQRES 7 A 317 GLY LEU ASP TRP VAL LYS GLU GLU ALA PRO ASP ILE LEU SEQRES 8 A 317 CYS LEU GLN GLU THR LYS CYS SER GLU ASN LYS LEU PRO SEQRES 9 A 317 ALA GLU LEU GLN GLU LEU PRO GLY LEU SER HIS GLN TYR SEQRES 10 A 317 TRP SER ALA PRO SER ASP LYS GLU GLY TYR SER GLY VAL SEQRES 11 A 317 GLY LEU LEU SER ARG GLN CYS PRO LEU LYS VAL SER TYR SEQRES 12 A 317 GLY ILE GLY ASP GLU GLU HIS ASP GLN GLU GLY ARG VAL SEQRES 13 A 317 ILE VAL ALA GLU PHE ASP SER PHE VAL LEU VAL THR ALA SEQRES 14 A 317 TYR VAL PRO ASN ALA GLY ARG GLY LEU VAL ARG LEU GLU SEQRES 15 A 317 TYR ARG GLN ARG TRP ASP GLU ALA PHE ARG LYS PHE LEU SEQRES 16 A 317 LYS GLY LEU ALA SER ARG LYS PRO LEU VAL LEU CYS GLY SEQRES 17 A 317 ASP LEU ASN VAL ALA HIS GLU GLU ILE ASP LEU ARG ASN SEQRES 18 A 317 PRO LYS GLY ASN LYS LYS ASN ALA GLY PHE THR PRO GLN SEQRES 19 A 317 GLU ARG GLN GLY PHE GLY GLU LEU LEU GLN ALA VAL PRO SEQRES 20 A 317 LEU ALA ASP SER PHE ARG HIS LEU TYR PRO ASN THR PRO SEQRES 21 A 317 TYR ALA TYR THR PHE TRP THR TYR MET MET ASN ALA ARG SEQRES 22 A 317 SER LYS ASN VAL GLY TRP ARG LEU ASP TYR PHE LEU LEU SEQRES 23 A 317 SER HIS SER LEU LEU PRO ALA LEU CYS ASP SER LYS ILE SEQRES 24 A 317 ARG SER LYS ALA LEU GLY SER ASP HIS CYS PRO ILE THR SEQRES 25 A 317 LEU TYR LEU ALA LEU SEQRES 1 B 317 PRO LYS ARG GLY LYS LYS GLY ALA VAL ALA GLU ASP GLY SEQRES 2 B 317 ASP GLU LEU ARG THR GLU PRO GLU ALA LYS LYS SER LYS SEQRES 3 B 317 THR ALA ALA LYS LYS ASN ASP LYS GLU ALA ALA GLY GLU SEQRES 4 B 317 GLY PRO ALA LEU TYR GLU ASP PRO PRO ASP GLN LYS THR SEQRES 5 B 317 SER PRO SER GLY LYS PRO ALA THR LEU LYS ILE CYS SER SEQRES 6 B 317 TRP ASN VAL ASP GLY LEU ARG ALA TRP ILE LYS LYS LYS SEQRES 7 B 317 GLY LEU ASP TRP VAL LYS GLU GLU ALA PRO ASP ILE LEU SEQRES 8 B 317 CYS LEU GLN GLU THR LYS CYS SER GLU ASN LYS LEU PRO SEQRES 9 B 317 ALA GLU LEU GLN GLU LEU PRO GLY LEU SER HIS GLN TYR SEQRES 10 B 317 TRP SER ALA PRO SER ASP LYS GLU GLY TYR SER GLY VAL SEQRES 11 B 317 GLY LEU LEU SER ARG GLN CYS PRO LEU LYS VAL SER TYR SEQRES 12 B 317 GLY ILE GLY ASP GLU GLU HIS ASP GLN GLU GLY ARG VAL SEQRES 13 B 317 ILE VAL ALA GLU PHE ASP SER PHE VAL LEU VAL THR ALA SEQRES 14 B 317 TYR VAL PRO ASN ALA GLY ARG GLY LEU VAL ARG LEU GLU SEQRES 15 B 317 TYR ARG GLN ARG TRP ASP GLU ALA PHE ARG LYS PHE LEU SEQRES 16 B 317 LYS GLY LEU ALA SER ARG LYS PRO LEU VAL LEU CYS GLY SEQRES 17 B 317 ASP LEU ASN VAL ALA HIS GLU GLU ILE ASP LEU ARG ASN SEQRES 18 B 317 PRO LYS GLY ASN LYS LYS ASN ALA GLY PHE THR PRO GLN SEQRES 19 B 317 GLU ARG GLN GLY PHE GLY GLU LEU LEU GLN ALA VAL PRO SEQRES 20 B 317 LEU ALA ASP SER PHE ARG HIS LEU TYR PRO ASN THR PRO SEQRES 21 B 317 TYR ALA TYR THR PHE TRP THR TYR MET MET ASN ALA ARG SEQRES 22 B 317 SER LYS ASN VAL GLY TRP ARG LEU ASP TYR PHE LEU LEU SEQRES 23 B 317 SER HIS SER LEU LEU PRO ALA LEU CYS ASP SER LYS ILE SEQRES 24 B 317 ARG SER LYS ALA LEU GLY SER ASP HIS CYS PRO ILE THR SEQRES 25 B 317 LEU TYR LEU ALA LEU SEQRES 1 C 317 PRO LYS ARG GLY LYS LYS GLY ALA VAL ALA GLU ASP GLY SEQRES 2 C 317 ASP GLU LEU ARG THR GLU PRO GLU ALA LYS LYS SER LYS SEQRES 3 C 317 THR ALA ALA LYS LYS ASN ASP LYS GLU ALA ALA GLY GLU SEQRES 4 C 317 GLY PRO ALA LEU TYR GLU ASP PRO PRO ASP GLN LYS THR SEQRES 5 C 317 SER PRO SER GLY LYS PRO ALA THR LEU LYS ILE CYS SER SEQRES 6 C 317 TRP ASN VAL ASP GLY LEU ARG ALA TRP ILE LYS LYS LYS SEQRES 7 C 317 GLY LEU ASP TRP VAL LYS GLU GLU ALA PRO ASP ILE LEU SEQRES 8 C 317 CYS LEU GLN GLU THR LYS CYS SER GLU ASN LYS LEU PRO SEQRES 9 C 317 ALA GLU LEU GLN GLU LEU PRO GLY LEU SER HIS GLN TYR SEQRES 10 C 317 TRP SER ALA PRO SER ASP LYS GLU GLY TYR SER GLY VAL SEQRES 11 C 317 GLY LEU LEU SER ARG GLN CYS PRO LEU LYS VAL SER TYR SEQRES 12 C 317 GLY ILE GLY ASP GLU GLU HIS ASP GLN GLU GLY ARG VAL SEQRES 13 C 317 ILE VAL ALA GLU PHE ASP SER PHE VAL LEU VAL THR ALA SEQRES 14 C 317 TYR VAL PRO ASN ALA GLY ARG GLY LEU VAL ARG LEU GLU SEQRES 15 C 317 TYR ARG GLN ARG TRP ASP GLU ALA PHE ARG LYS PHE LEU SEQRES 16 C 317 LYS GLY LEU ALA SER ARG LYS PRO LEU VAL LEU CYS GLY SEQRES 17 C 317 ASP LEU ASN VAL ALA HIS GLU GLU ILE ASP LEU ARG ASN SEQRES 18 C 317 PRO LYS GLY ASN LYS LYS ASN ALA GLY PHE THR PRO GLN SEQRES 19 C 317 GLU ARG GLN GLY PHE GLY GLU LEU LEU GLN ALA VAL PRO SEQRES 20 C 317 LEU ALA ASP SER PHE ARG HIS LEU TYR PRO ASN THR PRO SEQRES 21 C 317 TYR ALA TYR THR PHE TRP THR TYR MET MET ASN ALA ARG SEQRES 22 C 317 SER LYS ASN VAL GLY TRP ARG LEU ASP TYR PHE LEU LEU SEQRES 23 C 317 SER HIS SER LEU LEU PRO ALA LEU CYS ASP SER LYS ILE SEQRES 24 C 317 ARG SER LYS ALA LEU GLY SER ASP HIS CYS PRO ILE THR SEQRES 25 C 317 LEU TYR LEU ALA LEU HET PO4 A 400 5 HET MG A 402 1 HET PO4 B 401 5 HET MG B 403 1 HET MG C 404 1 HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION FORMUL 4 PO4 2(O4 P 3-) FORMUL 5 MG 3(MG 2+) FORMUL 9 HOH *37(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 1 6 HELIX 4 4 GLY A 176 VAL A 180 5 5 HELIX 5 5 ARG A 181 SER A 201 1 21 HELIX 6 6 GLU A 216 LEU A 220 5 5 HELIX 7 7 ASN A 222 ASN A 226 5 5 HELIX 8 8 THR A 233 VAL A 247 1 15 HELIX 9 9 SER A 252 TYR A 257 1 6 HELIX 10 10 TYR A 269 MET A 271 5 3 HELIX 11 11 ASN A 272 ASN A 277 1 6 HELIX 12 12 SER A 290 PRO A 293 5 4 HELIX 13 13 LEU B 72 LYS B 78 1 7 HELIX 14 14 LYS B 79 ALA B 88 1 10 HELIX 15 15 SER B 100 LEU B 104 5 5 HELIX 16 16 GLU B 107 LEU B 111 5 5 HELIX 17 17 ASP B 148 ASP B 152 5 5 HELIX 18 18 GLY B 176 VAL B 180 5 5 HELIX 19 19 ARG B 181 ARG B 202 1 22 HELIX 20 20 GLU B 216 LEU B 220 5 5 HELIX 21 21 ASN B 222 LYS B 227 1 6 HELIX 22 22 THR B 233 VAL B 247 1 15 HELIX 23 23 SER B 252 TYR B 257 1 6 HELIX 24 24 TYR B 269 MET B 271 5 3 HELIX 25 25 ASN B 272 ASN B 277 1 6 HELIX 26 26 HIS B 289 PRO B 293 5 5 HELIX 27 27 GLY C 71 LYS C 78 1 8 HELIX 28 28 LYS C 79 ALA C 88 1 10 HELIX 29 29 GLU C 107 LEU C 111 5 5 HELIX 30 30 GLY C 176 LEU C 182 5 7 HELIX 31 31 GLU C 183 SER C 201 1 19 HELIX 32 32 LYS C 224 ASN C 229 5 6 HELIX 33 33 THR C 233 GLN C 245 1 13 HELIX 34 34 SER C 252 TYR C 257 1 6 HELIX 35 35 HIS C 289 PRO C 293 5 5 SHEET 1 A 6 TRP A 119 SER A 120 0 SHEET 2 A 6 VAL A 131 SER A 135 -1 O VAL A 131 N SER A 120 SHEET 3 A 6 ILE A 91 GLN A 95 -1 N LEU A 94 O GLY A 132 SHEET 4 A 6 LEU A 62 ASN A 68 1 N CYS A 65 O ILE A 91 SHEET 5 A 6 ILE A 312 LEU A 316 -1 O ILE A 312 N SER A 66 SHEET 6 A 6 LEU A 295 SER A 298 -1 N ASP A 297 O TYR A 315 SHEET 1 B 6 LYS A 141 TYR A 144 0 SHEET 2 B 6 VAL A 157 PHE A 162 -1 O GLU A 161 N LYS A 141 SHEET 3 B 6 PHE A 165 TYR A 171 -1 O PHE A 165 N PHE A 162 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 SER A 288 -1 O LEU A 286 N LEU A 207 SHEET 6 B 6 LEU A 249 ASP A 251 -1 N ALA A 250 O LEU A 287 SHEET 1 C 6 HIS B 116 SER B 120 0 SHEET 2 C 6 VAL B 131 SER B 135 -1 O SER B 135 N HIS B 116 SHEET 3 C 6 ILE B 91 GLN B 95 -1 N LEU B 92 O LEU B 134 SHEET 4 C 6 LEU B 62 ASN B 68 1 N CYS B 65 O CYS B 93 SHEET 5 C 6 ILE B 312 LEU B 316 -1 O LEU B 314 N ILE B 64 SHEET 6 C 6 LEU B 295 ILE B 300 -1 N CYS B 296 O TYR B 315 SHEET 1 D 6 LYS B 141 TYR B 144 0 SHEET 2 D 6 VAL B 157 GLU B 161 -1 O VAL B 159 N SER B 143 SHEET 3 D 6 VAL B 166 TYR B 171 -1 O LEU B 167 N ALA B 160 SHEET 4 D 6 LEU B 205 ASP B 210 1 O VAL B 206 N VAL B 168 SHEET 5 D 6 ASP B 283 LEU B 287 -1 O LEU B 286 N LEU B 207 SHEET 6 D 6 ALA B 250 ASP B 251 -1 N ALA B 250 O LEU B 287 SHEET 1 E 6 GLN C 117 SER C 120 0 SHEET 2 E 6 VAL C 131 SER C 135 -1 O LEU C 133 N TYR C 118 SHEET 3 E 6 ILE C 91 GLN C 95 -1 N LEU C 92 O LEU C 134 SHEET 4 E 6 LEU C 62 ASN C 68 1 N TRP C 67 O CYS C 93 SHEET 5 E 6 ILE C 312 LEU C 316 -1 O LEU C 314 N ILE C 64 SHEET 6 E 6 LEU C 295 ILE C 300 -1 N ASP C 297 O TYR C 315 SHEET 1 F 6 LYS C 141 TYR C 144 0 SHEET 2 F 6 VAL C 157 GLU C 161 -1 O VAL C 159 N SER C 143 SHEET 3 F 6 VAL C 166 TYR C 171 -1 O LEU C 167 N ALA C 160 SHEET 4 F 6 LEU C 205 ASP C 210 1 O VAL C 206 N VAL C 168 SHEET 5 F 6 ASP C 283 LEU C 287 -1 O LEU C 286 N LEU C 207 SHEET 6 F 6 ALA C 250 ASP C 251 -1 N ALA C 250 O LEU C 287 SSBOND 1 CYS A 93 CYS A 208 1555 1555 2.07 LINK OD1 ASP A 70 MG MG A 402 1555 1555 2.51 LINK OE1 GLU A 96 MG MG A 402 1555 1555 2.48 LINK OE2 GLU A 96 MG MG A 402 1555 1555 2.24 LINK MG MG A 402 O HOH A 414 1555 1555 2.27 LINK OD1 ASP B 70 MG MG B 403 1555 1555 2.35 LINK OE1 GLU B 96 MG MG B 403 1555 1555 2.77 LINK OD1 ASP C 70 MG MG C 404 1555 1555 2.28 LINK OE1 GLU C 96 MG MG C 404 1555 1555 2.22 CISPEP 1 VAL B 247 PRO B 248 0 0.59 CISPEP 2 VAL C 247 PRO C 248 0 1.08 SITE 1 AC1 4 ASN A 174 ALA A 230 TRP A 280 HOH A 411 SITE 1 AC2 3 ASN B 174 ASN B 212 ALA B 230 SITE 1 AC3 3 ASP A 70 GLU A 96 HOH A 414 SITE 1 AC4 2 ASP B 70 GLU B 96 SITE 1 AC5 4 ASN C 68 ASP C 70 GLU C 96 ASP C 308 CRYST1 167.347 92.392 94.006 90.00 121.38 90.00 C 1 2 1 12 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 0.005976 0.000000 0.003644 0.00000 SCALE2 0.000000 0.010823 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012460 0.00000