HEADER DNA REPAIR 24-OCT-00 1E9N TITLE A SECOND DIVALENT METAL ION IN THE ACTIVE SITE OF A NEW CRYSTAL FORM TITLE 2 OF HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE, APE1, AND ITS TITLE 3 IMPLICATIONS FOR THE CATALYTIC MECHANISM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: AP ENDONUCLEASE 1, HAP1, REF1, APE1; 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 GENE: APE1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11D; SOURCE 10 EXPRESSION_SYSTEM_GENE: APE1 KEYWDS DNA REPAIR, DNA REPAIR ENDONUCLEASE, BASE EXCISION REPAIR, ABASIC KEYWDS 2 ENDONUCLEASE, APE1, HAP1, REF-1, ALPHA, BETA SANDWICH EXPDTA X-RAY DIFFRACTION AUTHOR P.T.BEERNINK,B.W.SEGELKE,B.RUPP REVDAT 6 08-MAY-19 1E9N 1 REMARK REVDAT 5 24-FEB-09 1E9N 1 VERSN REVDAT 4 04-APR-01 1E9N 1 JRNL REVDAT 3 27-MAR-01 1E9N 1 AUTHOR JRNL REVDAT 2 28-FEB-01 1E9N 1 AUTHOR REVDAT 1 16-FEB-01 1E9N 0 JRNL AUTH P.T.BEERNINK,B.W.SEGELKE,M.Z.HADI,J.P.ERZBERGER, JRNL AUTH 2 D.M.WILSON III,B.RUPP JRNL TITL TWO DIVALENT METAL IONS IN THE ACTIVE SITE OF A NEW CRYSTAL JRNL TITL 2 FORM OF HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE, APE1: JRNL TITL 3 IMPLICATIONS FOR THE CATALYTIC MECHANISM JRNL REF J.MOL.BIOL. V. 307 1023 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11286553 JRNL DOI 10.1006/JMBI.2001.4529 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5F REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 31342 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1860 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.00 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3499 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 34905 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4336 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 349 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.018 ; 0.600 ; 4450 REMARK 3 BOND ANGLES (DEGREES) : 2.320 ; 1.800 ; 5997 REMARK 3 TORSION ANGLES (DEGREES) : 18.920; 0.000 ; 2607 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.007 ; 2.000 ; 105 REMARK 3 GENERAL PLANES (A) : 0.016 ; 5.000 ; 642 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 3.200 ; 2.000 ; 4450 REMARK 3 NON-BONDED CONTACTS (A) : 0.228 ; 10.000; 50 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : 0 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : BABENET SCALING REMARK 3 KSOL : 0.80 REMARK 3 BSOL : 150.0 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT PROTGEO_V012 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : TNT BCORREL V1.0 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NCS WEIGHT 60, THEN RELAXED AT END OF REMARK 3 REFINEMENT REMARK 4 REMARK 4 1E9N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-OCT-00. REMARK 100 THE DEPOSITION ID IS D_1290004823. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-99 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2398 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : DUAL CRYSTAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34905 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 67.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08200 REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.37900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: TO BE PUBLISHED REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP, DROP 2+2 UL, 15MG/ML REMARK 280 PROTEIN, 1 ML WELL, 0.1M TRIS-HCL, PH 7.5, 0.2M NAOAC, 30% PEG4K, REMARK 280 20MM HECAMEG, 1MM PB(OAC)2, 1MM DTT, PH 7.50, VAPOR DIFFUSION, REMARK 280 HANGING DROP 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 68.76100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.50800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.76100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.50800 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 300 REMARK: THE BIOLOGICAL UNIT IS HALF OF THE REMARK 300 ASYMMETRIC UNIT 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: PQS 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 400 REMARK 400 COMPOUND REMARK 400 ENDONUCLEOLYTIC CLEAVAGE NEAR APURINIC OR APYRIMIDINIC SITES REMARK 400 TO PRODUCTS WITH 5'-PHOSPHATE. 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 MET A 1 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 ASP A 124 REMARK 465 LYS A 125 REMARK 465 MET B 1 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 ASP B 124 REMARK 465 LYS B 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 ASN A 102 CB CG OD1 ND2 REMARK 470 LYS A 103 CB CG CD CE NZ REMARK 470 GLU A 110 CG CD OE1 OE2 REMARK 470 SER A 123 CB OG REMARK 470 ASN B 102 CB CG OD1 ND2 REMARK 470 LYS B 103 CB CG CD CE NZ REMARK 470 SER B 123 CB OG 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 OE2 GLU A 96 O HOH A 2039 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 101 CD GLU A 101 OE2 0.075 REMARK 500 GLU A 107 CD GLU A 107 OE2 0.080 REMARK 500 GLU A 183 CD GLU A 183 OE2 0.082 REMARK 500 GLU B 86 CD GLU B 86 OE2 0.078 REMARK 500 GLU B 101 CD GLU B 101 OE2 0.078 REMARK 500 GLU B 154 CD GLU B 154 OE2 0.069 REMARK 500 GLU B 183 CD GLU B 183 OE2 0.084 REMARK 500 GLU B 217 CD GLU B 217 OE2 0.071 REMARK 500 GLU B 242 CD GLU B 242 OE2 0.066 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 ASP A 47 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES REMARK 500 ASP A 47 CB - CG - OD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 TRP A 67 CD1 - CG - CD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP A 90 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 PRO A 112 C - N - CA ANGL. DEV. = 10.9 DEGREES REMARK 500 PRO A 112 C - N - CD ANGL. DEV. = -16.1 DEGREES REMARK 500 TYR A 118 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ASP A 148 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG A 156 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ASP A 163 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 185 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP A 210 CB - CG - OD2 ANGL. DEV. = -7.8 DEGREES REMARK 500 ARG A 221 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP A 251 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 251 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 PRO A 258 C - N - CD ANGL. DEV. = -13.7 DEGREES REMARK 500 ARG A 281 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP B 47 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP B 50 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP B 90 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 PRO B 112 C - N - CA ANGL. DEV. = 11.9 DEGREES REMARK 500 PRO B 112 C - N - CD ANGL. DEV. = -16.3 DEGREES REMARK 500 ARG B 156 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG B 156 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG B 185 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 193 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 193 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP B 210 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP B 210 CB - CG - OD2 ANGL. DEV. = -7.8 DEGREES REMARK 500 ASP B 251 CB - CG - OD1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ASP B 251 CB - CG - OD2 ANGL. DEV. = -9.2 DEGREES REMARK 500 PRO B 261 C - N - CA ANGL. DEV. = 9.9 DEGREES REMARK 500 ASP B 297 CB - CG - OD1 ANGL. DEV. = 5.7 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 78 46.82 -91.84 REMARK 500 LEU A 111 103.70 -40.30 REMARK 500 SER A 129 -140.86 49.10 REMARK 500 PHE A 232 21.71 -145.77 REMARK 500 TYR A 262 18.40 41.36 REMARK 500 LYS B 78 48.86 -103.45 REMARK 500 LYS B 103 44.27 -72.24 REMARK 500 SER B 129 -142.30 56.47 REMARK 500 TYR B 262 16.44 58.33 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 PB A1319 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2164 O REMARK 620 2 GLU A 96 OE1 92.9 REMARK 620 3 ASP A 70 OD1 73.3 69.5 REMARK 620 4 HOH A2024 O 119.7 88.7 51.2 REMARK 620 5 HOH A2038 O 163.6 90.6 93.0 44.3 REMARK 620 6 HOH A2165 O 73.1 160.8 116.9 109.5 106.5 REMARK 620 7 HOH A2163 O 72.5 128.9 59.4 60.9 92.8 60.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PB A1320 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 210 OD1 REMARK 620 2 ASP A 210 OD2 43.6 REMARK 620 3 HIS A 309 NE2 91.7 83.1 REMARK 620 4 HOH A2080 O 117.8 91.5 129.6 REMARK 620 5 ASN A 212 ND2 75.8 101.9 153.9 76.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PB B1319 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 309 NE2 REMARK 620 2 ASP B 210 OD1 94.4 REMARK 620 3 ASP B 210 OD2 79.7 43.9 REMARK 620 4 HOH B2076 O 130.0 113.8 92.7 REMARK 620 5 ASN B 212 ND2 156.3 73.7 103.4 73.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PB B1320 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 96 OE1 REMARK 620 2 HOH B2178 O 89.7 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 PB A1319 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB A1320 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB B1319 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB B1320 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BIX RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF THE HUMAN DEOXYRIBONUCLEIC ACID REPAIR REMARK 900 ENDONUCLEASE HAP1 SUGGESTS THE RECOGNITION OF EXTRA-HELICAL REMARK 900 DEOXYRIBOSE AT DEOXYRIBONUCLEIC ACID ABASIC SITES REMARK 900 RELATED ID: 1CQG RELATED DB: PDB REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE REMARK 900 INTERMEDIATE BETWEEN HUMAN THIOREDOXIN (C35A, C62A, C69A, C73A) REMARK 900 MUTANT AND A 13 RESIDUE PEPTIDE COMPRISING ITS TARGET SITE IN HUMAN REMARK 900 REF-1 (RESIDUES 59 - 71 OF THE P50 SUBUNIT OF NFKB), NMR, 31 REMARK 900 STRUCTURES REMARK 900 RELATED ID: 1CQH RELATED DB: PDB REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE REMARK 900 INTERMEDIATE BETWEEN HUMAN THIOREDOXIN (C35A, C62A, C69A, C73A) REMARK 900 MUTANT AND A 13 RESIDUE PEPTIDE COMPRISING ITS TARGET SITE IN HUMAN REMARK 900 REF-1 (RESIDUES 59 - 71 OF THE P50 SUBUNIT OF NFKB), NMR, MINIMIZED REMARK 900 AVERAGE STRUCTURE DBREF 1E9N A 1 1 PDB 1E9N 1E9N 1 1 DBREF 1E9N A 2 318 UNP P27695 APE1_HUMAN 1 317 DBREF 1E9N B 1 1 PDB 1E9N 1E9N 1 1 DBREF 1E9N B 2 318 UNP P27695 APE1_HUMAN 1 317 SEQRES 1 A 318 MET PRO LYS ARG GLY LYS LYS GLY ALA VAL ALA GLU ASP SEQRES 2 A 318 GLY ASP GLU LEU ARG THR GLU PRO GLU ALA LYS LYS SER SEQRES 3 A 318 LYS THR ALA ALA LYS LYS ASN ASP LYS GLU ALA ALA GLY SEQRES 4 A 318 GLU GLY PRO ALA LEU TYR GLU ASP PRO PRO ASP GLN LYS SEQRES 5 A 318 THR SER PRO SER GLY LYS PRO ALA THR LEU LYS ILE CYS SEQRES 6 A 318 SER TRP ASN VAL ASP GLY LEU ARG ALA TRP ILE LYS LYS SEQRES 7 A 318 LYS GLY LEU ASP TRP VAL LYS GLU GLU ALA PRO ASP ILE SEQRES 8 A 318 LEU CYS LEU GLN GLU THR LYS CYS SER GLU ASN LYS LEU SEQRES 9 A 318 PRO ALA GLU LEU GLN GLU LEU PRO GLY LEU SER HIS GLN SEQRES 10 A 318 TYR TRP SER ALA PRO SER ASP LYS GLU GLY TYR SER GLY SEQRES 11 A 318 VAL GLY LEU LEU SER ARG GLN CYS PRO LEU LYS VAL SER SEQRES 12 A 318 TYR GLY ILE GLY ASP GLU GLU HIS ASP GLN GLU GLY ARG SEQRES 13 A 318 VAL ILE VAL ALA GLU PHE ASP SER PHE VAL LEU VAL THR SEQRES 14 A 318 ALA TYR VAL PRO ASN ALA GLY ARG GLY LEU VAL ARG LEU SEQRES 15 A 318 GLU TYR ARG GLN ARG TRP ASP GLU ALA PHE ARG LYS PHE SEQRES 16 A 318 LEU LYS GLY LEU ALA SER ARG LYS PRO LEU VAL LEU CYS SEQRES 17 A 318 GLY ASP LEU ASN VAL ALA HIS GLU GLU ILE ASP LEU ARG SEQRES 18 A 318 ASN PRO LYS GLY ASN LYS LYS ASN ALA GLY PHE THR PRO SEQRES 19 A 318 GLN GLU ARG GLN GLY PHE GLY GLU LEU LEU GLN ALA VAL SEQRES 20 A 318 PRO LEU ALA ASP SER PHE ARG HIS LEU TYR PRO ASN THR SEQRES 21 A 318 PRO TYR ALA TYR THR PHE TRP THR TYR MET MET ASN ALA SEQRES 22 A 318 ARG SER LYS ASN VAL GLY TRP ARG LEU ASP TYR PHE LEU SEQRES 23 A 318 LEU SER HIS SER LEU LEU PRO ALA LEU CYS ASP SER LYS SEQRES 24 A 318 ILE ARG SER LYS ALA LEU GLY SER ASP HIS CYS PRO ILE SEQRES 25 A 318 THR LEU TYR LEU ALA LEU SEQRES 1 B 318 MET PRO LYS ARG GLY LYS LYS GLY ALA VAL ALA GLU ASP SEQRES 2 B 318 GLY ASP GLU LEU ARG THR GLU PRO GLU ALA LYS LYS SER SEQRES 3 B 318 LYS THR ALA ALA LYS LYS ASN ASP LYS GLU ALA ALA GLY SEQRES 4 B 318 GLU GLY PRO ALA LEU TYR GLU ASP PRO PRO ASP GLN LYS SEQRES 5 B 318 THR SER PRO SER GLY LYS PRO ALA THR LEU LYS ILE CYS SEQRES 6 B 318 SER TRP ASN VAL ASP GLY LEU ARG ALA TRP ILE LYS LYS SEQRES 7 B 318 LYS GLY LEU ASP TRP VAL LYS GLU GLU ALA PRO ASP ILE SEQRES 8 B 318 LEU CYS LEU GLN GLU THR LYS CYS SER GLU ASN LYS LEU SEQRES 9 B 318 PRO ALA GLU LEU GLN GLU LEU PRO GLY LEU SER HIS GLN SEQRES 10 B 318 TYR TRP SER ALA PRO SER ASP LYS GLU GLY TYR SER GLY SEQRES 11 B 318 VAL GLY LEU LEU SER ARG GLN CYS PRO LEU LYS VAL SER SEQRES 12 B 318 TYR GLY ILE GLY ASP GLU GLU HIS ASP GLN GLU GLY ARG SEQRES 13 B 318 VAL ILE VAL ALA GLU PHE ASP SER PHE VAL LEU VAL THR SEQRES 14 B 318 ALA TYR VAL PRO ASN ALA GLY ARG GLY LEU VAL ARG LEU SEQRES 15 B 318 GLU TYR ARG GLN ARG TRP ASP GLU ALA PHE ARG LYS PHE SEQRES 16 B 318 LEU LYS GLY LEU ALA SER ARG LYS PRO LEU VAL LEU CYS SEQRES 17 B 318 GLY ASP LEU ASN VAL ALA HIS GLU GLU ILE ASP LEU ARG SEQRES 18 B 318 ASN PRO LYS GLY ASN LYS LYS ASN ALA GLY PHE THR PRO SEQRES 19 B 318 GLN GLU ARG GLN GLY PHE GLY GLU LEU LEU GLN ALA VAL SEQRES 20 B 318 PRO LEU ALA ASP SER PHE ARG HIS LEU TYR PRO ASN THR SEQRES 21 B 318 PRO TYR ALA TYR THR PHE TRP THR TYR MET MET ASN ALA SEQRES 22 B 318 ARG SER LYS ASN VAL GLY TRP ARG LEU ASP TYR PHE LEU SEQRES 23 B 318 LEU SER HIS SER LEU LEU PRO ALA LEU CYS ASP SER LYS SEQRES 24 B 318 ILE ARG SER LYS ALA LEU GLY SER ASP HIS CYS PRO ILE SEQRES 25 B 318 THR LEU TYR LEU ALA LEU HET PB A1319 1 HET PB A1320 1 HET PB B1319 1 HET PB B1320 1 HETNAM PB LEAD (II) ION FORMUL 3 PB 4(PB 2+) FORMUL 7 HOH *349(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 SER A 100 LEU A 104 5 5 HELIX 4 5 ALA A 106 LEU A 111 1 6 HELIX 5 6 ASP A 148 ASP A 152 5 5 HELIX 6 7 GLY A 176 VAL A 180 5 5 HELIX 7 8 ARG A 181 LYS A 203 1 23 HELIX 8 9 GLU A 216 ASP A 219 5 4 HELIX 9 10 PRO A 223 LYS A 227 5 5 HELIX 10 11 THR A 233 VAL A 247 1 15 HELIX 11 12 SER A 252 TYR A 257 1 6 HELIX 12 13 TYR A 269 ALA A 273 5 5 HELIX 13 14 HIS A 289 PRO A 293 5 5 HELIX 14 15 GLY B 71 LYS B 78 1 8 HELIX 15 16 LYS B 79 ALA B 88 1 10 HELIX 16 17 PRO B 105 GLN B 109 5 5 HELIX 17 18 ASP B 148 ASP B 152 5 5 HELIX 18 19 GLY B 176 VAL B 180 5 5 HELIX 19 20 ARG B 181 LYS B 203 1 23 HELIX 20 21 GLU B 216 ASP B 219 5 4 HELIX 21 22 PRO B 223 LYS B 227 5 5 HELIX 22 23 THR B 233 VAL B 247 1 15 HELIX 23 24 SER B 252 TYR B 257 1 6 HELIX 24 25 TYR B 269 ALA B 273 5 5 HELIX 25 26 HIS B 289 PRO B 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 VAL A 131 N SER A 120 SHEET 3 A 6 ILE A 91 GLN A 95 -1 O LEU A 92 N LEU A 134 SHEET 4 A 6 LEU A 62 ASN A 68 1 O CYS A 65 N CYS A 93 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 ILE A 300 -1 N CYS A 296 O TYR A 315 SHEET 1 B 6 LYS A 141 TYR A 144 0 SHEET 2 B 6 VAL A 157 GLU A 161 -1 O VAL A 159 N SER A 143 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 TYR A 284 N GLY A 209 SHEET 6 B 6 ALA A 250 ASP A 251 -1 O ALA A 250 N 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 VAL B 131 N SER B 120 SHEET 3 C 6 ILE B 91 GLN B 95 -1 O LEU B 92 N LEU B 134 SHEET 4 C 6 LEU B 62 ASN B 68 1 O CYS B 65 N CYS B 93 SHEET 5 C 6 ILE B 312 LEU B 316 -1 O ILE B 312 N SER B 66 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 TYR B 284 N GLY B 209 SHEET 6 D 6 ALA B 250 ASP B 251 -1 O ALA B 250 N LEU B 287 SSBOND 1 CYS A 138 CYS B 138 1555 1555 2.03 LINK PB PB A1319 O HOH A2164 1555 1555 2.77 LINK PB PB A1319 OE1 GLU A 96 1555 1555 1.99 LINK PB PB A1319 OD1 ASP A 70 1555 1555 3.48 LINK PB PB A1319 O HOH A2024 1555 1555 3.38 LINK PB PB A1319 O HOH A2038 1555 1555 3.44 LINK PB PB A1319 O HOH A2165 1555 1555 3.24 LINK PB PB A1319 O HOH A2163 1555 1555 3.34 LINK PB PB A1320 OD1 ASP A 210 1555 1555 3.19 LINK PB PB A1320 OD2 ASP A 210 1555 1555 2.79 LINK PB PB A1320 NE2 HIS A 309 1555 1555 3.01 LINK PB PB A1320 O HOH A2080 1555 1555 2.91 LINK PB PB A1320 ND2 ASN A 212 1555 1555 2.98 LINK PB PB B1319 NE2 HIS B 309 1555 1555 3.02 LINK PB PB B1319 OD1 ASP B 210 1555 1555 3.12 LINK PB PB B1319 OD2 ASP B 210 1555 1555 2.70 LINK PB PB B1319 O HOH B2076 1555 1555 3.15 LINK PB PB B1319 ND2 ASN B 212 1555 1555 3.09 LINK PB PB B1320 OE1 GLU B 96 1555 1555 1.98 LINK PB PB B1320 O HOH B2178 1555 1555 2.93 CISPEP 1 VAL A 247 PRO A 248 0 -0.17 CISPEP 2 VAL B 247 PRO B 248 0 -0.79 SITE 1 AC1 3 ASP A 70 GLU A 96 HOH A2164 SITE 1 AC2 4 ASP A 210 ASN A 212 HIS A 309 HOH A2080 SITE 1 AC3 4 ASP B 210 ASN B 212 LEU B 282 HIS B 309 SITE 1 AC4 2 GLU B 96 HOH B2178 CRYST1 137.522 45.016 125.702 90.00 108.03 90.00 C 1 2 1 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 0.007271 0.000000 0.002367 0.00000 SCALE2 0.000000 0.022214 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008366 0.00000 MTRIX1 1 -0.979000 -0.046000 -0.198000 27.18900 1 MTRIX2 1 -0.046000 0.999000 -0.004000 0.62630 1 MTRIX3 1 0.198000 0.005000 -0.980000 27.35010 1 MTRIX1 2 -0.989000 -0.005000 -0.149000 26.94680 1 MTRIX2 2 -0.006000 1.000000 0.003000 0.03010 1 MTRIX3 2 0.149000 0.003000 -0.989000 27.91270 1