HEADER DNA BINDING PROTEIN/DNA 20-NOV-17 6BOV
TITLE HUMAN APE1 SUBSTRATE COMPLEX WITH AN A/G MISMATCH ADJACENT THE THF
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: APEX NUCLEASE,APEN,APURINIC-APYRIMIDINIC ENDONUCLEASE 1,APE-
COMPND 5 1,REF-1,REDOX FACTOR-1;
COMPND 6 EC: 3.1.-.-,4.2.99.18;
COMPND 7 ENGINEERED: YES;
COMPND 8 MUTATION: YES;
COMPND 9 MOL_ID: 2;
COMPND 10 MOLECULE: 21-MER DNA;
COMPND 11 CHAIN: P;
COMPND 12 ENGINEERED: YES;
COMPND 13 MOL_ID: 3;
COMPND 14 MOLECULE: 21-MER DNA;
COMPND 15 CHAIN: V;
COMPND 16 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: APEX1, APE, APE1, APEX, APX, HAP1, REF1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 MOL_ID: 2;
SOURCE 9 SYNTHETIC: YES;
SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 11 ORGANISM_TAXID: 32630;
SOURCE 12 MOL_ID: 3;
SOURCE 13 SYNTHETIC: YES;
SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 15 ORGANISM_TAXID: 32630
KEYWDS HYDROLASE LYASE / DNA, DNA BINDING PROTEIN-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR B.D.FREUDENTHAL,A.M.WHITAKER,M.S.FAIRLAMB
REVDAT 4 04-OCT-23 6BOV 1 REMARK
REVDAT 3 18-DEC-19 6BOV 1 REMARK
REVDAT 2 20-FEB-19 6BOV 1 REMARK
REVDAT 1 15-AUG-18 6BOV 0
JRNL AUTH M.S.FAIRLAMB,A.M.WHITAKER,B.D.FREUDENTHAL
JRNL TITL APURINIC/APYRIMIDINIC (AP) ENDONUCLEASE 1 PROCESSING OF AP
JRNL TITL 2 SITES WITH 5' MISMATCHES.
JRNL REF ACTA CRYSTALLOGR D STRUCT V. 74 760 2018
JRNL REF 2 BIOL
JRNL REFN ISSN 2059-7983
JRNL PMID 30082511
JRNL DOI 10.1107/S2059798318003340
REMARK 2
REMARK 2 RESOLUTION. 1.98 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.10_2155
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) : 1.98
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.77
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960
REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0
REMARK 3 NUMBER OF REFLECTIONS : 98881
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.212
REMARK 3 R VALUE (WORKING SET) : 0.211
REMARK 3 FREE R VALUE : 0.242
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.870
REMARK 3 FREE R VALUE TEST SET COUNT : 3825
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 24.7730 - 5.8978 0.98 3635 149 0.1671 0.1913
REMARK 3 2 5.8978 - 4.6917 0.99 3660 148 0.1625 0.1659
REMARK 3 3 4.6917 - 4.1017 0.99 3651 146 0.1542 0.1563
REMARK 3 4 4.1017 - 3.7280 0.99 3647 147 0.1790 0.2102
REMARK 3 5 3.7280 - 3.4616 0.99 3682 147 0.1862 0.2177
REMARK 3 6 3.4616 - 3.2580 0.98 3695 148 0.1957 0.2602
REMARK 3 7 3.2580 - 3.0951 0.98 3593 144 0.2185 0.3075
REMARK 3 8 3.0951 - 2.9606 0.97 3594 145 0.2281 0.2172
REMARK 3 9 2.9606 - 2.8468 0.97 3567 144 0.2453 0.2879
REMARK 3 10 2.8468 - 2.7487 0.96 3591 144 0.2363 0.2859
REMARK 3 11 2.7487 - 2.6629 0.96 3603 145 0.2516 0.3410
REMARK 3 12 2.6629 - 2.5868 0.96 3508 144 0.2511 0.3082
REMARK 3 13 2.5868 - 2.5188 0.96 3516 143 0.2534 0.2853
REMARK 3 14 2.5188 - 2.4574 0.96 3527 142 0.2529 0.2660
REMARK 3 15 2.4574 - 2.4016 0.95 3604 142 0.2535 0.3543
REMARK 3 16 2.4016 - 2.3505 0.95 3455 140 0.2718 0.3488
REMARK 3 17 2.3505 - 2.3035 0.94 3492 141 0.2741 0.3218
REMARK 3 18 2.3035 - 2.2601 0.94 3572 146 0.2636 0.2858
REMARK 3 19 2.2601 - 2.2198 0.94 3334 134 0.2608 0.3048
REMARK 3 20 2.2198 - 2.1821 0.94 3554 144 0.2671 0.3209
REMARK 3 21 2.1821 - 2.1470 0.93 3470 133 0.2656 0.3092
REMARK 3 22 2.1470 - 2.1140 0.93 3353 133 0.2651 0.2985
REMARK 3 23 2.1140 - 2.0829 0.92 3461 140 0.2776 0.2943
REMARK 3 24 2.0829 - 2.0536 0.92 3409 135 0.2740 0.2892
REMARK 3 25 2.0536 - 2.0258 0.92 3440 138 0.2803 0.3343
REMARK 3 26 2.0258 - 1.9995 0.91 3331 132 0.3030 0.2866
REMARK 3 27 1.9995 - 1.9745 0.82 3112 131 0.3157 0.3805
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 : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.960
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 31.04
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
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 : 0.011 5381
REMARK 3 ANGLE : 1.176 7468
REMARK 3 CHIRALITY : 0.059 806
REMARK 3 PLANARITY : 0.007 811
REMARK 3 DIHEDRAL : 19.183 3063
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 6BOV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-17.
REMARK 100 THE DEPOSITION ID IS D_1000231174.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 07-APR-16
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 98881
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.975
REMARK 200 RESOLUTION RANGE LOW (A) : 25.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 4.300
REMARK 200 R MERGE (I) : 0.07100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8
REMARK 200 DATA REDUNDANCY IN SHELL : 2.50
REMARK 200 R MERGE FOR SHELL (I) : 0.47300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> 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: NULL
REMARK 200 STARTING MODEL: 5DFF
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 46.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 7% PEG 20K, 100MM SODIUM CITRATE, 15%
REMARK 280 GLYCEROL, 5MM CACL2, PH 5.0, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 TEMPERATURE 291K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,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
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: 4920 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 17510 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P, V
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: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 11940 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL
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 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 148
REMARK 465 GLU A 149
REMARK 465 GLU A 150
REMARK 465 HIS A 151
REMARK 465 ASP A 152
REMARK 465 GLN A 153
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 LYS B 125
REMARK 465 GLU B 126
REMARK 465 GLU B 149
REMARK 465 GLU B 150
REMARK 465 HIS B 151
REMARK 465 ASP B 152
REMARK 465 GLN B 153
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 A 124 CG OD1 OD2
REMARK 470 LYS A 125 CG CD CE NZ
REMARK 470 GLU A 126 CG CD OE1 OE2
REMARK 470 TYR A 128 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 470 GLU A 154 CG CD OE1 OE2
REMARK 470 ARG A 202 CG CD NE CZ NH1 NH2
REMARK 470 GLN B 51 CD OE1 NE2
REMARK 470 LYS B 79 CG CD CE NZ
REMARK 470 ASP B 124 CG OD1 OD2
REMARK 470 TYR B 128 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 470 ARG B 202 CG CD NE CZ NH1 NH2
REMARK 470 ASN B 272 CG OD1 ND2
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 DC P 12 O3' DC P 12 C3' -0.039
REMARK 500 DC V 9 O3' DC V 9 C3' -0.038
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 CYS B 310 CA - CB - SG ANGL. DEV. = 8.1 DEGREES
REMARK 500 DG P 4 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DC P 12 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DG V 1 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DC V 15 O4' - C1' - N1 ANGL. DEV. = 2.4 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 SER A 129 -147.21 59.50
REMARK 500 SER A 129 -142.63 51.34
REMARK 500 ARG A 202 -79.39 -109.07
REMARK 500 ASN A 222 63.72 -117.70
REMARK 500 PHE A 232 31.85 -144.21
REMARK 500 TYR A 262 17.30 59.63
REMARK 500 LEU B 114 49.37 -144.25
REMARK 500 SER B 129 -149.70 -128.10
REMARK 500 LEU B 199 -58.71 -120.42
REMARK 500 ALA B 200 -18.97 -48.15
REMARK 500 ARG B 202 -79.24 -112.90
REMARK 500 ASN B 222 67.63 -115.59
REMARK 500 ASN B 272 41.95 35.61
REMARK 500
REMARK 500 REMARK: NULL
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 PEG B 401
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 401
DBREF 6BOV A 1 318 UNP P27695 APEX1_HUMAN 1 318
DBREF 6BOV B 1 318 UNP P27695 APEX1_HUMAN 1 318
DBREF 6BOV P 1 21 PDB 6BOV 6BOV 1 21
DBREF 6BOV V 1 21 PDB 6BOV 6BOV 1 21
SEQADV 6BOV GLN A 96 UNP P27695 GLU 96 ENGINEERED MUTATION
SEQADV 6BOV ALA A 138 UNP P27695 CYS 138 ENGINEERED MUTATION
SEQADV 6BOV ASN A 210 UNP P27695 ASP 210 ENGINEERED MUTATION
SEQADV 6BOV GLN B 96 UNP P27695 GLU 96 ENGINEERED MUTATION
SEQADV 6BOV ALA B 138 UNP P27695 CYS 138 ENGINEERED MUTATION
SEQADV 6BOV ASN B 210 UNP P27695 ASP 210 ENGINEERED MUTATION
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 GLN 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 ALA 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 ASN 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 GLN 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 ALA 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 ASN 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
SEQRES 1 P 21 DG DC DT DG DA DT DG DC DG DG 3DR DC DG
SEQRES 2 P 21 DA DC DG DG DA DT DC DC
SEQRES 1 V 21 DG DG DA DT DC DC DG DT DC DG DA DA DC
SEQRES 2 V 21 DG DC DA DT DC DA DG DC
HET 3DR P 11 11
HET PEG B 401 5
HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
HETNAM PEG DI(HYDROXYETHYL)ETHER
HETSYN 3DR ABASIC DIDEOXYRIBOSE
FORMUL 3 3DR C5 H11 O6 P
FORMUL 5 PEG C4 H10 O3
FORMUL 6 HOH *281(H2 O)
HELIX 1 AA1 GLY A 71 LYS A 78 1 8
HELIX 2 AA2 LYS A 79 ALA A 88 1 10
HELIX 3 AA3 SER A 100 LEU A 104 5 5
HELIX 4 AA4 PRO A 105 SER A 115 5 11
HELIX 5 AA5 GLY A 176 VAL A 180 5 5
HELIX 6 AA6 ARG A 181 GLY A 198 1 18
HELIX 7 AA7 GLU A 216 LEU A 220 5 5
HELIX 8 AA8 PRO A 223 LYS A 227 5 5
HELIX 9 AA9 THR A 233 VAL A 247 1 15
HELIX 10 AB1 SER A 252 TYR A 257 1 6
HELIX 11 AB2 HIS A 289 PRO A 293 5 5
HELIX 12 AB3 GLY B 71 LYS B 78 1 8
HELIX 13 AB4 LYS B 79 ALA B 88 1 10
HELIX 14 AB5 SER B 100 LEU B 104 5 5
HELIX 15 AB6 PRO B 105 LEU B 111 5 7
HELIX 16 AB7 GLY B 176 VAL B 180 5 5
HELIX 17 AB8 ARG B 181 SER B 201 1 21
HELIX 18 AB9 GLU B 216 LEU B 220 5 5
HELIX 19 AC1 ASN B 222 LYS B 227 1 6
HELIX 20 AC2 THR B 233 VAL B 247 1 15
HELIX 21 AC3 SER B 252 TYR B 257 1 6
HELIX 22 AC4 ASN B 272 ASN B 277 1 6
HELIX 23 AC5 HIS B 289 PRO B 293 5 5
SHEET 1 AA1 6 HIS A 116 SER A 120 0
SHEET 2 AA1 6 VAL A 131 SER A 135 -1 O VAL A 131 N SER A 120
SHEET 3 AA1 6 ILE A 91 GLN A 95 -1 N LEU A 92 O LEU A 134
SHEET 4 AA1 6 LEU A 62 ASN A 68 1 N TRP A 67 O CYS A 93
SHEET 5 AA1 6 ILE A 312 LEU A 316 -1 O LEU A 314 N ILE A 64
SHEET 6 AA1 6 LEU A 295 ILE A 300 -1 N LYS A 299 O THR A 313
SHEET 1 AA2 6 LYS A 141 TYR A 144 0
SHEET 2 AA2 6 VAL A 157 GLU A 161 -1 O VAL A 159 N SER A 143
SHEET 3 AA2 6 VAL A 166 TYR A 171 -1 O LEU A 167 N ALA A 160
SHEET 4 AA2 6 LEU A 205 ASN A 210 1 O CYS A 208 N VAL A 168
SHEET 5 AA2 6 ASP A 283 LEU A 287 -1 O LEU A 286 N LEU A 207
SHEET 6 AA2 6 ALA A 250 ASP A 251 -1 N ALA A 250 O LEU A 287
SHEET 1 AA3 6 HIS B 116 SER B 120 0
SHEET 2 AA3 6 VAL B 131 SER B 135 -1 O SER B 135 N HIS B 116
SHEET 3 AA3 6 ILE B 91 GLN B 95 -1 N LEU B 92 O LEU B 134
SHEET 4 AA3 6 LEU B 62 ASN B 68 1 N CYS B 65 O CYS B 93
SHEET 5 AA3 6 ILE B 312 LEU B 316 -1 O LEU B 314 N ILE B 64
SHEET 6 AA3 6 LEU B 295 ILE B 300 -1 N LYS B 299 O THR B 313
SHEET 1 AA4 6 LYS B 141 TYR B 144 0
SHEET 2 AA4 6 VAL B 157 GLU B 161 -1 O GLU B 161 N LYS B 141
SHEET 3 AA4 6 VAL B 166 TYR B 171 -1 O LEU B 167 N ALA B 160
SHEET 4 AA4 6 LEU B 205 ASN B 210 1 O VAL B 206 N VAL B 168
SHEET 5 AA4 6 ASP B 283 LEU B 287 -1 O LEU B 286 N LEU B 207
SHEET 6 AA4 6 ALA B 250 ASP B 251 -1 N ALA B 250 O LEU B 287
LINK O3' DG P 10 P 3DR P 11 1555 1555 1.58
LINK O3' 3DR P 11 P DC P 12 1555 1555 1.59
CISPEP 1 VAL A 247 PRO A 248 0 -7.21
CISPEP 2 VAL B 247 PRO B 248 0 -16.41
SITE 1 AC1 4 TYR A 144 HIS B 116 GLN B 117 TYR B 118
CRYST1 44.358 60.371 73.343 83.56 78.43 88.30 P 1 2
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 0.022544 -0.000671 -0.004570 0.00000
SCALE2 0.000000 0.016572 -0.001808 0.00000
SCALE3 0.000000 0.000000 0.014000 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
