HEADER DNA BINDING PROTEIN/DNA 20-NOV-17 6BOW
TITLE HUMAN APE1 SUBSTRATE COMPLEX WITH AN T/T 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 BINDING PROTEIN-DNA
KEYWDS 2 COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR B.D.FREUDENTHAL,A.M.WHITAKER,M.S.FAIRLAMB
REVDAT 4 04-OCT-23 6BOW 1 REMARK
REVDAT 3 18-DEC-19 6BOW 1 REMARK
REVDAT 2 20-FEB-19 6BOW 1 REMARK
REVDAT 1 15-AUG-18 6BOW 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. 1.59 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) : 1.59
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.56
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960
REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0
REMARK 3 NUMBER OF REFLECTIONS : 190771
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.214
REMARK 3 R VALUE (WORKING SET) : 0.214
REMARK 3 FREE R VALUE : 0.241
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.020
REMARK 3 FREE R VALUE TEST SET COUNT : 3847
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 24.5643 - 4.7612 0.99 7223 149 0.1591 0.1776
REMARK 3 2 4.7612 - 3.7836 0.99 7222 147 0.1513 0.1789
REMARK 3 3 3.7836 - 3.3066 0.99 7217 152 0.1725 0.1630
REMARK 3 4 3.3066 - 3.0048 0.98 7146 146 0.1960 0.2478
REMARK 3 5 3.0048 - 2.7898 0.97 7020 146 0.2177 0.2535
REMARK 3 6 2.7898 - 2.6255 0.97 7069 147 0.2159 0.2090
REMARK 3 7 2.6255 - 2.4942 0.97 7055 145 0.2345 0.3165
REMARK 3 8 2.4942 - 2.3857 0.97 7110 144 0.2462 0.2830
REMARK 3 9 2.3857 - 2.2939 0.97 7034 148 0.2542 0.3054
REMARK 3 10 2.2939 - 2.2148 0.96 6921 141 0.2423 0.3263
REMARK 3 11 2.2148 - 2.1456 0.98 7198 152 0.2428 0.2366
REMARK 3 12 2.1456 - 2.0843 0.98 7172 150 0.2324 0.2348
REMARK 3 13 2.0843 - 2.0294 0.97 7013 142 0.2359 0.2317
REMARK 3 14 2.0294 - 1.9800 0.98 7129 144 0.2660 0.3283
REMARK 3 15 1.9800 - 1.9350 0.96 6964 137 0.2838 0.3282
REMARK 3 16 1.9350 - 1.8938 0.95 6998 148 0.2764 0.3406
REMARK 3 17 1.8938 - 1.8559 0.93 6782 139 0.3338 0.3555
REMARK 3 18 1.8559 - 1.8209 0.96 6989 145 0.3406 0.3385
REMARK 3 19 1.8209 - 1.7884 0.96 6970 143 0.3258 0.3324
REMARK 3 20 1.7884 - 1.7581 0.94 6844 136 0.3125 0.3988
REMARK 3 21 1.7581 - 1.7298 0.95 6996 147 0.3152 0.3805
REMARK 3 22 1.7298 - 1.7031 0.94 6747 136 0.3070 0.2969
REMARK 3 23 1.7031 - 1.6781 0.93 6892 142 0.3076 0.3143
REMARK 3 24 1.6781 - 1.6545 0.93 6668 137 0.3023 0.3379
REMARK 3 25 1.6545 - 1.6321 0.92 6735 142 0.3017 0.2780
REMARK 3 26 1.6321 - 1.6109 0.90 6632 135 0.3155 0.3294
REMARK 3 27 1.6109 - 1.5908 0.71 5178 107 0.3285 0.4033
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) : 0.210
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.370
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) : 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 : 0.012 5313
REMARK 3 ANGLE : 1.273 7380
REMARK 3 CHIRALITY : 0.069 801
REMARK 3 PLANARITY : 0.009 801
REMARK 3 DIHEDRAL : 19.481 3043
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 6BOW 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_1000231178.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 18-AUG-17
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 : 190771
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.591
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 (%) : 99.3
REMARK 200 DATA REDUNDANCY : 4.000
REMARK 200 R MERGE (I) : 0.06300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63
REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3
REMARK 200 DATA REDUNDANCY IN SHELL : 2.80
REMARK 200 R MERGE FOR SHELL (I) : 0.50800
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 (%): 46.50
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30
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: 4310 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 17670 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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: 12110 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 124
REMARK 465 LYS A 125
REMARK 465 GLU A 126
REMARK 465 GLY A 147
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 ASP B 124
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 TYR A 128 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 470 GLU A 154 CG CD OE1 OE2
REMARK 470 LYS A 197 CG CD CE NZ
REMARK 470 ARG A 202 CG CD NE CZ NH1 NH2
REMARK 470 LYS A 227 CG CD CE NZ
REMARK 470 GLN B 51 CD OE1 NE2
REMARK 470 LYS B 58 CG CD CE NZ
REMARK 470 GLN B 109 CG CD OE1 NE2
REMARK 470 ASP B 148 CG OD1 OD2
REMARK 470 GLU B 154 CG CD OE1 OE2
REMARK 470 ARG B 187 CG CD NE CZ NH1 NH2
REMARK 470 ARG B 202 CG CD NE CZ NH1 NH2
REMARK 470 LYS B 203 CG CD CE NZ
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 OP2 DV3 P 11 O HOH P 101 2.10
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 DC V 13 O3' DC V 13 C3' -0.049
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 DT P 10 C3' - O3' - P ANGL. DEV. = 9.1 DEGREES
REMARK 500 DT P 10 C3' - O3' - P ANGL. DEV. = -12.9 DEGREES
REMARK 500 DV3 P 11 O3' - P - O5' ANGL. DEV. = 15.8 DEGREES
REMARK 500 DV3 P 11 C3' - O3' - P ANGL. DEV. = 26.4 DEGREES
REMARK 500 DC P 12 O4' - C1' - N1 ANGL. DEV. = 1.8 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 -141.63 66.82
REMARK 500 PHE A 232 25.25 -141.90
REMARK 500 LEU B 114 55.37 -141.58
REMARK 500 SER B 129 -158.45 -152.17
REMARK 500 ASP B 163 -70.93 -47.46
REMARK 500 ASN B 222 63.49 -117.57
REMARK 500 PHE B 232 19.51 -143.44
REMARK 500
REMARK 500 REMARK: NULL
DBREF 6BOW A 1 318 UNP P27695 APEX1_HUMAN 1 318
DBREF 6BOW B 1 318 UNP P27695 APEX1_HUMAN 1 318
DBREF 6BOW P 1 21 PDB 6BOW 6BOW 1 21
DBREF 6BOW V 1 21 PDB 6BOW 6BOW 1 21
SEQADV 6BOW ALA A 138 UNP P27695 CYS 138 ENGINEERED MUTATION
SEQADV 6BOW ALA B 138 UNP P27695 CYS 138 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 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 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 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 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 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
SEQRES 1 P 21 DG DC DT DG DA DT DG DC DG DT DV3 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 DT DC
SEQRES 2 V 21 DG DC DA DT DC DA DG DC
HET DV3 P 11 22
HETNAM DV3 1,4-ANHYDRO-2-DEOXY-5-O-THIOPHOSPHONO-D-ERYTHRO-
HETNAM 2 DV3 PENTITOL
FORMUL 3 DV3 C5 H11 O5 P S
FORMUL 5 HOH *524(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 GLU A 110 5 6
HELIX 5 AA5 LEU A 111 SER A 115 5 5
HELIX 6 AA6 GLY A 176 VAL A 180 5 5
HELIX 7 AA7 ARG A 181 GLY A 198 1 18
HELIX 8 AA8 GLU A 216 LEU A 220 5 5
HELIX 9 AA9 PRO A 223 LYS A 227 5 5
HELIX 10 AB1 THR A 233 VAL A 247 1 15
HELIX 11 AB2 SER A 252 TYR A 257 1 6
HELIX 12 AB3 TYR A 269 ASN A 277 5 9
HELIX 13 AB4 HIS A 289 PRO A 293 5 5
HELIX 14 AB5 GLY B 71 LYS B 78 1 8
HELIX 15 AB6 LYS B 79 ALA B 88 1 10
HELIX 16 AB7 SER B 100 LEU B 104 5 5
HELIX 17 AB8 PRO B 105 SER B 115 5 11
HELIX 18 AB9 GLY B 176 VAL B 180 5 5
HELIX 19 AC1 ARG B 181 SER B 201 1 21
HELIX 20 AC2 GLU B 216 LEU B 220 5 5
HELIX 21 AC3 PRO B 223 LYS B 227 5 5
HELIX 22 AC4 THR B 233 VAL B 247 1 15
HELIX 23 AC5 SER B 252 TYR B 257 1 6
HELIX 24 AC6 ASN B 272 ASN B 277 1 6
HELIX 25 AC7 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 CYS A 65 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 ASP 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 ILE B 91
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 VAL B 159 N SER B 143
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 ASP 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' DT P 10 P ADV3 P 11 1555 1555 1.55
LINK O3' DT P 10 P BDV3 P 11 1555 1555 1.56
LINK O3'ADV3 P 11 P DC P 12 1555 1555 1.56
LINK O3'BDV3 P 11 P DC P 12 1555 1555 1.56
CISPEP 1 VAL A 247 PRO A 248 0 -8.34
CISPEP 2 VAL B 247 PRO B 248 0 -13.16
CRYST1 44.259 61.333 73.119 83.31 78.28 86.96 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 0.022594 -0.001199 -0.004584 0.00000
SCALE2 0.000000 0.016327 -0.001777 0.00000
SCALE3 0.000000 0.000000 0.014050 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
