PDB Short entry for 4Z47 HEADER DNA BINDING PROTEIN/DNA 01-APR-15 4Z47 TITLE STRUCTURE OF THE ENZYME-PRODUCT COMPLEX RESULTING FROM TDG ACTION ON A TITLE 2 GU MISMATCH IN THE PRESENCE OF EXCESS BASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: G/T MISMATCH-SPECIFIC THYMINE DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 111-308; COMPND 5 SYNONYM: THYMINE-DNA GLYCOSYLASE,HTDG; COMPND 6 EC: 3.2.2.29; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA; COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA; COMPND 14 CHAIN: D; COMPND 15 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: TDG; 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 PROTEIN-DNA COMPLEX, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.POZHARSKI,S.S.MALIK,A.C.DROHAT REVDAT 5 25-DEC-19 4Z47 1 REMARK REVDAT 4 13-SEP-17 4Z47 1 JRNL REMARK REVDAT 3 11-NOV-15 4Z47 1 JRNL REVDAT 2 30-SEP-15 4Z47 1 JRNL REVDAT 1 16-SEP-15 4Z47 0 JRNL AUTH S.S.MALIK,C.T.COEY,K.M.VARNEY,E.POZHARSKI,A.C.DROHAT JRNL TITL THYMINE DNA GLYCOSYLASE EXHIBITS NEGLIGIBLE AFFINITY FOR JRNL TITL 2 NUCLEOBASES THAT IT REMOVES FROM DNA. JRNL REF NUCLEIC ACIDS RES. V. 43 9541 2015 JRNL REFN ESSN 1362-4962 JRNL PMID 26358812 JRNL DOI 10.1093/NAR/GKV890 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 61716 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 + TEST SET) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 3110 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4497 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.3140 REMARK 3 BIN FREE R VALUE SET COUNT : 207 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1557 REMARK 3 NUCLEIC ACID ATOMS : 1135 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 273 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.60000 REMARK 3 B22 (A**2) : -0.28000 REMARK 3 B33 (A**2) : -1.18000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.65000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.060 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.982 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2961 ; 0.023 ; 0.016 REMARK 3 BOND LENGTHS OTHERS (A): 2240 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4248 ; 2.274 ; 1.595 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5214 ; 1.919 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 204 ; 6.665 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 74 ;34.638 ;24.054 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 291 ;13.329 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;17.134 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 412 ; 0.151 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2523 ; 0.019 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 667 ; 0.013 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 796 ; 4.961 ; 3.041 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 794 ; 4.938 ; 3.037 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 994 ; 6.399 ; 4.574 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 5199 ; 5.985 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 91 ;29.915 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5205 ;18.998 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4Z47 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208609. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64847 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 45.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 11.70 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.8 REMARK 200 DATA REDUNDANCY IN SHELL : 11.00 REMARK 200 R MERGE FOR SHELL (I) : 0.06700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4FNC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.2M AMMONIUM ACETATE, REMARK 280 0.1M SODIUM ACETATE, PH 6.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K 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 44.65250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.66100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.65250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.66100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 105 REMARK 465 SER A 106 REMARK 465 HIS A 107 REMARK 465 MET A 108 REMARK 465 ALA A 109 REMARK 465 SER A 110 REMARK 465 ASP A 307 REMARK 465 VAL A 308 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 LYS A 206 CG CD CE NZ REMARK 470 LYS A 248 CG CD CE NZ 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 TYR A 152 CG TYR A 152 CD2 -0.081 REMARK 500 GLU A 236 CD GLU A 236 OE1 0.116 REMARK 500 CYS A 276 CB CYS A 276 SG -0.139 REMARK 500 DT D 4 O3' DT D 4 C3' -0.042 REMARK 500 DT D 10 O3' DC D 11 P 0.087 REMARK 500 DC D 11 O3' DG D 12 P -0.092 REMARK 500 DA D 20 P DA D 20 OP2 -0.163 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 126 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 MET A 144 CG - SD - CE ANGL. DEV. = -10.1 DEGREES REMARK 500 ARG A 209 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 209 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP A 284 CB - CG - OD1 ANGL. DEV. = -6.5 DEGREES REMARK 500 DG C 3 C5' - C4' - O4' ANGL. DEV. = 10.6 DEGREES REMARK 500 DG C 3 C1' - O4' - C4' ANGL. DEV. = -6.6 DEGREES REMARK 500 DT C 7 O5' - P - OP2 ANGL. DEV. = -5.5 DEGREES REMARK 500 DT C 13 O5' - P - OP1 ANGL. DEV. = -9.1 DEGREES REMARK 500 DT C 13 O5' - C5' - C4' ANGL. DEV. = -10.5 DEGREES REMARK 500 DC C 24 C1' - O4' - C4' ANGL. DEV. = -6.8 DEGREES REMARK 500 DT C 28 P - O5' - C5' ANGL. DEV. = -13.6 DEGREES REMARK 500 DT D 10 C3' - O3' - P ANGL. DEV. = 9.6 DEGREES REMARK 500 DA D 20 O5' - P - OP2 ANGL. DEV. = -5.8 DEGREES REMARK 500 DG D 23 C3' - C2' - C1' ANGL. DEV. = -4.9 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 ASN A 112 41.81 39.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DC C 17 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 670 DISTANCE = 6.15 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACY A 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Z7Z RELATED DB: PDB REMARK 900 RELATED ID: 4Z7B RELATED DB: PDB REMARK 900 RELATED ID: 4XEG RELATED DB: PDB REMARK 900 RELATED ID: 4Z3A RELATED DB: PDB REMARK 900 RELATED ID: 5CYS RELATED DB: PDB DBREF 4Z47 A 111 308 UNP Q13569 TDG_HUMAN 111 308 DBREF 4Z47 C 1 28 PDB 4Z47 4Z47 1 28 DBREF 4Z47 D 1 28 PDB 4Z47 4Z47 1 28 SEQADV 4Z47 GLY A 105 UNP Q13569 EXPRESSION TAG SEQADV 4Z47 SER A 106 UNP Q13569 EXPRESSION TAG SEQADV 4Z47 HIS A 107 UNP Q13569 EXPRESSION TAG SEQADV 4Z47 MET A 108 UNP Q13569 EXPRESSION TAG SEQADV 4Z47 ALA A 109 UNP Q13569 EXPRESSION TAG SEQADV 4Z47 SER A 110 UNP Q13569 EXPRESSION TAG SEQRES 1 A 204 GLY SER HIS MET ALA SER PHE ASN GLY VAL SER GLU ALA SEQRES 2 A 204 GLU LEU LEU THR LYS THR LEU PRO ASP ILE LEU THR PHE SEQRES 3 A 204 ASN LEU ASP ILE VAL ILE ILE GLY ILE ASN PRO GLY LEU SEQRES 4 A 204 MET ALA ALA TYR LYS GLY HIS HIS TYR PRO GLY PRO GLY SEQRES 5 A 204 ASN HIS PHE TRP LYS CYS LEU PHE MET SER GLY LEU SER SEQRES 6 A 204 GLU VAL GLN LEU ASN HIS MET ASP ASP HIS THR LEU PRO SEQRES 7 A 204 GLY LYS TYR GLY ILE GLY PHE THR ASN MET VAL GLU ARG SEQRES 8 A 204 THR THR PRO GLY SER LYS ASP LEU SER SER LYS GLU PHE SEQRES 9 A 204 ARG GLU GLY GLY ARG ILE LEU VAL GLN LYS LEU GLN LYS SEQRES 10 A 204 TYR GLN PRO ARG ILE ALA VAL PHE ASN GLY LYS CYS ILE SEQRES 11 A 204 TYR GLU ILE PHE SER LYS GLU VAL PHE GLY VAL LYS VAL SEQRES 12 A 204 LYS ASN LEU GLU PHE GLY LEU GLN PRO HIS LYS ILE PRO SEQRES 13 A 204 ASP THR GLU THR LEU CYS TYR VAL MET PRO SER SER SER SEQRES 14 A 204 ALA ARG CYS ALA GLN PHE PRO ARG ALA GLN ASP LYS VAL SEQRES 15 A 204 HIS TYR TYR ILE LYS LEU LYS ASP LEU ARG ASP GLN LEU SEQRES 16 A 204 LYS GLY ILE GLU ARG ASN MET ASP VAL SEQRES 1 C 28 DC DA DG DC DT DC DT DG DT DA DC DG DT SEQRES 2 C 28 DG DA DG DC DG DA DT DG DG DA DC DA DG SEQRES 3 C 28 DC DT SEQRES 1 D 28 DA DG DC DT DG DT DC DC DA DT DC DG DC SEQRES 2 D 28 DT DC DA ORP DG DT DA DC DA DG DA DG DC SEQRES 3 D 28 DT DG HET ORP D 17 12 HET EDO A 401 4 HET EDO A 402 4 HET EDO A 403 4 HET ACY A 404 4 HETNAM ORP 2-DEOXY-5-PHOSPHONO-RIBOSE HETNAM EDO 1,2-ETHANEDIOL HETNAM ACY ACETIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ORP C5 H11 O7 P FORMUL 4 EDO 3(C2 H6 O2) FORMUL 7 ACY C2 H4 O2 FORMUL 8 HOH *273(H2 O) HELIX 1 AA1 SER A 115 LEU A 120 1 6 HELIX 2 AA2 GLY A 142 GLY A 149 1 8 HELIX 3 AA3 HIS A 158 SER A 166 1 9 HELIX 4 AA4 ASN A 174 HIS A 179 5 6 HELIX 5 AA5 THR A 180 GLY A 186 1 7 HELIX 6 AA6 GLY A 199 LEU A 203 5 5 HELIX 7 AA7 SER A 204 GLN A 223 1 20 HELIX 8 AA8 GLY A 231 GLY A 244 1 14 HELIX 9 AA9 ARG A 281 ASN A 305 1 25 SHEET 1 AA1 5 ILE A 187 ASN A 191 0 SHEET 2 AA1 5 ILE A 134 GLY A 138 1 N ILE A 136 O GLY A 188 SHEET 3 AA1 5 ILE A 226 ASN A 230 1 O VAL A 228 N VAL A 135 SHEET 4 AA1 5 LEU A 265 MET A 269 1 O LEU A 265 N ALA A 227 SHEET 5 AA1 5 GLY A 253 LEU A 254 -1 N GLY A 253 O VAL A 268 LINK O3' DA D 16 P ORP D 17 1555 1555 1.54 LINK O3 ORP D 17 P DG D 18 1555 1555 1.63 SITE 1 AC1 4 ASN A 131 LEU A 132 GLN A 223 ARG A 225 SITE 1 AC2 5 LEU A 254 GLN A 255 PRO A 256 LYS A 258 SITE 2 AC2 5 LEU A 265 SITE 1 AC3 5 LEU A 295 GLN A 298 LEU A 299 ILE A 302 SITE 2 AC3 5 HOH D 105 SITE 1 AC4 9 GLY A 138 ILE A 139 ASN A 140 TYR A 152 SITE 2 AC4 9 ASN A 191 HOH A 514 HOH A 555 HOH A 595 SITE 3 AC4 9 ORP D 17 CRYST1 89.305 53.322 82.297 90.00 95.31 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.011198 0.000000 0.001040 0.00000 SCALE2 0.000000 0.018754 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012203 0.00000