HEADER HYDROLASE/DNA 16-NOV-11 3UO7 TITLE CRYSTAL STRUCTURE OF HUMAN THYMINE DNA GLYCOSYLASE BOUND TO SUBSTRATE TITLE 2 5-CARBOXYLCYTOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*AP*GP*CP*TP*CP*TP*GP*TP*AP*CP*AP*TP*GP*AP*GP*CP*AP COMPND 3 *GP*TP*GP*GP*A)-3'; COMPND 4 CHAIN: C; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*CP*AP*CP*TP*GP*CP*TP*CP*AP*(1CC) COMPND 8 P*GP*TP*AP*CP*AP*GP*AP*GP*CP*TP*GP*T)-3'; COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: G/T MISMATCH-SPECIFIC THYMINE DNA GLYCOSYLASE; COMPND 13 CHAIN: A, B; COMPND 14 FRAGMENT: UNP RESIDUES 111-308; COMPND 15 SYNONYM: THYMINE-DNA GLYCOSYLASE, TDG; COMPND 16 EC: 3.2.2.29; COMPND 17 ENGINEERED: YES; COMPND 18 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 GENE: TDG; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DSDNA WITH 5CAC, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.ZHANG,C.HE REVDAT 3 13-SEP-23 3UO7 1 SEQADV LINK REVDAT 2 03-JUN-15 3UO7 1 JRNL REVDAT 1 15-FEB-12 3UO7 0 JRNL AUTH L.ZHANG,X.LU,J.LU,H.LIANG,Q.DAI,G.L.XU,C.LUO,H.JIANG,C.HE JRNL TITL THYMINE DNA GLYCOSYLASE SPECIFICALLY RECOGNIZES JRNL TITL 2 5-CARBOXYLCYTOSINE-MODIFIED DNA. JRNL REF NAT.CHEM.BIOL. V. 8 328 2012 JRNL REFN ISSN 1552-4450 JRNL PMID 22327402 JRNL DOI 10.1038/NCHEMBIO.914 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869) 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 81.2 REMARK 3 NUMBER OF REFLECTIONS : 14639 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 731 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 36.6156 - 6.4577 0.97 1634 177 0.2232 0.2750 REMARK 3 2 6.4577 - 5.1302 1.00 1641 181 0.2329 0.2679 REMARK 3 3 5.1302 - 4.4830 1.00 1623 180 0.1936 0.2722 REMARK 3 4 4.4830 - 4.0737 1.00 1623 181 0.1888 0.2389 REMARK 3 5 4.0737 - 3.7820 0.99 1588 172 0.2121 0.2448 REMARK 3 6 3.7820 - 3.5592 0.94 1527 173 0.2376 0.3107 REMARK 3 7 3.5592 - 3.3811 0.88 1420 156 0.2646 0.3322 REMARK 3 8 3.3811 - 3.2340 0.70 1130 121 0.3090 0.3335 REMARK 3 9 3.2340 - 3.1096 0.46 742 86 0.3395 0.4494 REMARK 3 10 3.1096 - 3.0020 0.16 254 30 0.4265 0.3226 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.29 REMARK 3 B_SOL : 27.46 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.880 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.190 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) : -7.41350 REMARK 3 B22 (A**2) : -7.41350 REMARK 3 B33 (A**2) : 14.82700 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.010 3956 REMARK 3 ANGLE : 1.428 5533 REMARK 3 CHIRALITY : 0.134 601 REMARK 3 PLANARITY : 0.007 547 REMARK 3 DIHEDRAL : 25.315 1551 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 3UO7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000069000. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 180 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03320 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL CRYO-COOLED REMARK 200 SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14639 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : 0.08000 REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.730 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 2BRA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.2 M TRIPOTASSIUM REMARK 280 CITRATE MONOHYDRATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.37933 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.18967 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.78450 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 9.59483 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 47.97417 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, A, 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 SER A 108 REMARK 465 ASN A 109 REMARK 465 ALA A 110 REMARK 465 PHE A 111 REMARK 465 ASN A 112 REMARK 465 GLY A 113 REMARK 465 VAL A 114 REMARK 465 SER A 115 REMARK 465 GLU A 116 REMARK 465 ALA A 117 REMARK 465 GLU A 118 REMARK 465 LEU A 119 REMARK 465 LEU A 120 REMARK 465 THR A 121 REMARK 465 LYS A 122 REMARK 465 ARG A 304 REMARK 465 ASN A 305 REMARK 465 MET A 306 REMARK 465 ASP A 307 REMARK 465 VAL A 308 REMARK 465 SER B 108 REMARK 465 ASN B 109 REMARK 465 ALA B 110 REMARK 465 PHE B 111 REMARK 465 ASN B 112 REMARK 465 GLY B 113 REMARK 465 VAL B 114 REMARK 465 SER B 115 REMARK 465 GLU B 116 REMARK 465 ALA B 117 REMARK 465 GLU B 118 REMARK 465 LEU B 119 REMARK 465 LEU B 120 REMARK 465 THR B 121 REMARK 465 LYS B 122 REMARK 465 ALA B 274 REMARK 465 ARG B 275 REMARK 465 CYS B 276 REMARK 465 ALA B 277 REMARK 465 GLN B 278 REMARK 465 PHE B 279 REMARK 465 PRO B 280 REMARK 465 ARG B 281 REMARK 465 ARG B 304 REMARK 465 ASN B 305 REMARK 465 MET B 306 REMARK 465 ASP B 307 REMARK 465 VAL B 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 DT C 5 C7 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 OP1 1CC D 11 ND2 ASN A 157 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CD1 ILE A 302 NE2 HIS B 257 6554 2.01 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 D 9 O3' DC D 9 C3' -0.050 REMARK 500 CYS A 162 CB CYS A 162 SG -0.116 REMARK 500 CYS A 266 CB CYS A 266 SG -0.149 REMARK 500 CYS B 266 CB CYS B 266 SG -0.123 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 DC C 1 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 DC C 1 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 DA C 2 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA C 10 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA C 12 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DT C 13 N3 - C4 - O4 ANGL. DEV. = 4.2 DEGREES REMARK 500 DC C 17 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG C 19 O4' - C1' - N9 ANGL. DEV. = 7.4 DEGREES REMARK 500 DG C 21 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DC D 4 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT D 5 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG D 6 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC D 7 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DT D 13 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA D 18 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG D 19 O4' - C4' - C3' ANGL. DEV. = -2.4 DEGREES REMARK 500 DG D 19 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 ILE A 139 CB - CA - C ANGL. DEV. = -12.3 DEGREES REMARK 500 ILE A 139 N - CA - C ANGL. DEV. = 18.0 DEGREES REMARK 500 GLY A 154 CA - C - N ANGL. DEV. = 20.3 DEGREES REMARK 500 GLY A 154 O - C - N ANGL. DEV. = -20.4 DEGREES REMARK 500 PRO A 155 C - N - CA ANGL. DEV. = -18.3 DEGREES REMARK 500 PRO A 155 C - N - CD ANGL. DEV. = 17.4 DEGREES REMARK 500 VAL A 247 N - CA - C ANGL. DEV. = 19.2 DEGREES REMARK 500 TYR B 222 CB - CG - CD2 ANGL. DEV. = -5.1 DEGREES REMARK 500 TYR B 222 CB - CG - CD1 ANGL. DEV. = 4.0 DEGREES REMARK 500 SER B 271 CB - CA - C ANGL. DEV. = -15.3 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 174 -177.73 -66.97 REMARK 500 LYS A 240 -77.31 -46.76 REMARK 500 VAL A 247 63.77 67.48 REMARK 500 ALA B 140 147.89 179.56 REMARK 500 TYR B 152 60.51 64.67 REMARK 500 PHE B 159 -27.85 -37.93 REMARK 500 GLN B 172 109.78 -49.82 REMARK 500 GLN B 223 78.07 48.39 REMARK 500 ASN B 249 83.19 54.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 154 PRO A 155 -81.70 REMARK 500 PRO A 155 GLY A 156 30.02 REMARK 500 GLY B 156 ASN B 157 144.18 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 TYR A 147 0.09 SIDE CHAIN REMARK 500 ARG A 281 0.10 SIDE CHAIN REMARK 500 TYR B 267 0.08 SIDE CHAIN REMARK 500 ARG B 296 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 PHE B 159 -13.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UOB RELATED DB: PDB DBREF 3UO7 A 111 308 UNP Q13569 TDG_HUMAN 111 308 DBREF 3UO7 B 111 308 UNP Q13569 TDG_HUMAN 111 308 DBREF 3UO7 D 1 23 PDB 3UO7 3UO7 1 23 DBREF 3UO7 C 1 23 PDB 3UO7 3UO7 1 23 SEQADV 3UO7 SER A 108 UNP Q13569 EXPRESSION TAG SEQADV 3UO7 ASN A 109 UNP Q13569 EXPRESSION TAG SEQADV 3UO7 ALA A 110 UNP Q13569 EXPRESSION TAG SEQADV 3UO7 ALA A 140 UNP Q13569 ASN 140 ENGINEERED MUTATION SEQADV 3UO7 SER B 108 UNP Q13569 EXPRESSION TAG SEQADV 3UO7 ASN B 109 UNP Q13569 EXPRESSION TAG SEQADV 3UO7 ALA B 110 UNP Q13569 EXPRESSION TAG SEQADV 3UO7 ALA B 140 UNP Q13569 ASN 140 ENGINEERED MUTATION SEQRES 1 C 23 DC DA DG DC DT DC DT DG DT DA DC DA DT SEQRES 2 C 23 DG DA DG DC DA DG DT DG DG DA SEQRES 1 D 23 DC DC DA DC DT DG DC DT DC DA 1CC DG DT SEQRES 2 D 23 DA DC DA DG DA DG DC DT DG DT SEQRES 1 A 201 SER ASN ALA PHE ASN GLY VAL SER GLU ALA GLU LEU LEU SEQRES 2 A 201 THR LYS THR LEU PRO ASP ILE LEU THR PHE ASN LEU ASP SEQRES 3 A 201 ILE VAL ILE ILE GLY ILE ALA PRO GLY LEU MET ALA ALA SEQRES 4 A 201 TYR LYS GLY HIS HIS TYR PRO GLY PRO GLY ASN HIS PHE SEQRES 5 A 201 TRP LYS CYS LEU PHE MET SER GLY LEU SER GLU VAL GLN SEQRES 6 A 201 LEU ASN HIS MET ASP ASP HIS THR LEU PRO GLY LYS TYR SEQRES 7 A 201 GLY ILE GLY PHE THR ASN MET VAL GLU ARG THR THR PRO SEQRES 8 A 201 GLY SER LYS ASP LEU SER SER LYS GLU PHE ARG GLU GLY SEQRES 9 A 201 GLY ARG ILE LEU VAL GLN LYS LEU GLN LYS TYR GLN PRO SEQRES 10 A 201 ARG ILE ALA VAL PHE ASN GLY LYS CYS ILE TYR GLU ILE SEQRES 11 A 201 PHE SER LYS GLU VAL PHE GLY VAL LYS VAL LYS ASN LEU SEQRES 12 A 201 GLU PHE GLY LEU GLN PRO HIS LYS ILE PRO ASP THR GLU SEQRES 13 A 201 THR LEU CYS TYR VAL MET PRO SER SER SER ALA ARG CYS SEQRES 14 A 201 ALA GLN PHE PRO ARG ALA GLN ASP LYS VAL HIS TYR TYR SEQRES 15 A 201 ILE LYS LEU LYS ASP LEU ARG ASP GLN LEU LYS GLY ILE SEQRES 16 A 201 GLU ARG ASN MET ASP VAL SEQRES 1 B 201 SER ASN ALA PHE ASN GLY VAL SER GLU ALA GLU LEU LEU SEQRES 2 B 201 THR LYS THR LEU PRO ASP ILE LEU THR PHE ASN LEU ASP SEQRES 3 B 201 ILE VAL ILE ILE GLY ILE ALA PRO GLY LEU MET ALA ALA SEQRES 4 B 201 TYR LYS GLY HIS HIS TYR PRO GLY PRO GLY ASN HIS PHE SEQRES 5 B 201 TRP LYS CYS LEU PHE MET SER GLY LEU SER GLU VAL GLN SEQRES 6 B 201 LEU ASN HIS MET ASP ASP HIS THR LEU PRO GLY LYS TYR SEQRES 7 B 201 GLY ILE GLY PHE THR ASN MET VAL GLU ARG THR THR PRO SEQRES 8 B 201 GLY SER LYS ASP LEU SER SER LYS GLU PHE ARG GLU GLY SEQRES 9 B 201 GLY ARG ILE LEU VAL GLN LYS LEU GLN LYS TYR GLN PRO SEQRES 10 B 201 ARG ILE ALA VAL PHE ASN GLY LYS CYS ILE TYR GLU ILE SEQRES 11 B 201 PHE SER LYS GLU VAL PHE GLY VAL LYS VAL LYS ASN LEU SEQRES 12 B 201 GLU PHE GLY LEU GLN PRO HIS LYS ILE PRO ASP THR GLU SEQRES 13 B 201 THR LEU CYS TYR VAL MET PRO SER SER SER ALA ARG CYS SEQRES 14 B 201 ALA GLN PHE PRO ARG ALA GLN ASP LYS VAL HIS TYR TYR SEQRES 15 B 201 ILE LYS LEU LYS ASP LEU ARG ASP GLN LEU LYS GLY ILE SEQRES 16 B 201 GLU ARG ASN MET ASP VAL MODRES 3UO7 1CC D 11 DC HET 1CC D 11 22 HETNAM 1CC 5-CARBOXY-2'-DEOXYCYTIDINE MONOPHOSPHATE FORMUL 2 1CC C10 H14 N3 O9 P HELIX 1 1 GLY A 142 GLY A 149 1 8 HELIX 2 2 HIS A 158 SER A 166 1 9 HELIX 3 3 ASN A 174 LEU A 181 5 8 HELIX 4 4 SER A 204 GLN A 223 1 20 HELIX 5 5 GLY A 231 VAL A 242 1 12 HELIX 6 6 ARG A 281 ASP A 284 5 4 HELIX 7 7 LYS A 285 ILE A 302 1 18 HELIX 8 8 GLY B 142 GLY B 149 1 8 HELIX 9 9 HIS B 158 SER B 166 1 9 HELIX 10 10 ASN B 174 HIS B 179 5 6 HELIX 11 11 THR B 180 TYR B 185 1 6 HELIX 12 12 SER B 204 GLN B 223 1 20 HELIX 13 13 LYS B 232 PHE B 243 1 12 HELIX 14 14 ALA B 282 ASP B 284 5 3 HELIX 15 15 LYS B 285 ILE B 302 1 18 SHEET 1 A 5 ILE A 187 ASN A 191 0 SHEET 2 A 5 ILE A 134 GLY A 138 1 N ILE A 136 O GLY A 188 SHEET 3 A 5 ILE A 226 ASN A 230 1 O VAL A 228 N VAL A 135 SHEET 4 A 5 LEU A 265 MET A 269 1 O LEU A 265 N ALA A 227 SHEET 5 A 5 GLY A 253 LYS A 258 -1 N GLN A 255 O CYS A 266 SHEET 1 B 5 ILE B 187 ASN B 191 0 SHEET 2 B 5 ILE B 134 GLY B 138 1 N ILE B 136 O GLY B 188 SHEET 3 B 5 ILE B 226 ASN B 230 1 O VAL B 228 N ILE B 137 SHEET 4 B 5 LEU B 265 MET B 269 1 O TYR B 267 N PHE B 229 SHEET 5 B 5 GLY B 253 LYS B 258 -1 N GLN B 255 O CYS B 266 LINK O3' DA D 10 P 1CC D 11 1555 1555 1.61 CISPEP 1 PRO A 198 GLY A 199 0 -15.35 CISPEP 2 GLY A 199 SER A 200 0 -15.74 CISPEP 3 GLY B 154 PRO B 155 0 13.37 CRYST1 164.352 164.352 57.569 90.00 90.00 120.00 P 65 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.006085 0.003513 0.000000 0.00000 SCALE2 0.000000 0.007026 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017370 0.00000