PDB Short entry for 4PCZ HEADER HYDROLASE/DNA 17-APR-14 4PCZ TITLE CRYSTAL STRUCTURE OF A COMPLEX BETWEEN R247G LLFPG MUTANT AND A THF TITLE 2 CONTAINING DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FAPY-DNA GLYCOSYLASE,DNA-(APURINIC OR APYRIMIDINIC SITE) COMPND 5 LYASE MUTM,AP LYASE MUTM; COMPND 6 EC: 3.2.2.23; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)- COMPND 11 3'); COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3'); COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS SUBSP. CREMORIS; SOURCE 3 ORGANISM_TAXID: 1359; SOURCE 4 GENE: MUTM, FPG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS DNA GLYCOSYLASE, THF, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR F.COSTE,B.CASTAING REVDAT 2 27-SEP-23 4PCZ 1 SOURCE JRNL REMARK REVDAT 1 01-APR-15 4PCZ 0 JRNL AUTH A.BIELA,F.COSTE,F.CULARD,M.GUERIN,S.GOFFINONT,K.GASTEIGER, JRNL AUTH 2 J.CIESLA,A.WINCZURA,Z.KAZIMIERCZUK,D.GASPARUTTO,T.CARELL, JRNL AUTH 3 B.TUDEK,B.CASTAING JRNL TITL ZINC FINGER OXIDATION OF FPG/NEI DNA GLYCOSYLASES BY JRNL TITL 2 2-THIOXANTHINE: BIOCHEMICAL AND X-RAY STRUCTURAL JRNL TITL 3 CHARACTERIZATION. JRNL REF NUCLEIC ACIDS RES. V. 42 10748 2014 JRNL REFN ESSN 1362-4962 JRNL PMID 25143530 JRNL DOI 10.1093/NAR/GKU613 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.120 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 120884 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 6213 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.370 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 : 0.019 2881 REMARK 3 ANGLE : 1.825 4004 REMARK 3 CHIRALITY : 0.101 449 REMARK 3 PLANARITY : 0.010 412 REMARK 3 DIHEDRAL : 18.582 1155 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 17 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.8143 182.3308 158.8573 REMARK 3 T TENSOR REMARK 3 T11: 0.2160 T22: 0.2065 REMARK 3 T33: 0.2421 T12: -0.0080 REMARK 3 T13: 0.0159 T23: -0.0126 REMARK 3 L TENSOR REMARK 3 L11: 0.1103 L22: 0.1904 REMARK 3 L33: 0.2983 L12: -0.1131 REMARK 3 L13: -0.0347 L23: -0.0565 REMARK 3 S TENSOR REMARK 3 S11: -0.0996 S12: -0.0668 S13: 0.2656 REMARK 3 S21: -0.0723 S22: 0.0702 S23: 0.1154 REMARK 3 S31: -0.2458 S32: -0.1218 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 18 THROUGH 72 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.8238 167.1853 156.0713 REMARK 3 T TENSOR REMARK 3 T11: 0.1959 T22: 0.1189 REMARK 3 T33: 0.1862 T12: -0.0363 REMARK 3 T13: -0.0119 T23: 0.0147 REMARK 3 L TENSOR REMARK 3 L11: 0.8667 L22: 0.5869 REMARK 3 L33: 0.5303 L12: -0.3681 REMARK 3 L13: 0.3537 L23: -0.3931 REMARK 3 S TENSOR REMARK 3 S11: 0.1121 S12: -0.0894 S13: -0.1188 REMARK 3 S21: -0.0659 S22: -0.0373 S23: 0.1420 REMARK 3 S31: 0.1312 S32: -0.0285 S33: 0.0238 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 73 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.1786 175.6347 146.3559 REMARK 3 T TENSOR REMARK 3 T11: 0.2159 T22: 0.1985 REMARK 3 T33: 0.1943 T12: -0.0044 REMARK 3 T13: -0.0138 T23: 0.0303 REMARK 3 L TENSOR REMARK 3 L11: 0.2560 L22: 0.2397 REMARK 3 L33: 0.4306 L12: -0.2786 REMARK 3 L13: 0.1741 L23: 0.0842 REMARK 3 S TENSOR REMARK 3 S11: 0.0542 S12: 0.1271 S13: -0.0010 REMARK 3 S21: -0.0686 S22: 0.0354 S23: 0.0540 REMARK 3 S31: -0.0544 S32: 0.0719 S33: -0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 113 THROUGH 141 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.1063 173.4832 169.6208 REMARK 3 T TENSOR REMARK 3 T11: 0.2481 T22: 0.1976 REMARK 3 T33: 0.1903 T12: -0.0019 REMARK 3 T13: 0.0234 T23: 0.0116 REMARK 3 L TENSOR REMARK 3 L11: 0.3864 L22: 0.3442 REMARK 3 L33: 0.0694 L12: 0.2940 REMARK 3 L13: -0.0093 L23: 0.1414 REMARK 3 S TENSOR REMARK 3 S11: 0.0356 S12: -0.1704 S13: -0.0389 REMARK 3 S21: 0.1046 S22: -0.0428 S23: 0.0464 REMARK 3 S31: 0.1513 S32: -0.0121 S33: 0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 142 THROUGH 193 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.0028 189.7850 173.1233 REMARK 3 T TENSOR REMARK 3 T11: 0.2082 T22: 0.1888 REMARK 3 T33: 0.2097 T12: -0.0259 REMARK 3 T13: 0.0110 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 1.0205 L22: 0.6351 REMARK 3 L33: 0.8383 L12: 0.4876 REMARK 3 L13: -0.5171 L23: 0.2428 REMARK 3 S TENSOR REMARK 3 S11: 0.0066 S12: -0.1129 S13: -0.0426 REMARK 3 S21: -0.0270 S22: -0.0050 S23: -0.0749 REMARK 3 S31: -0.0983 S32: 0.2040 S33: -0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 194 THROUGH 230 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.0326 192.4946 165.6181 REMARK 3 T TENSOR REMARK 3 T11: 0.2666 T22: 0.1421 REMARK 3 T33: 0.2377 T12: -0.0056 REMARK 3 T13: -0.0075 T23: -0.0147 REMARK 3 L TENSOR REMARK 3 L11: 0.7177 L22: 0.6262 REMARK 3 L33: 0.0719 L12: 0.0333 REMARK 3 L13: -0.2535 L23: -0.0799 REMARK 3 S TENSOR REMARK 3 S11: -0.1897 S12: 0.0236 S13: 0.2391 REMARK 3 S21: -0.1029 S22: -0.1042 S23: 0.2397 REMARK 3 S31: -0.2298 S32: -0.1503 S33: -0.0000 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 231 THROUGH 251 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.1472 202.9353 158.9566 REMARK 3 T TENSOR REMARK 3 T11: 0.4585 T22: 0.1942 REMARK 3 T33: 0.2956 T12: -0.0760 REMARK 3 T13: -0.0394 T23: 0.0220 REMARK 3 L TENSOR REMARK 3 L11: 0.1743 L22: 0.3262 REMARK 3 L33: 0.0928 L12: -0.0584 REMARK 3 L13: -0.0515 L23: -0.0817 REMARK 3 S TENSOR REMARK 3 S11: -0.2174 S12: 0.2179 S13: 0.1923 REMARK 3 S21: -0.4228 S22: 0.1266 S23: 0.3397 REMARK 3 S31: -0.3872 S32: -0.0863 S33: -0.0411 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 252 THROUGH 271 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.9021 197.9322 163.2950 REMARK 3 T TENSOR REMARK 3 T11: 0.3185 T22: 0.2527 REMARK 3 T33: 0.2448 T12: -0.0932 REMARK 3 T13: 0.0355 T23: -0.0229 REMARK 3 L TENSOR REMARK 3 L11: 0.1146 L22: 0.1237 REMARK 3 L33: 0.1175 L12: -0.0532 REMARK 3 L13: 0.1029 L23: -0.0871 REMARK 3 S TENSOR REMARK 3 S11: -0.2386 S12: 0.0922 S13: -0.0493 REMARK 3 S21: -0.1011 S22: 0.3212 S23: -0.0793 REMARK 3 S31: -0.3164 S32: 0.3765 S33: 0.0043 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.8211 179.7606 154.4696 REMARK 3 T TENSOR REMARK 3 T11: 0.2603 T22: 0.2716 REMARK 3 T33: 0.2578 T12: 0.0071 REMARK 3 T13: 0.0501 T23: 0.0192 REMARK 3 L TENSOR REMARK 3 L11: 0.0958 L22: 0.3677 REMARK 3 L33: 0.2129 L12: 0.2233 REMARK 3 L13: 0.0684 L23: 0.1730 REMARK 3 S TENSOR REMARK 3 S11: 0.0413 S12: -0.0512 S13: -0.0523 REMARK 3 S21: -0.1284 S22: 0.0113 S23: -0.1647 REMARK 3 S31: 0.0338 S32: 0.2654 S33: 0.0000 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 15 THROUGH 28 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.0725 180.9069 153.6371 REMARK 3 T TENSOR REMARK 3 T11: 0.2757 T22: 0.3377 REMARK 3 T33: 0.2284 T12: -0.0178 REMARK 3 T13: 0.0081 T23: 0.0194 REMARK 3 L TENSOR REMARK 3 L11: 0.6600 L22: 0.1807 REMARK 3 L33: 0.0470 L12: 0.1571 REMARK 3 L13: -0.0099 L23: -0.0974 REMARK 3 S TENSOR REMARK 3 S11: -0.1112 S12: 0.2118 S13: -0.0696 REMARK 3 S21: -0.0124 S22: 0.1351 S23: -0.0611 REMARK 3 S31: -0.1146 S32: 0.5959 S33: 0.0311 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 4PCZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000201177. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98011 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65739 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 47.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.41100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 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: PDB ENTRY 1PM5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, SODIUM CITRATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 71.16000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 45.86150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 45.86150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.58000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 45.86150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 45.86150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 106.74000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 45.86150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.86150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.58000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 45.86150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.86150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 106.74000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 71.16000 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: 4000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 417 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 463 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 470 LIES ON A SPECIAL POSITION. 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 15 CE NZ REMARK 470 ARG A 88 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 130 CE NZ REMARK 470 ARG A 220 CG CD NE CZ NH1 NH2 REMARK 470 THR A 221 OG1 CG2 REMARK 470 TYR A 222 CG CD1 CD2 CE1 CE2 CZ OH 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 O HOH A 603 O HOH A 691 2.12 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 DG C 17 O3' DG C 17 C3' -0.046 REMARK 500 DA C 20 O3' DA C 20 C3' -0.062 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 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 MET A 96 CA - CB - CG ANGL. DEV. = 10.5 DEGREES REMARK 500 DC B 11 O3' - P - OP2 ANGL. DEV. = 8.5 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 ASP A 66 28.05 -149.02 REMARK 500 ARG A 74 -124.45 48.36 REMARK 500 ASP A 107 104.06 -161.52 REMARK 500 VAL A 166 142.42 -171.40 REMARK 500 ARG A 220 -159.85 -111.93 REMARK 500 TYR A 222 -2.12 -144.19 REMARK 500 SER A 223 -3.51 77.82 REMARK 500 VAL A 237 -38.42 -133.07 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 641 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A 672 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A 735 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A 766 DISTANCE = 6.52 ANGSTROMS 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 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 245 SG REMARK 620 2 CYS A 248 SG 113.4 REMARK 620 3 CYS A 265 SG 108.0 97.7 REMARK 620 4 CYS A 268 SG 109.7 113.0 114.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4PD2 RELATED DB: PDB REMARK 900 RELATED ID: 4PDG RELATED DB: PDB REMARK 900 RELATED ID: 4PDI RELATED DB: PDB DBREF 4PCZ A 1 271 UNP P42371 FPG_LACLC 2 273 DBREF 4PCZ B 1 14 PDB 4PCZ 4PCZ 1 14 DBREF 4PCZ C 15 28 PDB 4PCZ 4PCZ 15 28 SEQADV 4PCZ A UNP P42371 ASP 139 DELETION SEQADV 4PCZ GLY A 247 UNP P42371 ARG 249 ENGINEERED MUTATION SEQRES 1 A 271 PRO GLU LEU PRO GLU VAL GLU THR VAL ARG ARG GLU LEU SEQRES 2 A 271 GLU LYS ARG ILE VAL GLY GLN LYS ILE ILE SER ILE GLU SEQRES 3 A 271 ALA THR TYR PRO ARG MET VAL LEU THR GLY PHE GLU GLN SEQRES 4 A 271 LEU LYS LYS GLU LEU THR GLY LYS THR ILE GLN GLY ILE SEQRES 5 A 271 SER ARG ARG GLY LYS TYR LEU ILE PHE GLU ILE GLY ASP SEQRES 6 A 271 ASP PHE ARG LEU ILE SER HIS LEU ARG MET GLU GLY LYS SEQRES 7 A 271 TYR ARG LEU ALA THR LEU ASP ALA PRO ARG GLU LYS HIS SEQRES 8 A 271 ASP HIS LEU THR MET LYS PHE ALA ASP GLY GLN LEU ILE SEQRES 9 A 271 TYR ALA ASP VAL ARG LYS PHE GLY THR TRP GLU LEU ILE SEQRES 10 A 271 SER THR ASP GLN VAL LEU PRO TYR PHE LEU LYS LYS LYS SEQRES 11 A 271 ILE GLY PRO GLU PRO THR TYR GLU ASP PHE ASP GLU LYS SEQRES 12 A 271 LEU PHE ARG GLU LYS LEU ARG LYS SER THR LYS LYS ILE SEQRES 13 A 271 LYS PRO TYR LEU LEU GLU GLN THR LEU VAL ALA GLY LEU SEQRES 14 A 271 GLY ASN ILE TYR VAL ASP GLU VAL LEU TRP LEU ALA LYS SEQRES 15 A 271 ILE HIS PRO GLU LYS GLU THR ASN GLN LEU ILE GLU SER SEQRES 16 A 271 SER ILE HIS LEU LEU HIS ASP SER ILE ILE GLU ILE LEU SEQRES 17 A 271 GLN LYS ALA ILE LYS LEU GLY GLY SER SER ILE ARG THR SEQRES 18 A 271 TYR SER ALA LEU GLY SER THR GLY LYS MET GLN ASN GLU SEQRES 19 A 271 LEU GLN VAL TYR GLY LYS THR GLY GLU LYS CYS SER GLY SEQRES 20 A 271 CYS GLY ALA GLU ILE GLN LYS ILE LYS VAL ALA GLY ARG SEQRES 21 A 271 GLY THR HIS PHE CYS PRO VAL CYS GLN GLN LYS SEQRES 1 B 14 DC DT DC DT DT DT 3DR DT DT DT DC DT DC SEQRES 2 B 14 DG SEQRES 1 C 14 DG DC DG DA DG DA DA DA DC DA DA DA DG SEQRES 2 C 14 DA HET 3DR B 7 11 HET ZN A 301 1 HET GOL A 302 12 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN 3DR ABASIC DIDEOXYRIBOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 3DR C5 H11 O6 P FORMUL 4 ZN ZN 2+ FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *453(H2 O) HELIX 1 AA1 GLU A 2 VAL A 18 1 17 HELIX 2 AA2 TYR A 29 VAL A 33 5 5 HELIX 3 AA3 GLY A 36 THR A 45 1 10 HELIX 4 AA4 GLN A 121 LYS A 130 1 10 HELIX 5 AA5 ASP A 141 SER A 152 1 12 HELIX 6 AA6 LYS A 155 GLU A 162 1 8 HELIX 7 AA7 GLY A 170 ALA A 181 1 12 HELIX 8 AA8 GLU A 188 LEU A 192 5 5 HELIX 9 AA9 ILE A 193 LEU A 214 1 22 HELIX 10 AB1 LYS A 230 LEU A 235 5 6 SHEET 1 AA1 4 SER A 24 ALA A 27 0 SHEET 2 AA1 4 ASP A 92 LYS A 97 -1 O LYS A 97 N SER A 24 SHEET 3 AA1 4 GLN A 102 ALA A 106 -1 O TYR A 105 N HIS A 93 SHEET 4 AA1 4 LYS A 78 ALA A 82 -1 N ALA A 82 O GLN A 102 SHEET 1 AA2 4 ILE A 49 ARG A 55 0 SHEET 2 AA2 4 TYR A 58 ILE A 63 -1 O ILE A 60 N SER A 53 SHEET 3 AA2 4 PHE A 67 HIS A 72 -1 O SER A 71 N LEU A 59 SHEET 4 AA2 4 THR A 113 SER A 118 -1 O GLU A 115 N ILE A 70 SHEET 1 AA3 2 GLN A 253 VAL A 257 0 SHEET 2 AA3 2 ARG A 260 PHE A 264 -1 O PHE A 264 N GLN A 253 LINK O3' DT B 6 P 3DR B 7 1555 1555 1.61 LINK O3' 3DR B 7 P DT B 8 1555 1555 1.58 LINK SG CYS A 245 ZN ZN A 301 1555 1555 2.36 LINK SG CYS A 248 ZN ZN A 301 1555 1555 2.31 LINK SG CYS A 265 ZN ZN A 301 1555 1555 2.32 LINK SG CYS A 268 ZN ZN A 301 1555 1555 2.28 CISPEP 1 ILE A 219 ARG A 220 0 -0.14 SITE 1 AC1 4 CYS A 245 CYS A 248 CYS A 265 CYS A 268 SITE 1 AC2 12 TYR A 58 HIS A 72 ARG A 74 THR A 113 SITE 2 AC2 12 GLU A 115 TYR A 125 LYS A 129 HOH A 406 SITE 3 AC2 12 HOH A 424 HOH A 449 DT B 9 DT B 10 CRYST1 91.723 91.723 142.320 90.00 90.00 90.00 P 41 21 2 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 0.010902 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010902 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007026 0.00000