PDB Short entry for 4LB5 HEADER TRANSFERASE/DNA 20-JUN-13 4LB5 TITLE CRYSTAL STRUCTURE OF PKZ ZALPHA IN COMPLEX WITH DS(CG)6 (HEXAGONAL TITLE 2 FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN KINASE CONTAINING Z-DNA BINDING DOMAINS; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: ZALPHA DOMAIN, UNP RESIDUES 5-70; COMPND 5 SYNONYM: UNCHARACTERIZED PROTEIN, Z-DNA BINDING PROTEIN KINASE; COMPND 6 EC: 2.7.11.1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3'; COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: PKZ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: SYNTHETIC OLIGONUCLEOTIDE KEYWDS WHTH, ZALPHA, ZBD, KINASE, INNATE IMMUNITY, Z-DNA, Z-RNA, EIF2A, KEYWDS 2 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.DE ROSA,S.ZACARIAS,A.ATHANASIADIS REVDAT 3 28-FEB-24 4LB5 1 REMARK SEQADV REVDAT 2 04-DEC-13 4LB5 1 JRNL REVDAT 1 18-SEP-13 4LB5 0 JRNL AUTH M.DE ROSA,S.ZACARIAS,A.ATHANASIADIS JRNL TITL STRUCTURAL BASIS FOR Z-DNA BINDING AND STABILIZATION BY THE JRNL TITL 2 ZEBRAFISH Z-DNA DEPENDENT PROTEIN KINASE PKZ. JRNL REF NUCLEIC ACIDS RES. V. 41 9924 2013 JRNL REFN ISSN 0305-1048 JRNL PMID 23975196 JRNL DOI 10.1093/NAR/GKT743 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 15006 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1501 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 29.3061 - 4.4433 0.95 1333 148 0.1953 0.2194 REMARK 3 2 4.4433 - 3.5287 1.00 1265 141 0.1561 0.1903 REMARK 3 3 3.5287 - 3.0832 1.00 1251 139 0.1783 0.2082 REMARK 3 4 3.0832 - 2.8016 1.00 1229 136 0.1989 0.2554 REMARK 3 5 2.8016 - 2.6009 1.00 1212 136 0.2186 0.2443 REMARK 3 6 2.6009 - 2.4476 1.00 1224 135 0.2059 0.2253 REMARK 3 7 2.4476 - 2.3251 1.00 1209 135 0.1872 0.2571 REMARK 3 8 2.3251 - 2.2239 1.00 1205 134 0.1993 0.2404 REMARK 3 9 2.2239 - 2.1383 1.00 1192 132 0.1925 0.2469 REMARK 3 10 2.1383 - 2.0646 1.00 1188 132 0.2126 0.2806 REMARK 3 11 2.0646 - 2.0000 1.00 1197 133 0.2308 0.2681 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) : 20.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.88 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 : 0.006 1299 REMARK 3 ANGLE : 1.074 1796 REMARK 3 CHIRALITY : 0.067 202 REMARK 3 PLANARITY : 0.004 186 REMARK 3 DIHEDRAL : 18.351 506 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 9 THROUGH 36 ) REMARK 3 ORIGIN FOR THE GROUP (A): -41.9703 9.9961 -3.6062 REMARK 3 T TENSOR REMARK 3 T11: 0.2512 T22: 0.9225 REMARK 3 T33: 0.7245 T12: 0.0023 REMARK 3 T13: 0.0567 T23: -0.2697 REMARK 3 L TENSOR REMARK 3 L11: 8.3084 L22: 4.6754 REMARK 3 L33: 5.5586 L12: -3.8165 REMARK 3 L13: 4.6189 L23: 0.6409 REMARK 3 S TENSOR REMARK 3 S11: 0.1098 S12: -0.2357 S13: -0.6282 REMARK 3 S21: 0.7331 S22: -0.5397 S23: 1.4338 REMARK 3 S31: 1.1461 S32: -1.0677 S33: -0.0937 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 37 THROUGH 68 ) REMARK 3 ORIGIN FOR THE GROUP (A): -34.3158 16.2834 -5.3033 REMARK 3 T TENSOR REMARK 3 T11: 0.2657 T22: 0.5418 REMARK 3 T33: 0.4410 T12: 0.0975 REMARK 3 T13: 0.0145 T23: -0.1597 REMARK 3 L TENSOR REMARK 3 L11: 7.3137 L22: 6.1943 REMARK 3 L33: 6.8779 L12: -1.1486 REMARK 3 L13: 0.6668 L23: 1.2298 REMARK 3 S TENSOR REMARK 3 S11: -0.2336 S12: -0.2734 S13: 0.2581 REMARK 3 S21: 0.2087 S22: 0.0786 S23: 0.5567 REMARK 3 S31: -0.4256 S32: -0.4075 S33: 0.1048 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 7 THROUGH 21 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.5153 -9.6143 -24.5172 REMARK 3 T TENSOR REMARK 3 T11: 0.6011 T22: 0.4596 REMARK 3 T33: 0.6386 T12: 0.2332 REMARK 3 T13: -0.1140 T23: -0.0694 REMARK 3 L TENSOR REMARK 3 L11: 2.6641 L22: 8.1820 REMARK 3 L33: 8.9641 L12: 0.9286 REMARK 3 L13: -0.0505 L23: 5.2665 REMARK 3 S TENSOR REMARK 3 S11: 0.2003 S12: -0.2279 S13: -1.4957 REMARK 3 S21: 0.3124 S22: -0.1057 S23: -0.9925 REMARK 3 S31: 1.1401 S32: 0.6990 S33: -0.3932 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 22 THROUGH 36 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.3239 -4.7903 -16.8146 REMARK 3 T TENSOR REMARK 3 T11: 0.5636 T22: 0.3391 REMARK 3 T33: 0.3572 T12: 0.0616 REMARK 3 T13: -0.0242 T23: 0.0578 REMARK 3 L TENSOR REMARK 3 L11: 1.7274 L22: 8.5269 REMARK 3 L33: 8.4793 L12: 1.8129 REMARK 3 L13: 0.1674 L23: 5.0263 REMARK 3 S TENSOR REMARK 3 S11: 0.2559 S12: -0.8430 S13: -1.0200 REMARK 3 S21: 0.7690 S22: -0.2791 S23: 0.0018 REMARK 3 S31: 1.4374 S32: -0.2905 S33: -0.0187 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 37 THROUGH 56 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.9266 -1.1573 -28.0775 REMARK 3 T TENSOR REMARK 3 T11: 0.4789 T22: 0.4055 REMARK 3 T33: 0.3619 T12: 0.1447 REMARK 3 T13: -0.0516 T23: -0.1092 REMARK 3 L TENSOR REMARK 3 L11: 8.8225 L22: 5.1062 REMARK 3 L33: 8.0445 L12: 3.8731 REMARK 3 L13: -1.1121 L23: 3.1401 REMARK 3 S TENSOR REMARK 3 S11: -0.1105 S12: 1.0735 S13: -0.5233 REMARK 3 S21: -0.6274 S22: 0.1699 S23: -0.2007 REMARK 3 S31: 0.4012 S32: -0.1798 S33: -0.0507 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 57 THROUGH 63 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.3482 1.7259 -19.7306 REMARK 3 T TENSOR REMARK 3 T11: 0.6468 T22: 0.7258 REMARK 3 T33: 0.6685 T12: 0.1289 REMARK 3 T13: -0.1527 T23: -0.2478 REMARK 3 L TENSOR REMARK 3 L11: 7.5560 L22: 2.6843 REMARK 3 L33: 9.1552 L12: 1.2087 REMARK 3 L13: -6.9880 L23: 1.4629 REMARK 3 S TENSOR REMARK 3 S11: 0.0406 S12: 0.1817 S13: -0.6675 REMARK 3 S21: 0.0516 S22: -0.8168 S23: 1.4890 REMARK 3 S31: 0.0867 S32: -1.7621 S33: 0.6540 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 64 THROUGH 69 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.3358 -8.4294 -27.4117 REMARK 3 T TENSOR REMARK 3 T11: 0.6479 T22: 0.3448 REMARK 3 T33: 0.5488 T12: 0.0999 REMARK 3 T13: -0.1020 T23: -0.1072 REMARK 3 L TENSOR REMARK 3 L11: 5.1094 L22: 5.8855 REMARK 3 L33: 4.1304 L12: -3.9107 REMARK 3 L13: -4.5338 L23: 3.9979 REMARK 3 S TENSOR REMARK 3 S11: -0.8443 S12: -0.0463 S13: -0.6272 REMARK 3 S21: 0.4840 S22: 0.2157 S23: 0.7661 REMARK 3 S31: 1.3191 S32: 0.0974 S33: 0.7042 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 0 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.6664 11.1739 -17.5527 REMARK 3 T TENSOR REMARK 3 T11: 0.2275 T22: 0.3330 REMARK 3 T33: 0.2041 T12: 0.0948 REMARK 3 T13: -0.0524 T23: -0.0537 REMARK 3 L TENSOR REMARK 3 L11: 3.1870 L22: 1.8398 REMARK 3 L33: 8.8144 L12: 0.2384 REMARK 3 L13: -3.8675 L23: -0.4493 REMARK 3 S TENSOR REMARK 3 S11: 0.0163 S12: 0.0292 S13: 0.0283 REMARK 3 S21: -0.1834 S22: -0.1615 S23: 0.0197 REMARK 3 S31: -0.1099 S32: -0.2048 S33: 0.0940 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 4LB5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUL-13. REMARK 100 THE DEPOSITION ID IS D_1000080409. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 70 REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15007 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 29.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.53000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: PDB ENTRY 1QBJ REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 ACETATE, PH 5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 72.92333 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 145.84667 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 109.38500 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 182.30833 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 36.46167 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 72.92333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 145.84667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 182.30833 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 109.38500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 36.46167 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 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 350 BIOMT1 2 0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -36.46167 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 C 132 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 149 LIES ON A SPECIAL POSITION. 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 -1 REMARK 465 SER A 0 REMARK 465 HIS A 1 REMARK 465 MET A 2 REMARK 465 ALA A 3 REMARK 465 SER A 4 REMARK 465 SER A 5 REMARK 465 ALA A 6 REMARK 465 GLU A 7 REMARK 465 ASN A 8 REMARK 465 GLU A 58 REMARK 465 ASP A 59 REMARK 465 ASN A 60 REMARK 465 GLU A 69 REMARK 465 SER A 70 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 HIS B 1 REMARK 465 MET B 2 REMARK 465 ALA B 3 REMARK 465 SER B 4 REMARK 465 SER B 5 REMARK 465 ALA B 6 REMARK 465 SER B 70 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 31 CD CE NZ REMARK 470 LYS A 34 CG CD CE NZ REMARK 470 LYS A 51 CE NZ REMARK 470 LYS A 61 CE NZ REMARK 470 LYS B 34 CE NZ REMARK 470 GLU B 58 CG CD OE1 OE2 REMARK 470 GLU B 69 CD OE1 OE2 REMARK 470 DT C 0 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DT C 0 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT C 0 C7 C6 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 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC C 7 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG C 10 O4' - C1' - N9 ANGL. DEV. = -5.3 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 ARG A 62 80.64 51.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4LB6 RELATED DB: PDB DBREF 4LB5 A 5 70 UNP Q5NE14 Q5NE14_DANRE 5 70 DBREF 4LB5 B 5 70 UNP Q5NE14 Q5NE14_DANRE 5 70 DBREF 4LB5 C 0 12 PDB 4LB5 4LB5 0 12 SEQADV 4LB5 GLY A -1 UNP Q5NE14 EXPRESSION TAG SEQADV 4LB5 SER A 0 UNP Q5NE14 EXPRESSION TAG SEQADV 4LB5 HIS A 1 UNP Q5NE14 EXPRESSION TAG SEQADV 4LB5 MET A 2 UNP Q5NE14 EXPRESSION TAG SEQADV 4LB5 ALA A 3 UNP Q5NE14 EXPRESSION TAG SEQADV 4LB5 SER A 4 UNP Q5NE14 EXPRESSION TAG SEQADV 4LB5 GLY B -1 UNP Q5NE14 EXPRESSION TAG SEQADV 4LB5 SER B 0 UNP Q5NE14 EXPRESSION TAG SEQADV 4LB5 HIS B 1 UNP Q5NE14 EXPRESSION TAG SEQADV 4LB5 MET B 2 UNP Q5NE14 EXPRESSION TAG SEQADV 4LB5 ALA B 3 UNP Q5NE14 EXPRESSION TAG SEQADV 4LB5 SER B 4 UNP Q5NE14 EXPRESSION TAG SEQRES 1 A 72 GLY SER HIS MET ALA SER SER ALA GLU ASN GLU ILE GLU SEQRES 2 A 72 MET ARG ILE CYS ASP TYR LEU ARG ARG HIS GLY ARG SER SEQRES 3 A 72 THR VAL GLN ASP ILE PHE LYS GLU LEU LYS LEU GLU LYS SEQRES 4 A 72 SER THR VAL ASN ARG HIS LEU TYR SER LEU GLN ALA SER SEQRES 5 A 72 LYS GLN VAL PHE LYS THR VAL GLU ASP ASN LYS ARG PRO SEQRES 6 A 72 VAL TRP ASN LEU VAL GLU SER SEQRES 1 B 72 GLY SER HIS MET ALA SER SER ALA GLU ASN GLU ILE GLU SEQRES 2 B 72 MET ARG ILE CYS ASP TYR LEU ARG ARG HIS GLY ARG SER SEQRES 3 B 72 THR VAL GLN ASP ILE PHE LYS GLU LEU LYS LEU GLU LYS SEQRES 4 B 72 SER THR VAL ASN ARG HIS LEU TYR SER LEU GLN ALA SER SEQRES 5 B 72 LYS GLN VAL PHE LYS THR VAL GLU ASP ASN LYS ARG PRO SEQRES 6 B 72 VAL TRP ASN LEU VAL GLU SER SEQRES 1 C 13 DT DC DG DC DG DC DG DC DG DC DG DC DG HET ACT A 101 4 HET ACT A 102 4 HET ACT B 101 4 HETNAM ACT ACETATE ION FORMUL 4 ACT 3(C2 H3 O2 1-) FORMUL 7 HOH *110(H2 O) HELIX 1 1 GLU A 9 GLY A 22 1 14 HELIX 2 2 THR A 25 LYS A 34 1 10 HELIX 3 3 GLU A 36 SER A 50 1 15 HELIX 4 4 ASN B 8 GLY B 22 1 15 HELIX 5 5 THR B 25 LYS B 34 1 10 HELIX 6 6 GLU B 36 SER B 50 1 15 SHEET 1 A 2 VAL A 53 THR A 56 0 SHEET 2 A 2 VAL A 64 LEU A 67 -1 O ASN A 66 N PHE A 54 SHEET 1 B 2 VAL B 53 THR B 56 0 SHEET 2 B 2 VAL B 64 LEU B 67 -1 O VAL B 64 N THR B 56 SITE 1 AC1 2 GLU A 36 THR A 39 SITE 1 AC2 3 HIS A 21 GLY A 22 ARG A 23 SITE 1 AC3 2 LYS B 61 ARG B 62 CRYST1 56.860 56.860 218.770 90.00 90.00 120.00 P 61 2 2 24 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 0.017587 0.010154 0.000000 0.00000 SCALE2 0.000000 0.020308 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004571 0.00000