HEADER TRANSCRIPTION/DNA 28-APR-17 5VMX TITLE KAISO (ZBTB33) ZINC FINGER DNA BINDING DOMAIN IN COMPLEX WITH A HEMI TITLE 2 CPG-METHYLATED DNA RESEMBLING THE SPECIFIC KAISO BINDING SEQUENCE TITLE 3 (KBS) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR KAISO; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 471-604; COMPND 5 SYNONYM: ZINC FINGER AND BTB DOMAIN-CONTAINING PROTEIN 33; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*TP*GP*CP*TP*TP*CP*CP*(5CM)P*GP*(5CM) COMPND 9 P*GP*AP*AP*TP*AP*AP*CP*G)-3'); COMPND 10 CHAIN: D; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'- COMPND 14 D(*CP*GP*TP*TP*AP*TP*TP*CP*GP*CP*GP*GP*GP*AP*AP*GP*CP*A)-3'); COMPND 15 CHAIN: E; 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: ZBTB33, KAISO, ZNF348; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) [DNAY]; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21D; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS DNA METHYLATION, ZINC FINGER, TRANSCRIPTIONAL REGULATOR, KEYWDS 2 TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.N.NIKOLOVA,R.L.STANFIELD,M.A.MARTINEZ-YAMOUT,H.J.DYSON,P.E.WRIGHT REVDAT 4 04-OCT-23 5VMX 1 REMARK REVDAT 3 23-MAR-22 5VMX 1 SOURCE REVDAT 2 25-APR-18 5VMX 1 JRNL REVDAT 1 04-APR-18 5VMX 0 JRNL AUTH E.N.NIKOLOVA,R.L.STANFIELD,H.J.DYSON,P.E.WRIGHT JRNL TITL CH···O HYDROGEN BONDS MEDIATE HIGHLY SPECIFIC JRNL TITL 2 RECOGNITION OF METHYLATED CPG SITES BY THE ZINC FINGER JRNL TITL 3 PROTEIN KAISO. JRNL REF BIOCHEMISTRY V. 57 2109 2018 JRNL REFN ISSN 1520-4995 JRNL PMID 29546986 JRNL DOI 10.1021/ACS.BIOCHEM.8B00065 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 27000 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2700 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 43.1135 - 5.0533 1.00 1788 200 0.1536 0.1755 REMARK 3 2 5.0533 - 4.0118 0.99 1674 186 0.1347 0.1601 REMARK 3 3 4.0118 - 3.5050 1.00 1675 186 0.1436 0.1757 REMARK 3 4 3.5050 - 3.1846 1.00 1640 182 0.1633 0.1718 REMARK 3 5 3.1846 - 2.9564 1.00 1658 183 0.1821 0.2029 REMARK 3 6 2.9564 - 2.7822 1.00 1637 183 0.1822 0.2195 REMARK 3 7 2.7822 - 2.6428 1.00 1649 183 0.1863 0.2254 REMARK 3 8 2.6428 - 2.5278 1.00 1638 182 0.1651 0.1970 REMARK 3 9 2.5278 - 2.4305 0.99 1620 180 0.1832 0.1875 REMARK 3 10 2.4305 - 2.3466 0.99 1600 178 0.1745 0.2194 REMARK 3 11 2.3466 - 2.2733 0.99 1637 182 0.1808 0.2085 REMARK 3 12 2.2733 - 2.2083 0.98 1575 174 0.1868 0.2357 REMARK 3 13 2.2083 - 2.1502 0.97 1575 177 0.1986 0.2486 REMARK 3 14 2.1502 - 2.0977 0.95 1550 171 0.1975 0.2202 REMARK 3 15 2.0977 - 2.0500 0.85 1384 153 0.2233 0.2258 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.070 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 : 0.010 1959 REMARK 3 ANGLE : 1.217 2780 REMARK 3 CHIRALITY : 0.054 289 REMARK 3 PLANARITY : 0.007 227 REMARK 3 DIHEDRAL : 25.012 764 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 481 THROUGH 496 ) REMARK 3 ORIGIN FOR THE GROUP (A): 64.8369 373.0427 27.6828 REMARK 3 T TENSOR REMARK 3 T11: 0.9210 T22: 0.3216 REMARK 3 T33: 0.7963 T12: 0.0867 REMARK 3 T13: -0.0124 T23: -0.0717 REMARK 3 L TENSOR REMARK 3 L11: 4.4918 L22: 4.5958 REMARK 3 L33: 7.3073 L12: -4.3917 REMARK 3 L13: 4.7767 L23: -4.8871 REMARK 3 S TENSOR REMARK 3 S11: -0.3075 S12: 0.2340 S13: -0.8788 REMARK 3 S21: 0.3068 S22: 0.3807 S23: -0.3207 REMARK 3 S31: 0.2385 S32: 0.1465 S33: -0.1198 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 497 THROUGH 517 ) REMARK 3 ORIGIN FOR THE GROUP (A): 57.4667 379.7493 23.4931 REMARK 3 T TENSOR REMARK 3 T11: 0.5750 T22: 0.2367 REMARK 3 T33: 0.6012 T12: -0.0024 REMARK 3 T13: 0.0403 T23: 0.0041 REMARK 3 L TENSOR REMARK 3 L11: 7.5222 L22: 4.8727 REMARK 3 L33: 4.4878 L12: -3.6164 REMARK 3 L13: 1.6574 L23: 0.9128 REMARK 3 S TENSOR REMARK 3 S11: 0.1189 S12: 0.1663 S13: -1.1516 REMARK 3 S21: -0.0280 S22: 0.0929 S23: 0.8455 REMARK 3 S31: 0.9581 S32: -0.0405 S33: -0.2302 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 518 THROUGH 545 ) REMARK 3 ORIGIN FOR THE GROUP (A): 47.7163 395.7869 20.5675 REMARK 3 T TENSOR REMARK 3 T11: 0.3424 T22: 0.3481 REMARK 3 T33: 0.6039 T12: -0.0193 REMARK 3 T13: -0.0830 T23: -0.0443 REMARK 3 L TENSOR REMARK 3 L11: 7.4005 L22: 6.9527 REMARK 3 L33: 4.2051 L12: -2.4260 REMARK 3 L13: 0.3863 L23: -1.7688 REMARK 3 S TENSOR REMARK 3 S11: -0.0764 S12: -0.1643 S13: -0.7707 REMARK 3 S21: -0.7404 S22: 0.2236 S23: 1.6724 REMARK 3 S31: 0.5417 S32: -0.3336 S33: -0.1912 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 546 THROUGH 586 ) REMARK 3 ORIGIN FOR THE GROUP (A): 68.5978 408.6052 21.4174 REMARK 3 T TENSOR REMARK 3 T11: 0.1702 T22: 0.2860 REMARK 3 T33: 0.2152 T12: 0.0491 REMARK 3 T13: -0.0376 T23: -0.0065 REMARK 3 L TENSOR REMARK 3 L11: 7.8858 L22: 6.5009 REMARK 3 L33: 3.7711 L12: 1.9353 REMARK 3 L13: -3.3917 L23: 0.6764 REMARK 3 S TENSOR REMARK 3 S11: 0.0497 S12: -0.0887 S13: -0.0434 REMARK 3 S21: 0.1307 S22: 0.0239 S23: -0.2936 REMARK 3 S31: 0.1894 S32: 0.4316 S33: -0.0942 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 587 THROUGH 602) REMARK 3 ORIGIN FOR THE GROUP (A): 56.3753 405.9819 32.3668 REMARK 3 T TENSOR REMARK 3 T11: 0.5454 T22: 0.4327 REMARK 3 T33: 0.4015 T12: 0.0579 REMARK 3 T13: 0.0308 T23: -0.0165 REMARK 3 L TENSOR REMARK 3 L11: 6.2128 L22: 5.8724 REMARK 3 L33: 4.1523 L12: -2.7998 REMARK 3 L13: 2.4032 L23: -4.9031 REMARK 3 S TENSOR REMARK 3 S11: 0.0803 S12: -0.7072 S13: -0.1905 REMARK 3 S21: 1.1348 S22: 0.1108 S23: 0.2238 REMARK 3 S31: 0.3242 S32: 0.1551 S33: -0.2037 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 18 ) REMARK 3 ORIGIN FOR THE GROUP (A): 58.4658 392.7729 27.6877 REMARK 3 T TENSOR REMARK 3 T11: 0.4140 T22: 0.3494 REMARK 3 T33: 0.2924 T12: 0.0916 REMARK 3 T13: 0.0881 T23: 0.0354 REMARK 3 L TENSOR REMARK 3 L11: 4.5442 L22: 6.3441 REMARK 3 L33: 6.1614 L12: -0.3003 REMARK 3 L13: 0.7202 L23: 3.6357 REMARK 3 S TENSOR REMARK 3 S11: -0.1329 S12: -0.3997 S13: -0.3214 REMARK 3 S21: 0.2735 S22: 0.1834 S23: 0.7420 REMARK 3 S31: 0.0061 S32: -0.5038 S33: -0.2161 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 19 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 53.1537 388.1331 43.6816 REMARK 3 T TENSOR REMARK 3 T11: 1.6740 T22: 1.3593 REMARK 3 T33: 0.5023 T12: -0.2647 REMARK 3 T13: 0.7109 T23: 0.1670 REMARK 3 L TENSOR REMARK 3 L11: 0.2977 L22: 2.5419 REMARK 3 L33: 3.7197 L12: 0.6483 REMARK 3 L13: -0.8868 L23: -2.7383 REMARK 3 S TENSOR REMARK 3 S11: 0.9297 S12: -2.4333 S13: -0.4749 REMARK 3 S21: 2.2374 S22: -0.6416 S23: 1.0731 REMARK 3 S31: 1.2431 S32: -1.1971 S33: 0.2137 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 27 THROUGH 36 ) REMARK 3 ORIGIN FOR THE GROUP (A): 63.8298 394.4763 16.3534 REMARK 3 T TENSOR REMARK 3 T11: 0.5699 T22: 0.3757 REMARK 3 T33: 0.2608 T12: 0.0269 REMARK 3 T13: 0.0616 T23: 0.0057 REMARK 3 L TENSOR REMARK 3 L11: 4.9269 L22: 4.6510 REMARK 3 L33: 7.3564 L12: -0.6343 REMARK 3 L13: -0.6261 L23: -0.2877 REMARK 3 S TENSOR REMARK 3 S11: -0.0844 S12: 0.8577 S13: -0.0534 REMARK 3 S21: -0.9794 S22: 0.1488 S23: -0.1465 REMARK 3 S31: 0.8822 S32: 0.1816 S33: -0.0405 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 5VMX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000227651. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 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) : 0.97946 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27026 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 43.104 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : 0.08910 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.47300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.870 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.9_1692 REMARK 200 STARTING MODEL: 4F6N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M DISODIUM TARTRATE, 20 % PEG REMARK 280 3350, PH 7.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y+1/2,-Z REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 22.16900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 91.99200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 22.16900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 91.99200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 22.16900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 91.99200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 22.16900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 91.99200 REMARK 290 SMTRY3 8 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: 6290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, E 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 CL CL A 704 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 MET A 471 REMARK 465 ALA A 472 REMARK 465 ASN A 473 REMARK 465 LYS A 474 REMARK 465 ARG A 475 REMARK 465 MET A 476 REMARK 465 LYS A 477 REMARK 465 VAL A 478 REMARK 465 LYS A 479 REMARK 465 HIS A 480 REMARK 465 ARG A 603 REMARK 465 SER A 604 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 OG SER A 517 OE1 GLU A 519 2.07 REMARK 500 NH1 ARG A 525 OE1 GLU A 541 2.19 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 DG D 11 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG E 30 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 DG E 30 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 496 SG REMARK 620 2 CYS A 499 SG 117.2 REMARK 620 3 HIS A 512 NE2 112.0 102.2 REMARK 620 4 HIS A 516 NE2 111.2 109.4 103.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 702 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 524 SG REMARK 620 2 CYS A 527 SG 115.1 REMARK 620 3 HIS A 540 NE2 104.7 112.3 REMARK 620 4 HIS A 544 NE2 100.7 119.2 102.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 703 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 552 SG REMARK 620 2 CYS A 555 SG 116.6 REMARK 620 3 HIS A 568 NE2 110.5 107.8 REMARK 620 4 HIS A 573 NE2 102.9 115.3 102.9 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 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 704 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5VMZ RELATED DB: PDB REMARK 900 RELATED ID: 5VMU RELATED DB: PDB REMARK 900 RELATED ID: 5VMV RELATED DB: PDB REMARK 900 RELATED ID: 5VMW RELATED DB: PDB REMARK 900 RELATED ID: 5VMY RELATED DB: PDB DBREF 5VMX A 471 604 UNP Q86T24 KAISO_HUMAN 471 604 DBREF 5VMX D 1 18 PDB 5VMX 5VMX 1 18 DBREF 5VMX E 19 36 PDB 5VMX 5VMX 19 36 SEQRES 1 A 134 MET ALA ASN LYS ARG MET LYS VAL LYS HIS ASP ASP HIS SEQRES 2 A 134 TYR GLU LEU ILE VAL ASP GLY ARG VAL TYR TYR ILE CYS SEQRES 3 A 134 ILE VAL CYS LYS ARG SER TYR VAL CYS LEU THR SER LEU SEQRES 4 A 134 ARG ARG HIS PHE ASN ILE HIS SER TRP GLU LYS LYS TYR SEQRES 5 A 134 PRO CYS ARG TYR CYS GLU LYS VAL PHE PRO LEU ALA GLU SEQRES 6 A 134 TYR ARG THR LYS HIS GLU ILE HIS HIS THR GLY GLU ARG SEQRES 7 A 134 ARG TYR GLN CYS LEU ALA CYS GLY LYS SER PHE ILE ASN SEQRES 8 A 134 TYR GLN PHE MET SER SER HIS ILE LYS SER VAL HIS SER SEQRES 9 A 134 GLN ASP PRO SER GLY ASP SER LYS LEU TYR ARG LEU HIS SEQRES 10 A 134 PRO CYS ARG SER LEU GLN ILE ARG GLN TYR ALA TYR LEU SEQRES 11 A 134 SER ASP ARG SER SEQRES 1 D 18 DT DG DC DT DT DC DC 5CM DG 5CM DG DA DA SEQRES 2 D 18 DT DA DA DC DG SEQRES 1 E 18 DC DG DT DT DA DT DT DC DG DC DG DG DG SEQRES 2 E 18 DA DA DG DC DA HET 5CM D 8 20 HET 5CM D 10 20 HET ZN A 701 1 HET ZN A 702 1 HET ZN A 703 1 HET CL A 704 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION FORMUL 2 5CM 2(C10 H16 N3 O7 P) FORMUL 4 ZN 3(ZN 2+) FORMUL 7 CL CL 1- FORMUL 8 HOH *101(H2 O) HELIX 1 AA1 CYS A 505 TRP A 518 1 14 HELIX 2 AA2 LEU A 533 GLY A 546 1 14 HELIX 3 AA3 ASN A 561 SER A 574 1 14 HELIX 4 AA4 TYR A 597 SER A 601 5 5 SHEET 1 AA1 3 HIS A 483 VAL A 488 0 SHEET 2 AA1 3 ARG A 491 CYS A 496 -1 O ILE A 495 N TYR A 484 SHEET 3 AA1 3 SER A 502 TYR A 503 -1 O TYR A 503 N TYR A 494 SHEET 1 AA2 2 TYR A 522 PRO A 523 0 SHEET 2 AA2 2 VAL A 530 PHE A 531 -1 O PHE A 531 N TYR A 522 SHEET 1 AA3 3 SER A 558 PHE A 559 0 SHEET 2 AA3 3 TYR A 550 CYS A 552 -1 N TYR A 550 O PHE A 559 SHEET 3 AA3 3 TYR A 584 LEU A 586 -1 O ARG A 585 N GLN A 551 LINK O3' DC D 7 P 5CM D 8 1555 1555 1.61 LINK O3' 5CM D 8 P DG D 9 1555 1555 1.61 LINK O3' DG D 9 P 5CM D 10 1555 1555 1.61 LINK O3' 5CM D 10 P DG D 11 1555 1555 1.60 LINK SG CYS A 496 ZN ZN A 701 1555 1555 2.33 LINK SG CYS A 499 ZN ZN A 701 1555 1555 2.22 LINK NE2 HIS A 512 ZN ZN A 701 1555 1555 2.10 LINK NE2 HIS A 516 ZN ZN A 701 1555 1555 1.97 LINK SG CYS A 524 ZN ZN A 702 1555 1555 2.17 LINK SG CYS A 527 ZN ZN A 702 1555 1555 2.30 LINK NE2 HIS A 540 ZN ZN A 702 1555 1555 2.05 LINK NE2 HIS A 544 ZN ZN A 702 1555 1555 2.07 LINK SG CYS A 552 ZN ZN A 703 1555 1555 2.29 LINK SG CYS A 555 ZN ZN A 703 1555 1555 2.29 LINK NE2 HIS A 568 ZN ZN A 703 1555 1555 2.03 LINK NE2 HIS A 573 ZN ZN A 703 1555 1555 2.11 SITE 1 AC1 4 CYS A 496 CYS A 499 HIS A 512 HIS A 516 SITE 1 AC2 4 CYS A 524 CYS A 527 HIS A 540 HIS A 544 SITE 1 AC3 4 CYS A 552 CYS A 555 HIS A 568 HIS A 573 SITE 1 AC4 1 ARG A 548 CRYST1 44.338 183.984 105.072 90.00 90.00 90.00 C 2 2 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 0.022554 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005435 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009517 0.00000