HEADER TRANSCRIPTION/DNA 28-APR-17 5VMU TITLE KAISO (ZBTB33) ZINC FINGER DNA BINDING DOMAIN IN COMPLEX WITH A DOUBLE 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'-D(*CP*GP*TP*TP*AP*TP*TP*(5CM)P*GP*(5CM) COMPND 14 P*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: HOMO SAPIENS; SOURCE 14 ORGANISM_TAXID: 9606; 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, TRANSCRIPTION- KEYWDS 2 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 5VMU 1 REMARK REVDAT 3 23-MAR-22 5VMU 1 SOURCE REVDAT 2 25-APR-18 5VMU 1 JRNL REVDAT 1 04-APR-18 5VMU 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. 2.35 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 17789 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1782 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 42.3425 - 5.5124 1.00 1382 154 0.1632 0.2003 REMARK 3 2 5.5124 - 4.3768 1.00 1307 145 0.1514 0.1673 REMARK 3 3 4.3768 - 3.8240 1.00 1307 145 0.1452 0.1975 REMARK 3 4 3.8240 - 3.4745 1.00 1284 142 0.1595 0.2035 REMARK 3 5 3.4745 - 3.2256 1.00 1269 141 0.1808 0.2161 REMARK 3 6 3.2256 - 3.0355 0.99 1263 141 0.1919 0.2432 REMARK 3 7 3.0355 - 2.8835 1.00 1258 140 0.2194 0.2604 REMARK 3 8 2.8835 - 2.7580 1.00 1260 140 0.2304 0.2916 REMARK 3 9 2.7580 - 2.6518 1.00 1263 141 0.2340 0.2692 REMARK 3 10 2.6518 - 2.5603 1.00 1264 141 0.2289 0.2355 REMARK 3 11 2.5603 - 2.4803 0.97 1219 136 0.2424 0.3056 REMARK 3 12 2.4803 - 2.4094 0.94 1182 132 0.2726 0.2821 REMARK 3 13 2.4094 - 2.3460 0.59 749 84 0.3503 0.3855 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.260 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 1960 REMARK 3 ANGLE : 1.174 2784 REMARK 3 CHIRALITY : 0.052 287 REMARK 3 PLANARITY : 0.005 227 REMARK 3 DIHEDRAL : 25.769 752 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 522 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.7327 -10.1701 25.0648 REMARK 3 T TENSOR REMARK 3 T11: 0.7925 T22: 0.3664 REMARK 3 T33: 0.8714 T12: -0.0424 REMARK 3 T13: -0.0289 T23: 0.0180 REMARK 3 L TENSOR REMARK 3 L11: 5.9123 L22: 6.6750 REMARK 3 L33: 4.3720 L12: -4.7585 REMARK 3 L13: -2.2966 L23: 0.5557 REMARK 3 S TENSOR REMARK 3 S11: 0.1708 S12: 0.0384 S13: 1.3707 REMARK 3 S21: 0.1749 S22: 0.0629 S23: -0.8548 REMARK 3 S31: -1.0307 S32: 0.0852 S33: -0.2437 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 523 THROUGH 545 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.7620 -30.5419 20.0646 REMARK 3 T TENSOR REMARK 3 T11: 0.4764 T22: 0.3905 REMARK 3 T33: 0.6899 T12: 0.0288 REMARK 3 T13: 0.0827 T23: 0.0730 REMARK 3 L TENSOR REMARK 3 L11: 9.1514 L22: 4.0143 REMARK 3 L33: 7.0806 L12: -4.0195 REMARK 3 L13: 0.8815 L23: 3.5697 REMARK 3 S TENSOR REMARK 3 S11: -0.2937 S12: 0.1545 S13: 0.5854 REMARK 3 S21: -0.3079 S22: 0.2833 S23: -1.4153 REMARK 3 S31: -0.3038 S32: 0.4269 S33: -0.0455 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 546 THROUGH 586 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.0771 -40.8486 21.4557 REMARK 3 T TENSOR REMARK 3 T11: 0.3542 T22: 0.3227 REMARK 3 T33: 0.3526 T12: 0.0655 REMARK 3 T13: 0.0422 T23: 0.0104 REMARK 3 L TENSOR REMARK 3 L11: 8.9127 L22: 7.5659 REMARK 3 L33: 5.3592 L12: 3.3180 REMARK 3 L13: 4.0076 L23: 0.4719 REMARK 3 S TENSOR REMARK 3 S11: -0.0161 S12: -0.0074 S13: 0.1679 REMARK 3 S21: 0.0702 S22: -0.1426 S23: 0.3343 REMARK 3 S31: -0.2688 S32: -0.4023 S33: 0.1094 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 587 THROUGH 601 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.6224 -37.8718 32.0994 REMARK 3 T TENSOR REMARK 3 T11: 0.7618 T22: 0.4257 REMARK 3 T33: 0.6158 T12: 0.0561 REMARK 3 T13: -0.0127 T23: 0.0423 REMARK 3 L TENSOR REMARK 3 L11: 2.5190 L22: 4.9600 REMARK 3 L33: 8.5490 L12: -2.5439 REMARK 3 L13: -2.6094 L23: 6.1955 REMARK 3 S TENSOR REMARK 3 S11: -0.1697 S12: -0.9710 S13: 0.4783 REMARK 3 S21: 1.3420 S22: 0.5415 S23: 0.5577 REMARK 3 S31: -0.5015 S32: 0.2146 S33: -0.4138 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.9551 -28.1785 12.0147 REMARK 3 T TENSOR REMARK 3 T11: 1.9044 T22: 0.5549 REMARK 3 T33: 0.4141 T12: -0.0451 REMARK 3 T13: 0.1329 T23: 0.0897 REMARK 3 L TENSOR REMARK 3 L11: 3.0253 L22: 4.6494 REMARK 3 L33: 9.9351 L12: -1.1628 REMARK 3 L13: 0.7777 L23: 5.9180 REMARK 3 S TENSOR REMARK 3 S11: -0.2325 S12: 0.6342 S13: 0.0371 REMARK 3 S21: -2.8959 S22: 0.4628 S23: -1.5720 REMARK 3 S31: 1.6982 S32: -0.1303 S33: 0.0999 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 9 THROUGH 18 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.1257 -22.5285 39.3830 REMARK 3 T TENSOR REMARK 3 T11: 1.4902 T22: 1.0391 REMARK 3 T33: 0.6401 T12: 0.1272 REMARK 3 T13: -0.5150 T23: -0.1545 REMARK 3 L TENSOR REMARK 3 L11: 8.2719 L22: 2.4138 REMARK 3 L33: 5.5848 L12: 2.3480 REMARK 3 L13: 0.5777 L23: 1.1713 REMARK 3 S TENSOR REMARK 3 S11: -0.7328 S12: -2.1358 S13: -0.2689 REMARK 3 S21: 3.0247 S22: 0.7701 S23: -0.7859 REMARK 3 S31: -1.5653 S32: 0.8118 S33: -0.1778 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 19 THROUGH 28 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.0801 -22.3533 40.4935 REMARK 3 T TENSOR REMARK 3 T11: 1.6218 T22: 1.0902 REMARK 3 T33: 0.5573 T12: -0.0939 REMARK 3 T13: -0.3613 T23: -0.1539 REMARK 3 L TENSOR REMARK 3 L11: 5.0688 L22: 0.7307 REMARK 3 L33: 3.9761 L12: 0.4815 REMARK 3 L13: -0.9177 L23: 1.2434 REMARK 3 S TENSOR REMARK 3 S11: 0.2053 S12: -2.2404 S13: 0.1424 REMARK 3 S21: 2.6279 S22: -0.1244 S23: -1.0186 REMARK 3 S31: -0.4987 S32: 0.2578 S33: -0.2143 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 29 THROUGH 36 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.4465 -25.8684 13.3565 REMARK 3 T TENSOR REMARK 3 T11: 1.4531 T22: 0.6178 REMARK 3 T33: 0.4498 T12: -0.0576 REMARK 3 T13: 0.0300 T23: 0.0292 REMARK 3 L TENSOR REMARK 3 L11: 4.7397 L22: 0.7828 REMARK 3 L33: 6.8849 L12: -1.5509 REMARK 3 L13: 2.2455 L23: -1.0575 REMARK 3 S TENSOR REMARK 3 S11: -0.0185 S12: 1.2164 S13: 0.1992 REMARK 3 S21: -1.9777 S22: 0.2668 S23: 0.1809 REMARK 3 S31: -1.4262 S32: 0.1085 S33: -0.1174 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 5VMU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000226558. 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 : 17827 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.346 REMARK 200 RESOLUTION RANGE LOW (A) : 42.336 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : 0.11800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.62900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.040 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 (%): 68.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M DI-SODIUM 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 21.99250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 92.50700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 21.99250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 92.50700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 21.99250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 92.50700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 21.99250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 92.50700 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: 7460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 ASP A 602 REMARK 465 ARG A 603 REMARK 465 SER A 604 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 ARG A 491 CG CD NE CZ NH1 NH2 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 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG D 11 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT D 14 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG E 30 O4' - C1' - N9 ANGL. DEV. = 3.7 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 CYS A 527 -155.91 -140.59 REMARK 500 CYS A 555 -10.96 -140.57 REMARK 500 LYS A 582 -0.79 66.76 REMARK 500 LEU A 600 48.31 -72.58 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 115.5 REMARK 620 3 HIS A 512 NE2 105.7 100.5 REMARK 620 4 HIS A 516 NE2 114.8 111.6 107.0 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 114.7 REMARK 620 3 HIS A 540 NE2 110.2 114.0 REMARK 620 4 HIS A 544 NE2 105.0 111.0 100.7 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 111.8 REMARK 620 3 HIS A 568 NE2 109.0 110.4 REMARK 620 4 HIS A 573 NE2 100.8 114.8 109.7 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 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: 5VMV RELATED DB: PDB REMARK 900 RELATED ID: 5VMW RELATED DB: PDB REMARK 900 RELATED ID: 5VMX RELATED DB: PDB REMARK 900 RELATED ID: 5VMY RELATED DB: PDB REMARK 900 RELATED ID: 5VMZ RELATED DB: PDB DBREF 5VMU A 471 604 UNP Q86T24 KAISO_HUMAN 471 604 DBREF 5VMU D 1 18 PDB 5VMU 5VMU 1 18 DBREF 5VMU E 19 36 PDB 5VMU 5VMU 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 5CM DG 5CM DG DG DG SEQRES 2 E 18 DA DA DG DC DA HET 5CM D 8 20 HET 5CM D 10 20 HET 5CM E 26 20 HET 5CM E 28 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 4(C10 H16 N3 O7 P) FORMUL 4 ZN 3(ZN 2+) FORMUL 7 CL CL 1- FORMUL 8 HOH *27(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 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 1.61 LINK O3' DT E 25 P 5CM E 26 1555 1555 1.60 LINK O3' 5CM E 26 P DG E 27 1555 1555 1.60 LINK O3' DG E 27 P 5CM E 28 1555 1555 1.61 LINK O3' 5CM E 28 P DG E 29 1555 1555 1.61 LINK SG CYS A 496 ZN ZN A 701 1555 1555 2.31 LINK SG CYS A 499 ZN ZN A 701 1555 1555 2.24 LINK NE2 HIS A 512 ZN ZN A 701 1555 1555 2.02 LINK NE2 HIS A 516 ZN ZN A 701 1555 1555 2.02 LINK SG CYS A 524 ZN ZN A 702 1555 1555 2.19 LINK SG CYS A 527 ZN ZN A 702 1555 1555 2.26 LINK NE2 HIS A 540 ZN ZN A 702 1555 1555 1.98 LINK NE2 HIS A 544 ZN ZN A 702 1555 1555 2.07 LINK SG CYS A 552 ZN ZN A 703 1555 1555 2.24 LINK SG CYS A 555 ZN ZN A 703 1555 1555 2.38 LINK NE2 HIS A 568 ZN ZN A 703 1555 1555 2.04 LINK NE2 HIS A 573 ZN ZN A 703 1555 1555 2.05 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 3 ARG A 548 ARG A 590 HOH A 807 CRYST1 43.985 185.014 105.108 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 0.022735 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005405 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009514 0.00000