PDB Short entry for 4F6N HEADER DNA BINDING PROTEIN/DNA 15-MAY-12 4F6N TITLE CRYSTAL STRUCTURE OF KAISO ZINC FINGER DNA BINDING PROTEIN IN COMPLEX TITLE 2 WITH METHYLATED CPG SITE DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR KAISO; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZINC FINGER DNA BINDING DOMAIN; 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(*GP*TP*GP*TP*CP*AP*CP*(5CM)P*GP*(5CM) COMPND 9 P*GP*TP*CP*TP*AP*TP*AP*CP*G)-3'); COMPND 10 CHAIN: D; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: MEECAD DNA STRAND 1; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*CP*GP*TP*AP*TP*AP*GP*AP*(5CM)P*GP*(5CM) COMPND 15 P*GP*GP*TP*GP*AP*CP*AP*C)-3'); COMPND 16 CHAIN: E; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: MEECAD DNA STRAND 2 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; 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 OTHER_DETAILS: THIS SEQUENCE OCCURS IN HUMANS; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_TAXID: 9606; SOURCE 20 OTHER_DETAILS: THIS SEQUENCE OCCURS IN HUMANS KEYWDS ZINC FINGER, PROTEIN-DNA COMPLEX, DOUBLE HELIX, DNA BINDING, DNA, DNA KEYWDS 2 BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.A.BUCK-KOEHNTOP,R.L.STANFIELD,D.C.EKIERT,M.A.MARTINEZ-YAMOUT, AUTHOR 2 H.J.DYSON,I.A.WILSON,P.E.WRIGHT REVDAT 5 03-APR-24 4F6N 1 REMARK REVDAT 4 28-FEB-24 4F6N 1 REMARK LINK REVDAT 3 03-OCT-12 4F6N 1 JRNL REVDAT 2 26-SEP-12 4F6N 1 JRNL REVDAT 1 05-SEP-12 4F6N 0 JRNL AUTH B.A.BUCK-KOEHNTOP,R.L.STANFIELD,D.C.EKIERT, JRNL AUTH 2 M.A.MARTINEZ-YAMOUT,H.J.DYSON,I.A.WILSON,P.E.WRIGHT JRNL TITL MOLECULAR BASIS FOR RECOGNITION OF METHYLATED AND SPECIFIC JRNL TITL 2 DNA SEQUENCES BY THE ZINC FINGER PROTEIN KAISO. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 15229 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22949637 JRNL DOI 10.1073/PNAS.1213726109 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 11779 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 558 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 763 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.3890 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.4580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1020 REMARK 3 NUCLEIC ACID ATOMS : 761 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 15 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 72.00 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.440 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.300 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.228 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1965 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2755 ; 1.579 ; 2.435 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 119 ; 6.364 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 55 ;30.590 ;21.273 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 185 ;18.155 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;18.264 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1201 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 481 A 600 REMARK 3 ORIGIN FOR THE GROUP (A): -14.6827 -27.2737 24.1289 REMARK 3 T TENSOR REMARK 3 T11: 0.1805 T22: 0.1884 REMARK 3 T33: 0.2151 T12: 0.0506 REMARK 3 T13: 0.0302 T23: 0.0050 REMARK 3 L TENSOR REMARK 3 L11: 2.1190 L22: 8.7494 REMARK 3 L33: 1.8565 L12: 0.3415 REMARK 3 L13: 0.6568 L23: 0.6478 REMARK 3 S TENSOR REMARK 3 S11: -0.0354 S12: -0.0430 S13: 0.3029 REMARK 3 S21: 0.5372 S22: 0.1238 S23: -0.2909 REMARK 3 S31: -0.4351 S32: 0.0419 S33: -0.0885 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 19 REMARK 3 RESIDUE RANGE : E 21 E 38 REMARK 3 ORIGIN FOR THE GROUP (A): -16.8148 -23.0558 29.4536 REMARK 3 T TENSOR REMARK 3 T11: 0.4464 T22: 0.3147 REMARK 3 T33: 0.2965 T12: 0.0321 REMARK 3 T13: 0.0665 T23: -0.0183 REMARK 3 L TENSOR REMARK 3 L11: 4.2832 L22: 5.1503 REMARK 3 L33: 7.5288 L12: 0.4622 REMARK 3 L13: -1.4029 L23: 0.1268 REMARK 3 S TENSOR REMARK 3 S11: 0.1324 S12: -0.8271 S13: 0.2844 REMARK 3 S21: 0.8652 S22: 0.0594 S23: -0.1733 REMARK 3 S31: -1.0375 S32: 0.3513 S33: -0.1918 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4F6N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072521. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11780 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 65.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 7.360 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : 0.08700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.58100 REMARK 200 R SYM FOR SHELL (I) : 0.58100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: KAISO FROM COMPLEX WITH KAISO BINDING SITE PROTEIN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M NACL, 0.1M SODIUM CACODYLATE, 10% REMARK 280 GLYCEROL, 30% PEG 600, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: F 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,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z+1/2 REMARK 290 7555 -X,Y+1/2,-Z+1/2 REMARK 290 8555 X,-Y+1/2,-Z+1/2 REMARK 290 9555 X+1/2,Y,Z+1/2 REMARK 290 10555 -X+1/2,-Y,Z+1/2 REMARK 290 11555 -X+1/2,Y,-Z+1/2 REMARK 290 12555 X+1/2,-Y,-Z+1/2 REMARK 290 13555 X+1/2,Y+1/2,Z REMARK 290 14555 -X+1/2,-Y+1/2,Z REMARK 290 15555 -X+1/2,Y+1/2,-Z REMARK 290 16555 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 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 91.70100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 115.06900 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 91.70100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 115.06900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 91.70100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 115.06900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 91.70100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 115.06900 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 22.02450 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 115.06900 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 22.02450 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 115.06900 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 22.02450 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 115.06900 REMARK 290 SMTRY1 12 1.000000 0.000000 0.000000 22.02450 REMARK 290 SMTRY2 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 115.06900 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 22.02450 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 91.70100 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 22.02450 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 91.70100 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 22.02450 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 91.70100 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 22.02450 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 91.70100 REMARK 290 SMTRY3 16 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: 7950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 5.0 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 HOH A 802 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 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 SER A 601 REMARK 465 ASP A 602 REMARK 465 ARG A 603 REMARK 465 SER A 604 REMARK 465 DC E 20 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 D 19 C2 DG D 19 N3 0.171 REMARK 500 DG D 19 C2 DG D 19 N2 0.157 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 DA D 6 O4' - C1' - N9 ANGL. DEV. = -4.6 DEGREES REMARK 500 DC D 7 O4' - C1' - N1 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT D 12 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 DT D 12 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC D 13 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA D 17 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC D 18 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG D 19 N1 - C2 - N3 ANGL. DEV. = -7.5 DEGREES REMARK 500 DG D 19 N1 - C2 - N2 ANGL. DEV. = -14.0 DEGREES REMARK 500 DG D 19 N3 - C2 - N2 ANGL. DEV. = 21.6 DEGREES REMARK 500 DG E 21 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT E 22 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DT E 24 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA E 25 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG E 29 O4' - C1' - N9 ANGL. DEV. = -4.9 DEGREES REMARK 500 DG E 31 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 DG E 32 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA E 35 O4' - C1' - N9 ANGL. DEV. = -5.5 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 489 73.97 25.43 REMARK 500 ILE A 515 -37.51 -39.19 REMARK 500 SER A 574 49.22 38.66 REMARK 500 ASP A 580 -38.48 57.50 REMARK 500 ALA A 598 -7.86 -58.05 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 109.6 REMARK 620 3 HIS A 512 NE2 109.5 109.3 REMARK 620 4 HIS A 516 NE2 109.6 109.6 109.3 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 109.7 REMARK 620 3 HIS A 540 NE2 109.4 109.5 REMARK 620 4 HIS A 544 NE2 109.5 109.5 109.2 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 109.5 REMARK 620 3 HIS A 568 NE2 109.6 109.6 REMARK 620 4 HIS A 573 NE2 109.2 109.6 109.4 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 GOL A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4F6M RELATED DB: PDB DBREF 4F6N A 472 604 UNP Q86T24 KAISO_HUMAN 472 604 DBREF 4F6N D 1 19 PDB 4F6N 4F6N 1 19 DBREF 4F6N E 20 38 PDB 4F6N 4F6N 20 38 SEQRES 1 A 133 ALA ASN LYS ARG MET LYS VAL LYS HIS ASP ASP HIS TYR SEQRES 2 A 133 GLU LEU ILE VAL ASP GLY ARG VAL TYR TYR ILE CYS ILE SEQRES 3 A 133 VAL CYS LYS ARG SER TYR VAL CYS LEU THR SER LEU ARG SEQRES 4 A 133 ARG HIS PHE ASN ILE HIS SER TRP GLU LYS LYS TYR PRO SEQRES 5 A 133 CYS ARG TYR CYS GLU LYS VAL PHE PRO LEU ALA GLU TYR SEQRES 6 A 133 ARG THR LYS HIS GLU ILE HIS HIS THR GLY GLU ARG ARG SEQRES 7 A 133 TYR GLN CYS LEU ALA CYS GLY LYS SER PHE ILE ASN TYR SEQRES 8 A 133 GLN PHE MET SER SER HIS ILE LYS SER VAL HIS SER GLN SEQRES 9 A 133 ASP PRO SER GLY ASP SER LYS LEU TYR ARG LEU HIS PRO SEQRES 10 A 133 CYS ARG SER LEU GLN ILE ARG GLN TYR ALA TYR LEU SER SEQRES 11 A 133 ASP ARG SER SEQRES 1 D 19 DG DT DG DT DC DA DC 5CM DG 5CM DG DT DC SEQRES 2 D 19 DT DA DT DA DC DG SEQRES 1 E 19 DC DG DT DA DT DA DG DA 5CM DG 5CM DG DG SEQRES 2 E 19 DT DG DA DC DA DC MODRES 4F6N 5CM D 8 DC MODRES 4F6N 5CM D 10 DC MODRES 4F6N 5CM E 28 DC MODRES 4F6N 5CM E 30 DC HET 5CM D 8 20 HET 5CM D 10 20 HET 5CM E 28 20 HET 5CM E 30 20 HET ZN A 701 1 HET ZN A 702 1 HET ZN A 703 1 HET GOL A 704 6 HET GOL D 101 6 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 5CM 4(C10 H16 N3 O7 P) FORMUL 4 ZN 3(ZN 2+) FORMUL 7 GOL 2(C3 H8 O3) FORMUL 9 HOH *15(H2 O) HELIX 1 1 CYS A 505 TRP A 518 1 14 HELIX 2 2 LEU A 533 GLY A 546 1 14 HELIX 3 3 ASN A 561 SER A 574 1 14 SHEET 1 A 3 HIS A 483 VAL A 488 0 SHEET 2 A 3 ARG A 491 CYS A 496 -1 O ILE A 495 N TYR A 484 SHEET 3 A 3 SER A 502 TYR A 503 -1 O TYR A 503 N TYR A 494 SHEET 1 B 2 TYR A 522 PRO A 523 0 SHEET 2 B 2 VAL A 530 PHE A 531 -1 O PHE A 531 N TYR A 522 SHEET 1 C 3 SER A 558 PHE A 559 0 SHEET 2 C 3 TYR A 550 CYS A 552 -1 N TYR A 550 O PHE A 559 SHEET 3 C 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 1.58 LINK O3' 5CM D 8 P DG D 9 1555 1555 1.58 LINK O3' DG D 9 P 5CM D 10 1555 1555 1.58 LINK O3' 5CM D 10 P DG D 11 1555 1555 1.61 LINK O3' DA E 27 P 5CM E 28 1555 1555 1.59 LINK O3' 5CM E 28 P DG E 29 1555 1555 1.58 LINK O3' DG E 29 P 5CM E 30 1555 1555 1.59 LINK O3' 5CM E 30 P DG E 31 1555 1555 1.58 LINK SG CYS A 496 ZN ZN A 701 1555 1555 2.29 LINK SG CYS A 499 ZN ZN A 701 1555 1555 2.29 LINK NE2 HIS A 512 ZN ZN A 701 1555 1555 2.06 LINK NE2 HIS A 516 ZN ZN A 701 1555 1555 2.07 LINK SG CYS A 524 ZN ZN A 702 1555 1555 2.29 LINK SG CYS A 527 ZN ZN A 702 1555 1555 2.28 LINK NE2 HIS A 540 ZN ZN A 702 1555 1555 2.07 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 2.27 LINK NE2 HIS A 568 ZN ZN A 703 1555 1555 2.04 LINK NE2 HIS A 573 ZN ZN A 703 1555 1555 2.07 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 TYR A 536 LYS A 539 DA D 6 SITE 1 AC5 6 DG D 3 DT D 4 DC D 5 HOH D 201 SITE 2 AC5 6 DC E 36 DA E 37 CRYST1 44.049 183.402 230.138 90.00 90.00 90.00 F 2 2 2 16 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 0.022702 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005453 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004345 0.00000