HEADER TRANSCRIPTION/DNA 14-AUG-13 4M9E TITLE STRUCTURE OF KLF4 ZINC FINGER DNA BINDING DOMAIN IN COMPLEX WITH TITLE 2 METHYLATED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: KRUEPPEL-LIKE FACTOR 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 396-483; COMPND 5 SYNONYM: EPITHELIAL ZINC FINGER PROTEIN EZF, GUT-ENRICHED KRUEPPEL- COMPND 6 LIKE FACTOR; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*AP*GP*GP*(5CM)P*GP*TP*GP*GP*C)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*GP*CP*CP*AP*(5CM)P*GP*CP*CP*TP*C)-3'); COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: KLF4, EZF, GKLF, ZIE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PXC1248; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: DNA SYNTHESIS; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 OTHER_DETAILS: DNA SYNTHESIS KEYWDS DNA METHYLATION, TRANSCRIPTION FACTOR, CELLULAR REPROGRAMMING, C2H2 KEYWDS 2 ZINC FINGER, DNA BINDING, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,Y.O.OLANREWAJU,R.M.BLUMENTHAL,X.ZHANG,X.CHENG REVDAT 4 20-SEP-23 4M9E 1 REMARK LINK REVDAT 3 21-MAY-14 4M9E 1 JRNL REVDAT 2 19-MAR-14 4M9E 1 JRNL REVDAT 1 12-FEB-14 4M9E 0 JRNL AUTH Y.LIU,Y.O.OLANREWAJU,Y.ZHENG,H.HASHIMOTO,R.M.BLUMENTHAL, JRNL AUTH 2 X.ZHANG,X.CHENG JRNL TITL STRUCTURAL BASIS FOR KLF4 RECOGNITION OF METHYLATED DNA. JRNL REF NUCLEIC ACIDS RES. V. 42 4859 2014 JRNL REFN ISSN 0305-1048 JRNL PMID 24520114 JRNL DOI 10.1093/NAR/GKU134 REMARK 2 REMARK 2 RESOLUTION. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 13843 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 689 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 34.4456 - 3.1645 0.99 2872 131 0.1648 0.1873 REMARK 3 2 3.1645 - 2.5120 1.00 2697 143 0.2094 0.3047 REMARK 3 3 2.5120 - 2.1946 1.00 2651 146 0.1940 0.2297 REMARK 3 4 2.1946 - 1.9939 1.00 2638 133 0.1978 0.2477 REMARK 3 5 1.9939 - 1.8510 0.89 2296 136 0.2345 0.2768 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) : 20.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.90 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 1230 REMARK 3 ANGLE : 1.313 1753 REMARK 3 CHIRALITY : 0.063 166 REMARK 3 PLANARITY : 0.005 147 REMARK 3 DIHEDRAL : 26.221 512 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 53.3137 72.2660 141.9154 REMARK 3 T TENSOR REMARK 3 T11: 0.1230 T22: 0.1368 REMARK 3 T33: 0.0927 T12: -0.0184 REMARK 3 T13: 0.0158 T23: 0.0155 REMARK 3 L TENSOR REMARK 3 L11: 1.5052 L22: 1.6636 REMARK 3 L33: 1.1247 L12: -0.8003 REMARK 3 L13: -0.2145 L23: 0.7061 REMARK 3 S TENSOR REMARK 3 S11: 0.0111 S12: 0.0839 S13: 0.0685 REMARK 3 S21: 0.0487 S22: 0.0233 S23: -0.0075 REMARK 3 S31: 0.0555 S32: -0.1108 S33: -0.0315 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 4M9E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000081631. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL - LIQUED NITROGEN REMARK 200 COOLED REMARK 200 OPTICS : ROSENBAUM-ROCK DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR: LIQUID NITROGEN REMARK 200 COOLED; SAGITALLY FOCUSING 2ND REMARK 200 CRYSTAL, ROSENBAUM-ROCK VERTICAL REMARK 200 FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13918 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 70.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 12.00 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.50100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 2WBU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, 0.25M NACL AND 20% REMARK 280 POLYETHYLENE GLYCOL 8000, PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 65.50750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 24.35250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 24.35250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 98.26125 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 24.35250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 24.35250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.75375 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 24.35250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 24.35250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 98.26125 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 24.35250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 24.35250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 32.75375 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 65.50750 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: 4880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 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 ARG A 396 REMARK 465 THR A 397 REMARK 465 ALA A 398 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 453 CE NZ REMARK 470 ARG A 458 NE CZ NH1 NH2 REMARK 470 LYS A 480 CE NZ REMARK 470 ARG A 481 CG CD NE CZ NH1 NH2 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 638 O HOH B 126 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 B 1 O4' - C1' - N9 ANGL. DEV. = -4.6 DEGREES REMARK 500 DT B 7 N1 - C1' - C2' ANGL. DEV. = 8.8 DEGREES REMARK 500 DC B 10 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DA C 4 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DA C 4 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG C 6 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DG C 6 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG C 6 O4' - C1' - N9 ANGL. DEV. = 7.5 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 ALA A 405 -136.32 46.15 REMARK 500 CYS A 407 -75.09 -116.25 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 505 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 402 SG REMARK 620 2 CYS A 407 SG 113.5 REMARK 620 3 HIS A 420 NE2 109.2 108.4 REMARK 620 4 HIS A 424 NE2 108.0 112.4 104.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 432 SG REMARK 620 2 CYS A 437 SG 118.7 REMARK 620 3 HIS A 450 NE2 108.9 108.3 REMARK 620 4 HIS A 454 NE2 111.8 109.6 97.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 462 SG REMARK 620 2 CYS A 465 SG 121.2 REMARK 620 3 HIS A 478 NE2 107.2 102.0 REMARK 620 4 HIS A 482 NE2 108.2 115.8 99.6 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 GOL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 505 DBREF 4M9E A 396 483 UNP Q60793 KLF4_MOUSE 396 483 DBREF 4M9E B 1 10 PDB 4M9E 4M9E 1 10 DBREF 4M9E C 1 10 PDB 4M9E 4M9E 1 10 SEQRES 1 A 88 ARG THR ALA THR HIS THR CYS ASP TYR ALA GLY CYS GLY SEQRES 2 A 88 LYS THR TYR THR LYS SER SER HIS LEU LYS ALA HIS LEU SEQRES 3 A 88 ARG THR HIS THR GLY GLU LYS PRO TYR HIS CYS ASP TRP SEQRES 4 A 88 ASP GLY CYS GLY TRP LYS PHE ALA ARG SER ASP GLU LEU SEQRES 5 A 88 THR ARG HIS TYR ARG LYS HIS THR GLY HIS ARG PRO PHE SEQRES 6 A 88 GLN CYS GLN LYS CYS ASP ARG ALA PHE SER ARG SER ASP SEQRES 7 A 88 HIS LEU ALA LEU HIS MET LYS ARG HIS PHE SEQRES 1 B 10 DG DA DG DG 5CM DG DT DG DG DC SEQRES 1 C 10 DG DC DC DA 5CM DG DC DC DT DC MODRES 4M9E 5CM B 5 DC MODRES 4M9E 5CM C 5 DC HET 5CM B 5 20 HET 5CM C 5 31 HET GOL A 501 6 HET ACT A 502 4 HET ZN A 503 1 HET ZN A 504 1 HET ZN A 505 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION HETNAM ZN ZINC ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 5CM 2(C10 H16 N3 O7 P) FORMUL 4 GOL C3 H8 O3 FORMUL 5 ACT C2 H3 O2 1- FORMUL 6 ZN 3(ZN 2+) FORMUL 9 HOH *134(H2 O) HELIX 1 1 LYS A 413 GLY A 426 1 14 HELIX 2 2 ARG A 443 GLY A 456 1 14 HELIX 3 3 ARG A 471 ARG A 481 1 11 SHEET 1 A 2 HIS A 400 THR A 401 0 SHEET 2 A 2 THR A 410 TYR A 411 -1 O TYR A 411 N HIS A 400 SHEET 1 B 2 TYR A 430 HIS A 431 0 SHEET 2 B 2 LYS A 440 PHE A 441 -1 O PHE A 441 N TYR A 430 SHEET 1 C 2 PHE A 460 GLN A 461 0 SHEET 2 C 2 ALA A 468 PHE A 469 -1 O PHE A 469 N PHE A 460 LINK O3' DG B 4 P 5CM B 5 1555 1555 1.61 LINK O3' 5CM B 5 P DG B 6 1555 1555 1.61 LINK O3'A DA C 4 P A5CM C 5 1555 1555 1.61 LINK O3'B DA C 4 P B5CM C 5 1555 1555 1.61 LINK O3'A5CM C 5 P DG C 6 1555 1555 1.61 LINK O3'B5CM C 5 P DG C 6 1555 1555 1.61 LINK SG CYS A 402 ZN ZN A 505 1555 1555 2.24 LINK SG CYS A 407 ZN ZN A 505 1555 1555 2.28 LINK NE2 HIS A 420 ZN ZN A 505 1555 1555 2.05 LINK NE2 HIS A 424 ZN ZN A 505 1555 1555 2.07 LINK SG CYS A 432 ZN ZN A 504 1555 1555 2.26 LINK SG CYS A 437 ZN ZN A 504 1555 1555 2.30 LINK NE2 HIS A 450 ZN ZN A 504 1555 1555 2.04 LINK NE2 HIS A 454 ZN ZN A 504 1555 1555 2.04 LINK SG CYS A 462 ZN ZN A 503 1555 1555 2.33 LINK SG CYS A 465 ZN ZN A 503 1555 1555 2.28 LINK NE2 HIS A 478 ZN ZN A 503 1555 1555 2.03 LINK NE2 HIS A 482 ZN ZN A 503 1555 1555 2.03 SITE 1 AC1 6 THR A 448 ARG A 452 THR A 455 HIS A 457 SITE 2 AC1 6 HOH A 665 HOH A 668 SITE 1 AC2 4 ARG A 452 HOH A 603 HOH A 652 DA C 4 SITE 1 AC3 4 CYS A 462 CYS A 465 HIS A 478 HIS A 482 SITE 1 AC4 4 CYS A 432 CYS A 437 HIS A 450 HIS A 454 SITE 1 AC5 4 CYS A 402 CYS A 407 HIS A 420 HIS A 424 CRYST1 48.705 48.705 131.015 90.00 90.00 90.00 P 43 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 0.020532 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020532 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007633 0.00000