HEADER TRANSCRIPTION/DNA 03-MAR-09 2WBS TITLE CRYSTAL STRUCTURE OF THE ZINC FINGER DOMAIN OF KLF4 BOUND TITLE 2 TO ITS TARGET DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: KRUEPPEL-LIKE FACTOR 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNA-BINDING DOMAIN, RESIDUES 395-483; COMPND 5 SYNONYM: GUT-ENRICHED KRUEPPEL-LIKE FACTOR, EPITHELIAL ZINC FINGER COMPND 6 PROTEIN EZF; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*GP*AP*GP*GP*CP*GP*CP)-3'; COMPND 10 CHAIN: F; COMPND 11 SYNONYM: HEPTAMERIC DNA BINDING SEQUENCE OF KLF4; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(*GP*CP*GP*CP*CP*TP*CP)-3'; COMPND 14 CHAIN: G; COMPND 15 SYNONYM: HEPTAMERIC DNA BINDING SEQUENCE OF KLF4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 STRAIN: C57BL/6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 11 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 12 ORGANISM_TAXID: 10090; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 16 ORGANISM_COMMON: MOUSE; SOURCE 17 ORGANISM_TAXID: 10090 KEYWDS TRANSCRIPTION-DNA COMPLEX, DNA-BINDING, TRANSCRIPTION, KEYWDS 2 METAL-BINDING, DNA, PROTEIN, NUCLEUS, ACTIVATOR, ZINC-FINGER, KEYWDS 3 TRANSCRIPTION REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR G.ZOCHER,A.SCHUETZ,D.CARSTANJEN,U.HEINEMANN REVDAT 3 05-OCT-11 2WBS 1 SOURCE JRNL REVDAT 2 13-JUL-11 2WBS 1 VERSN REVDAT 1 07-APR-10 2WBS 0 JRNL AUTH A.SCHUETZ,D.NANA,C.ROSE,G.ZOCHER,M.MILANOVIC, JRNL AUTH 2 J.KOENIGSMANN,R.BLASIG,U.HEINEMANN,D.CARSTANJEN JRNL TITL THE STRUCTURE OF THE KLF4 DNA-BINDING DOMAIN LINKS JRNL TITL 2 TO SELF-RENEWAL AND MACROPHAGE DIFFERENTIATION. JRNL REF CELL.MOL.LIFE SCI. V. 68 3121 2011 JRNL REFN ISSN 1420-682X JRNL PMID 21290164 JRNL DOI 10.1007/S00018-010-0618-X REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0082 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 14649 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 770 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1026 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.18 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 54 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 727 REMARK 3 NUCLEIC ACID ATOMS : 281 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 131 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.84000 REMARK 3 B22 (A**2) : 0.18000 REMARK 3 B33 (A**2) : 0.66000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : -0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.118 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.113 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.090 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.489 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1072 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 665 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1502 ; 1.644 ; 2.243 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1603 ; 0.969 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 90 ; 4.681 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 41 ;35.536 ;20.976 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 123 ;13.116 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;19.510 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 151 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1003 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 214 ; 0.001 ; 0.020 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): 437 ; 2.758 ; 6.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 697 ; 3.580 ; 7.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 635 ; 3.516 ; 7.500 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 803 ; 4.578 ; 7.000 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 : 4 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 397 A 428 REMARK 3 ORIGIN FOR THE GROUP (A): 19.3174 30.8401 10.9354 REMARK 3 T TENSOR REMARK 3 T11: 0.1787 T22: 0.1986 REMARK 3 T33: 0.2199 T12: 0.1802 REMARK 3 T13: -0.0132 T23: -0.0233 REMARK 3 L TENSOR REMARK 3 L11: 10.9068 L22: 3.2251 REMARK 3 L33: 4.5017 L12: -2.0744 REMARK 3 L13: 6.8488 L23: -0.6343 REMARK 3 S TENSOR REMARK 3 S11: -0.3963 S12: -0.4428 S13: 0.3229 REMARK 3 S21: 0.0035 S22: 0.0379 S23: 0.6784 REMARK 3 S31: -0.3432 S32: -0.3578 S33: 0.3584 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 429 A 483 REMARK 3 ORIGIN FOR THE GROUP (A): 38.4018 17.1271 9.1400 REMARK 3 T TENSOR REMARK 3 T11: 0.0568 T22: 0.0351 REMARK 3 T33: 0.0649 T12: -0.0072 REMARK 3 T13: 0.0035 T23: -0.0024 REMARK 3 L TENSOR REMARK 3 L11: 1.8088 L22: 0.9600 REMARK 3 L33: 2.6822 L12: -0.0062 REMARK 3 L13: 0.3309 L23: 0.6003 REMARK 3 S TENSOR REMARK 3 S11: 0.0176 S12: -0.0838 S13: -0.1243 REMARK 3 S21: -0.0476 S22: 0.0245 S23: -0.0932 REMARK 3 S31: -0.0469 S32: -0.0182 S33: -0.0422 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : G 1 G 7 REMARK 3 ORIGIN FOR THE GROUP (A): 43.9865 17.9665 19.5026 REMARK 3 T TENSOR REMARK 3 T11: 0.0372 T22: 0.1055 REMARK 3 T33: 0.1404 T12: -0.0181 REMARK 3 T13: -0.0479 T23: 0.1037 REMARK 3 L TENSOR REMARK 3 L11: 0.9560 L22: 0.4798 REMARK 3 L33: 3.2531 L12: -0.6516 REMARK 3 L13: -1.7596 L23: 1.2217 REMARK 3 S TENSOR REMARK 3 S11: -0.0121 S12: -0.1374 S13: -0.0228 REMARK 3 S21: 0.0121 S22: 0.0259 S23: -0.0497 REMARK 3 S31: 0.0103 S32: 0.2182 S33: -0.0138 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 1 F 7 REMARK 3 ORIGIN FOR THE GROUP (A): 38.8876 18.3767 20.4086 REMARK 3 T TENSOR REMARK 3 T11: 0.0809 T22: 0.0920 REMARK 3 T33: 0.0154 T12: -0.0409 REMARK 3 T13: -0.0112 T23: 0.0121 REMARK 3 L TENSOR REMARK 3 L11: 2.2969 L22: 1.1078 REMARK 3 L33: 2.2049 L12: -0.4308 REMARK 3 L13: 2.0126 L23: 0.2913 REMARK 3 S TENSOR REMARK 3 S11: 0.2112 S12: -0.1652 S13: 0.0715 REMARK 3 S21: 0.0353 S22: -0.2489 S23: -0.0695 REMARK 3 S31: 0.2099 S32: -0.3292 S33: 0.0378 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: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2WBS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-MAR-09. REMARK 100 THE PDBE ID CODE IS EBI-38944. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841, 2.0, 1.28204, REMARK 200 1.28312, 1.16967 REMARK 200 MONOCHROMATOR : SI111 CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15421 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.70 REMARK 200 RESOLUTION RANGE LOW (A) : 29.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.7 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 4.4 REMARK 200 R MERGE (I) : 0.08 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.20 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.4 REMARK 200 R MERGE FOR SHELL (I) : 0.68 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.70 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX SHARP REFMAC5 COOT REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 20.50000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.95500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.98500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.95500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.50000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.98500 REMARK 290 SMTRY3 4 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: 2260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, F, G 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 LYS A 395 REMARK 465 ARG A 396 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 440 CG CD CE NZ 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 OP2 DG F 3 O HOH F 2009 2.06 REMARK 500 REMARK 500 REMARK: NULL 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 DC G 7 C3' DC G 7 O3' -0.040 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 F 3 O5' - P - OP2 ANGL. DEV. = -6.5 DEGREES REMARK 500 DC F 7 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DG G 1 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DC G 5 C5' - C4' - C3' ANGL. DEV. = -12.9 DEGREES REMARK 500 DC G 5 O4' - C4' - C3' ANGL. DEV. = 5.0 DEGREES REMARK 500 DC G 5 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 DT G 6 C5 - C4 - O4 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT G 6 N3 - C4 - O4 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC G 7 O4' - C1' - N1 ANGL. DEV. = 2.3 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 CYS A 407 -78.45 -97.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 GLYCEROL (GOL): CRYO PROTECTANT REMARK 600 ZINC ION (ZN): ZINC FINGER MOTIF 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 A1484 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 437 SG REMARK 620 2 CYS A 432 SG 121.8 REMARK 620 3 HIS A 450 NE2 104.6 109.9 REMARK 620 4 HIS A 454 NE2 108.9 105.9 104.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1485 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 465 SG REMARK 620 2 HIS A 478 NE2 99.4 REMARK 620 3 HIS A 482 NE2 111.7 100.3 REMARK 620 4 CYS A 462 SG 121.5 109.7 111.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1486 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 407 SG REMARK 620 2 HIS A 420 NE2 102.1 REMARK 620 3 HIS A 424 NE2 110.6 85.8 REMARK 620 4 CYS A 402 SG 128.9 111.7 109.1 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 A1484 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1485 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1486 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1487 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WBU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE IN COMPLEX WITH DNA DBREF 2WBS A 395 483 UNP Q60793 KLF4_MOUSE 395 483 DBREF 2WBS F 1 7 PDB 2WBS 2WBS 1 7 DBREF 2WBS G 1 7 PDB 2WBS 2WBS 1 7 SEQRES 1 A 89 LYS ARG THR ALA THR HIS THR CYS ASP TYR ALA GLY CYS SEQRES 2 A 89 GLY LYS THR TYR THR LYS SER SER HIS LEU LYS ALA HIS SEQRES 3 A 89 LEU ARG THR HIS THR GLY GLU LYS PRO TYR HIS CYS ASP SEQRES 4 A 89 TRP ASP GLY CYS GLY TRP LYS PHE ALA ARG SER ASP GLU SEQRES 5 A 89 LEU THR ARG HIS TYR ARG LYS HIS THR GLY HIS ARG PRO SEQRES 6 A 89 PHE GLN CYS GLN LYS CYS ASP ARG ALA PHE SER ARG SER SEQRES 7 A 89 ASP HIS LEU ALA LEU HIS MET LYS ARG HIS PHE SEQRES 1 F 7 DG DA DG DG DC DG DC SEQRES 1 G 7 DG DC DG DC DC DT DC HET ZN A1484 1 HET ZN A1485 1 HET ZN A1486 1 HET GOL A1487 6 HETNAM GOL GLYCEROL HETNAM ZN ZINC ION FORMUL 4 GOL C3 H8 O3 FORMUL 5 ZN 3(ZN 2+) FORMUL 6 HOH *131(H2 O) HELIX 1 1 LYS A 413 ARG A 422 1 10 HELIX 2 2 ARG A 443 GLY A 456 1 14 HELIX 3 3 ARG A 471 MET A 479 1 9 HELIX 4 4 LYS A 480 PHE A 483 5 4 SHEET 1 AA 2 HIS A 400 THR A 401 0 SHEET 2 AA 2 THR A 410 TYR A 411 -1 O TYR A 411 N HIS A 400 SHEET 1 AB 2 TYR A 430 HIS A 431 0 SHEET 2 AB 2 LYS A 440 PHE A 441 -1 O PHE A 441 N TYR A 430 SHEET 1 AC 2 PHE A 460 GLN A 461 0 SHEET 2 AC 2 ALA A 468 PHE A 469 -1 O PHE A 469 N PHE A 460 LINK ZN ZN A1484 SG CYS A 437 1555 1555 2.31 LINK ZN ZN A1484 SG CYS A 432 1555 1555 2.21 LINK ZN ZN A1484 NE2 HIS A 450 1555 1555 2.12 LINK ZN ZN A1484 NE2 HIS A 454 1555 1555 1.97 LINK ZN ZN A1485 SG CYS A 465 1555 1555 2.33 LINK ZN ZN A1485 NE2 HIS A 478 1555 1555 2.03 LINK ZN ZN A1485 NE2 HIS A 482 1555 1555 2.10 LINK ZN ZN A1485 SG CYS A 462 1555 1555 2.24 LINK ZN ZN A1486 NE2 HIS A 420 1555 1555 2.00 LINK ZN ZN A1486 NE2 HIS A 424 1555 1555 1.93 LINK ZN ZN A1486 SG CYS A 402 1555 1555 2.20 LINK ZN ZN A1486 SG CYS A 407 1555 1555 2.29 SITE 1 AC1 4 CYS A 432 CYS A 437 HIS A 450 HIS A 454 SITE 1 AC2 4 CYS A 462 CYS A 465 HIS A 478 HIS A 482 SITE 1 AC3 4 CYS A 402 CYS A 407 HIS A 420 HIS A 424 SITE 1 AC4 4 TRP A 434 ASP A 435 LYS A 464 HOH A2079 CRYST1 41.000 45.970 73.910 90.00 90.00 90.00 P 21 21 21 4 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 0.024390 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021753 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013530 0.00000