PDB Short entry for 4DK9 HEADER HYDROLASE/DNA 03-FEB-12 4DK9 TITLE CRYSTAL STRUCTURE OF MBD4 CATALYTIC DOMAIN BOUND TO ABASIC DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: COMPLEMENTARY DNA STRAND; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3'; COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: ABASIC DNA STRAND; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 4; COMPND 13 CHAIN: A; COMPND 14 FRAGMENT: CATALYTIC DOMAIN (UNP RESIDUES 426-580); COMPND 15 SYNONYM: METHYL-CPG-BINDING ENDONUCLEASE 1, METHYL-CPG-BINDING COMPND 16 PROTEIN MBD4, MISMATCH-SPECIFIC DNA N-GLYCOSYLASE; COMPND 17 EC: 3.2.2.-; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 GENE: MBD4, MED1; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) GOLD; SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PROTEIN-DNA COMPLEX, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.A.MANVILLA,E.A.TOTH,A.C.DROHAT REVDAT 4 28-FEB-24 4DK9 1 REMARK SEQADV LINK REVDAT 3 25-JUL-12 4DK9 1 JRNL REVDAT 2 16-MAY-12 4DK9 1 JRNL REVDAT 1 25-APR-12 4DK9 0 JRNL AUTH B.A.MANVILLA,A.MAITI,M.C.BEGLEY,E.A.TOTH,A.C.DROHAT JRNL TITL CRYSTAL STRUCTURE OF HUMAN METHYL-BINDING DOMAIN IV JRNL TITL 2 GLYCOSYLASE BOUND TO ABASIC DNA. JRNL REF J.MOL.BIOL. V. 420 164 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22560993 JRNL DOI 10.1016/J.JMB.2012.04.028 REMARK 2 REMARK 2 RESOLUTION. 2.76 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) : 2.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 7583 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 350 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) : 2.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.83 REMARK 3 REFLECTION IN BIN (WORKING SET) : 494 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.3620 REMARK 3 BIN FREE R VALUE SET COUNT : 22 REMARK 3 BIN FREE R VALUE : 0.3140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1162 REMARK 3 NUCLEIC ACID ATOMS : 437 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 1 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 105.3 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.64000 REMARK 3 B22 (A**2) : 2.81000 REMARK 3 B33 (A**2) : -0.17000 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): 0.948 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.362 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.302 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 34.007 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.915 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.897 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1694 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2398 ; 1.824 ; 2.262 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 139 ; 6.469 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 56 ;31.699 ;23.750 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 188 ;21.048 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;22.732 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 257 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1148 ; 0.008 ; 0.021 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): 703 ; 4.238 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1141 ; 6.114 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 991 ; 2.683 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1257 ; 4.456 ; 4.500 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 438 A 576 REMARK 3 ORIGIN FOR THE GROUP (A): -10.5629 13.1560 -15.8617 REMARK 3 T TENSOR REMARK 3 T11: 0.2498 T22: 0.2952 REMARK 3 T33: 0.2745 T12: 0.0240 REMARK 3 T13: -0.0098 T23: -0.0126 REMARK 3 L TENSOR REMARK 3 L11: 1.8493 L22: 0.3620 REMARK 3 L33: 1.5430 L12: 0.2577 REMARK 3 L13: -0.4300 L23: -0.0663 REMARK 3 S TENSOR REMARK 3 S11: 0.1787 S12: 0.0760 S13: -0.0779 REMARK 3 S21: -0.0555 S22: -0.1320 S23: 0.0684 REMARK 3 S31: -0.0780 S32: 0.1054 S33: -0.0467 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 : B 1 B 11 REMARK 3 RESIDUE RANGE : C 12 C 22 REMARK 3 ORIGIN FOR THE GROUP (A): -13.6454 32.0644 -21.9874 REMARK 3 T TENSOR REMARK 3 T11: 0.3964 T22: 0.2906 REMARK 3 T33: 0.0708 T12: -0.0527 REMARK 3 T13: -0.1164 T23: 0.1109 REMARK 3 L TENSOR REMARK 3 L11: 0.9142 L22: 2.5311 REMARK 3 L33: 1.1892 L12: -1.5238 REMARK 3 L13: 1.5435 L23: -2.0949 REMARK 3 S TENSOR REMARK 3 S11: -0.2055 S12: 0.2171 S13: -0.1225 REMARK 3 S21: 0.3369 S22: 0.2048 S23: 0.1188 REMARK 3 S31: -0.6066 S32: 0.0136 S33: 0.0008 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 RIDING REMARK 3 POSITIONS. U VALUES: WITH TLS ADDED REMARK 4 REMARK 4 4DK9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070434. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7618 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 150.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : 0.15600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.70 REMARK 200 R MERGE FOR SHELL (I) : 0.94100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M POTASSIUM ACETATE, 20% PEG 3350, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 298K 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 20.49950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.09650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.58050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.09650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.49950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.58050 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: 3520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, A 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 GLY A 424 REMARK 465 SER A 425 REMARK 465 ALA A 426 REMARK 465 LEU A 427 REMARK 465 SER A 428 REMARK 465 PRO A 429 REMARK 465 PRO A 430 REMARK 465 ARG A 431 REMARK 465 ARG A 432 REMARK 465 LYS A 433 REMARK 465 ALA A 434 REMARK 465 PHE A 435 REMARK 465 LYS A 436 REMARK 465 LYS A 437 REMARK 465 SER A 578 REMARK 465 LEU A 579 REMARK 465 SER A 580 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 442 NH1 NH2 REMARK 470 SER A 470 OG REMARK 470 LYS A 472 CD CE NZ REMARK 470 ILE A 475 CD1 REMARK 470 LYS A 480 CE NZ REMARK 470 GLU A 483 CG CD OE1 OE2 REMARK 470 LYS A 484 CE NZ REMARK 470 ARG A 497 CD NE CZ NH1 NH2 REMARK 470 LYS A 504 CG CD CE NZ REMARK 470 LEU A 506 CD2 REMARK 470 LYS A 514 CE NZ REMARK 470 LYS A 529 CE NZ REMARK 470 GLU A 575 OE1 OE2 REMARK 470 LYS A 576 CD CE NZ 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 C 19 O3' - P - OP2 ANGL. DEV. = 7.8 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 K A 601 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC C 21 OP1 REMARK 620 2 ILE A 532 O 167.0 REMARK 620 3 LEU A 534 O 86.1 83.6 REMARK 620 4 ILE A 537 O 91.9 80.2 90.0 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 K A 601 DBREF 4DK9 A 426 580 UNP O95243 MBD4_HUMAN 426 580 DBREF 4DK9 B 1 11 PDB 4DK9 4DK9 1 11 DBREF 4DK9 C 12 22 PDB 4DK9 4DK9 12 22 SEQADV 4DK9 GLY A 424 UNP O95243 EXPRESSION TAG SEQADV 4DK9 SER A 425 UNP O95243 EXPRESSION TAG SEQRES 1 B 11 DA DA DG DA DC DG DT DG DG DA DC SEQRES 1 C 11 DT DG DT DC DC DA 3DR DG DT DC DT SEQRES 1 A 157 GLY SER ALA LEU SER PRO PRO ARG ARG LYS ALA PHE LYS SEQRES 2 A 157 LYS TRP THR PRO PRO ARG SER PRO PHE ASN LEU VAL GLN SEQRES 3 A 157 GLU THR LEU PHE HIS ASP PRO TRP LYS LEU LEU ILE ALA SEQRES 4 A 157 THR ILE PHE LEU ASN ARG THR SER GLY LYS MET ALA ILE SEQRES 5 A 157 PRO VAL LEU TRP LYS PHE LEU GLU LYS TYR PRO SER ALA SEQRES 6 A 157 GLU VAL ALA ARG THR ALA ASP TRP ARG ASP VAL SER GLU SEQRES 7 A 157 LEU LEU LYS PRO LEU GLY LEU TYR ASP LEU ARG ALA LYS SEQRES 8 A 157 THR ILE VAL LYS PHE SER ASP GLU TYR LEU THR LYS GLN SEQRES 9 A 157 TRP LYS TYR PRO ILE GLU LEU HIS GLY ILE GLY LYS TYR SEQRES 10 A 157 GLY ASN ASP SER TYR ARG ILE PHE CYS VAL ASN GLU TRP SEQRES 11 A 157 LYS GLN VAL HIS PRO GLU ASP HIS LYS LEU ASN LYS TYR SEQRES 12 A 157 HIS ASP TRP LEU TRP GLU ASN HIS GLU LYS LEU SER LEU SEQRES 13 A 157 SER HET 3DR C 18 11 HET K A 601 1 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM K POTASSIUM ION HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 2 3DR C5 H11 O6 P FORMUL 4 K K 1+ FORMUL 5 HOH *(H2 O) HELIX 1 1 VAL A 448 PHE A 453 1 6 HELIX 2 2 ASP A 455 LEU A 466 1 12 HELIX 3 3 SER A 470 TYR A 485 1 16 HELIX 4 4 SER A 487 ARG A 492 1 6 HELIX 5 5 ASP A 495 LYS A 504 1 10 HELIX 6 6 LEU A 508 LYS A 526 1 19 HELIX 7 7 TYR A 530 LEU A 534 5 5 HELIX 8 8 GLY A 538 CYS A 549 1 12 HELIX 9 9 GLU A 552 VAL A 556 5 5 HELIX 10 10 ASP A 560 HIS A 574 1 15 LINK O3' DA C 17 P 3DR C 18 1555 1555 1.58 LINK O3' 3DR C 18 P DG C 19 1555 1555 1.60 LINK OP1 DC C 21 K K A 601 1555 1555 2.78 LINK O ILE A 532 K K A 601 1555 1555 2.74 LINK O LEU A 534 K K A 601 1555 1555 2.61 LINK O ILE A 537 K K A 601 1555 1555 2.65 CISPEP 1 LYS A 504 PRO A 505 0 8.52 SITE 1 AC1 4 ILE A 532 LEU A 534 ILE A 537 DC C 21 CRYST1 40.999 55.161 122.193 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 0.024391 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018129 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008184 0.00000