HEADER HYDROLASE/DNA 10-JUL-15 5CHZ TITLE STRUCTURE OF WILD-TYPE HUMAN MBD4 BOUND TO A G:T MISMATCH COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 426-580; COMPND 5 SYNONYM: METHYL-CPG-BINDING ENDONUCLEASE 1,METHYL-CPG-BINDING PROTEIN COMPND 6 MBD4,MISMATCH-SPECIFIC DNA N-GLYCOSYLASE; COMPND 7 EC: 3.2.2.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 7-MER DNA; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 12-MER DNA(G); COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: 5-MER DNA; COMPND 19 CHAIN: B; COMPND 20 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: MBD4, MED1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630 KEYWDS HMBD4, DNA GLYCOSYLASE, G:T MISMATCH, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.OUZON-SHUBEITA,Y.-L.LIN,S.LEE REVDAT 4 27-SEP-23 5CHZ 1 LINK REVDAT 3 18-DEC-19 5CHZ 1 REMARK REVDAT 2 27-SEP-17 5CHZ 1 REMARK REVDAT 1 20-JUL-16 5CHZ 0 JRNL AUTH H.OUZON-SHUBEITA,Y.-L.LIN,S.LEE JRNL TITL STRUCTURE OF WILD-TYPE HUMAN MBD4 BOUND TO A G:T MISMATCH JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 19653 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1067 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) : 1.83 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1271 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.2030 REMARK 3 BIN FREE R VALUE SET COUNT : 79 REMARK 3 BIN FREE R VALUE : 0.2440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1196 REMARK 3 NUCLEIC ACID ATOMS : 488 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 156 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.35000 REMARK 3 B22 (A**2) : 0.09000 REMARK 3 B33 (A**2) : -0.43000 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): 0.128 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.121 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.077 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.480 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1783 ; 0.017 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): 1434 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2519 ; 1.766 ; 1.707 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3322 ; 1.055 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 139 ; 5.629 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 60 ;32.242 ;23.500 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 213 ;15.573 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;24.644 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 245 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1643 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 430 ; 0.002 ; 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): 559 ; 2.050 ; 2.094 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 558 ; 2.022 ; 2.087 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 697 ; 2.804 ; 3.121 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 698 ; 2.802 ; 3.129 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1224 ; 3.724 ; 2.877 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1223 ; 3.725 ; 2.877 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1822 ; 5.288 ; 4.233 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2362 ; 6.982 ;22.862 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2363 ; 6.981 ;22.867 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 REMARK 4 REMARK 4 5CHZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211604. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97648 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20686 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 38.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.54400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.150 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4OFA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% ETHYLENE GLYCOL, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 20.94300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.26100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.43750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.26100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.94300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.43750 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D, B 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 MET A 389 REMARK 465 GLY A 390 REMARK 465 SER A 391 REMARK 465 SER A 392 REMARK 465 HIS A 393 REMARK 465 HIS A 394 REMARK 465 HIS A 395 REMARK 465 HIS A 396 REMARK 465 HIS A 397 REMARK 465 HIS A 398 REMARK 465 SER A 399 REMARK 465 SER A 400 REMARK 465 GLY A 401 REMARK 465 LEU A 402 REMARK 465 VAL A 403 REMARK 465 PRO A 404 REMARK 465 ARG A 405 REMARK 465 GLY A 406 REMARK 465 SER A 407 REMARK 465 HIS A 408 REMARK 465 MET A 409 REMARK 465 ALA A 410 REMARK 465 SER A 411 REMARK 465 MET A 412 REMARK 465 THR A 413 REMARK 465 GLY A 414 REMARK 465 GLY A 415 REMARK 465 GLN A 416 REMARK 465 GLN A 417 REMARK 465 MET A 418 REMARK 465 GLY A 419 REMARK 465 ARG A 420 REMARK 465 GLY A 421 REMARK 465 SER A 422 REMARK 465 GLU A 423 REMARK 465 PHE A 424 REMARK 465 MET 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 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 NE2 HIS A 574 O HOH A 701 2.06 REMARK 500 OP1 DG D 12 O HOH D 101 2.18 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 DG B 8 C6 DG B 8 N1 -0.089 REMARK 500 DG B 8 N9 DG B 8 C4 -0.053 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 ARG A 468 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 512 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASP A 568 CB - CG - OD1 ANGL. DEV. = 7.4 DEGREES REMARK 500 DC C 2 O5' - P - OP1 ANGL. DEV. = -6.7 DEGREES REMARK 500 DG B 8 OP1 - P - OP2 ANGL. DEV. = -18.2 DEGREES REMARK 500 DG B 8 O5' - P - OP2 ANGL. DEV. = -12.1 DEGREES REMARK 500 DG B 8 C2 - N3 - C4 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG B 8 N3 - C4 - C5 ANGL. DEV. = -5.7 DEGREES REMARK 500 DG B 8 C5 - C6 - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 DG B 8 C4 - C5 - N7 ANGL. DEV. = -2.4 DEGREES REMARK 500 DG B 8 N7 - C8 - N9 ANGL. DEV. = -3.2 DEGREES REMARK 500 DG B 8 C8 - N9 - C4 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG B 8 N3 - C4 - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 DG B 8 C6 - C5 - N7 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG B 8 C5 - C6 - O6 ANGL. DEV. = -8.4 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 ASN A 551 58.45 -94.10 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 MG A 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 532 O REMARK 620 2 LEU A 534 O 96.7 REMARK 620 3 ILE A 537 O 94.8 96.4 REMARK 620 4 DA B 10 OP1 173.1 90.2 84.3 REMARK 620 5 HOH B 103 O 91.4 170.7 87.4 81.8 REMARK 620 6 HOH B 117 O 98.9 92.8 162.4 80.7 81.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OFA RELATED DB: PDB REMARK 900 RELATED ID: 4OFE RELATED DB: PDB REMARK 900 RELATED ID: 4OFH RELATED DB: PDB DBREF 5CHZ A 426 580 UNP O95243 MBD4_HUMAN 426 580 DBREF 5CHZ C 1 7 PDB 5CHZ 5CHZ 1 7 DBREF 5CHZ D 1 12 PDB 5CHZ 5CHZ 1 12 DBREF 5CHZ B 8 12 PDB 5CHZ 5CHZ 8 12 SEQADV 5CHZ MET A 389 UNP O95243 INITIATING METHIONINE SEQADV 5CHZ GLY A 390 UNP O95243 EXPRESSION TAG SEQADV 5CHZ SER A 391 UNP O95243 EXPRESSION TAG SEQADV 5CHZ SER A 392 UNP O95243 EXPRESSION TAG SEQADV 5CHZ HIS A 393 UNP O95243 EXPRESSION TAG SEQADV 5CHZ HIS A 394 UNP O95243 EXPRESSION TAG SEQADV 5CHZ HIS A 395 UNP O95243 EXPRESSION TAG SEQADV 5CHZ HIS A 396 UNP O95243 EXPRESSION TAG SEQADV 5CHZ HIS A 397 UNP O95243 EXPRESSION TAG SEQADV 5CHZ HIS A 398 UNP O95243 EXPRESSION TAG SEQADV 5CHZ SER A 399 UNP O95243 EXPRESSION TAG SEQADV 5CHZ SER A 400 UNP O95243 EXPRESSION TAG SEQADV 5CHZ GLY A 401 UNP O95243 EXPRESSION TAG SEQADV 5CHZ LEU A 402 UNP O95243 EXPRESSION TAG SEQADV 5CHZ VAL A 403 UNP O95243 EXPRESSION TAG SEQADV 5CHZ PRO A 404 UNP O95243 EXPRESSION TAG SEQADV 5CHZ ARG A 405 UNP O95243 EXPRESSION TAG SEQADV 5CHZ GLY A 406 UNP O95243 EXPRESSION TAG SEQADV 5CHZ SER A 407 UNP O95243 EXPRESSION TAG SEQADV 5CHZ HIS A 408 UNP O95243 EXPRESSION TAG SEQADV 5CHZ MET A 409 UNP O95243 EXPRESSION TAG SEQADV 5CHZ ALA A 410 UNP O95243 EXPRESSION TAG SEQADV 5CHZ SER A 411 UNP O95243 EXPRESSION TAG SEQADV 5CHZ MET A 412 UNP O95243 EXPRESSION TAG SEQADV 5CHZ THR A 413 UNP O95243 EXPRESSION TAG SEQADV 5CHZ GLY A 414 UNP O95243 EXPRESSION TAG SEQADV 5CHZ GLY A 415 UNP O95243 EXPRESSION TAG SEQADV 5CHZ GLN A 416 UNP O95243 EXPRESSION TAG SEQADV 5CHZ GLN A 417 UNP O95243 EXPRESSION TAG SEQADV 5CHZ MET A 418 UNP O95243 EXPRESSION TAG SEQADV 5CHZ GLY A 419 UNP O95243 EXPRESSION TAG SEQADV 5CHZ ARG A 420 UNP O95243 EXPRESSION TAG SEQADV 5CHZ GLY A 421 UNP O95243 EXPRESSION TAG SEQADV 5CHZ SER A 422 UNP O95243 EXPRESSION TAG SEQADV 5CHZ GLU A 423 UNP O95243 EXPRESSION TAG SEQADV 5CHZ PHE A 424 UNP O95243 EXPRESSION TAG SEQADV 5CHZ MET A 425 UNP O95243 EXPRESSION TAG SEQRES 1 A 192 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 192 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET THR GLY SEQRES 3 A 192 GLY GLN GLN MET GLY ARG GLY SER GLU PHE MET ALA LEU SEQRES 4 A 192 SER PRO PRO ARG ARG LYS ALA PHE LYS LYS TRP THR PRO SEQRES 5 A 192 PRO ARG SER PRO PHE ASN LEU VAL GLN GLU THR LEU PHE SEQRES 6 A 192 HIS ASP PRO TRP LYS LEU LEU ILE ALA THR ILE PHE LEU SEQRES 7 A 192 ASN ARG THR SER GLY LYS MET ALA ILE PRO VAL LEU TRP SEQRES 8 A 192 LYS PHE LEU GLU LYS TYR PRO SER ALA GLU VAL ALA ARG SEQRES 9 A 192 THR ALA ASP TRP ARG ASP VAL SER GLU LEU LEU LYS PRO SEQRES 10 A 192 LEU GLY LEU TYR ASP LEU ARG ALA LYS THR ILE VAL LYS SEQRES 11 A 192 PHE SER ASP GLU TYR LEU THR LYS GLN TRP LYS TYR PRO SEQRES 12 A 192 ILE GLU LEU HIS GLY ILE GLY LYS TYR GLY ASN ASP SER SEQRES 13 A 192 TYR ARG ILE PHE CYS VAL ASN GLU TRP LYS GLN VAL HIS SEQRES 14 A 192 PRO GLU ASP HIS LYS LEU ASN LYS TYR HIS ASP TRP LEU SEQRES 15 A 192 TRP GLU ASN HIS GLU LYS LEU SER LEU SER SEQRES 1 C 7 DC DC DA DG DC DG DT SEQRES 1 D 12 DG DC DT DG DC DG DC DG DC DT DG DG SEQRES 1 B 5 DG DC DA DG DC HET MG A 601 1 HETNAM MG MAGNESIUM ION FORMUL 5 MG MG 2+ FORMUL 6 HOH *156(H2 O) HELIX 1 AA1 VAL A 448 PHE A 453 1 6 HELIX 2 AA2 ASP A 455 LEU A 466 1 12 HELIX 3 AA3 SER A 470 TYR A 485 1 16 HELIX 4 AA4 SER A 487 ARG A 492 1 6 HELIX 5 AA5 ASP A 495 LYS A 504 1 10 HELIX 6 AA6 PRO A 505 GLY A 507 5 3 HELIX 7 AA7 LEU A 508 LYS A 526 1 19 HELIX 8 AA8 TYR A 530 LEU A 534 5 5 HELIX 9 AA9 GLY A 538 CYS A 549 1 12 HELIX 10 AB1 GLU A 552 VAL A 556 5 5 HELIX 11 AB2 ASP A 560 HIS A 574 1 15 LINK O ILE A 532 MG MG A 601 1555 1555 2.32 LINK O LEU A 534 MG MG A 601 1555 1555 2.29 LINK O ILE A 537 MG MG A 601 1555 1555 2.37 LINK MG MG A 601 OP1 DA B 10 1555 1555 2.68 LINK MG MG A 601 O HOH B 103 1555 1555 2.56 LINK MG MG A 601 O HOH B 117 1555 1555 2.45 SITE 1 AC1 6 ILE A 532 LEU A 534 ILE A 537 DA B 10 SITE 2 AC1 6 HOH B 103 HOH B 117 CRYST1 41.886 54.875 104.522 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 0.023874 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018223 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009567 0.00000