HEADER HYDROLASE/DNA 27-JUN-13 4LG7 TITLE CRYSTAL STRUCTURE MBD4 MBD DOMAIN IN COMPLEX WITH METHYLATED CPG DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 83-149; COMPND 5 SYNONYM: METHYL-CPG-BINDING ENDONUCLEASE 1, METHYL-CPG-BINDING COMPND 6 PROTEIN MBD4, MISMATCH-SPECIFIC DNA N-GLYCOSYLASE; COMPND 7 EC: 3.2.2.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3'); COMPND 11 CHAIN: B, C; COMPND 12 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: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-MHL; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: SYNTHETIC KEYWDS STRUCTURAL GENOMICS CONSORTIUM, SGC, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.XU,W.TEMPEL,A.K.WERNIMONT,C.BOUNTRA,C.H.ARROWSMITH,A.M.EDWARDS, AUTHOR 2 J.MIN,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 2 20-SEP-23 4LG7 1 REMARK SEQADV LINK REVDAT 1 17-JUL-13 4LG7 0 JRNL AUTH C.XU,W.TEMPEL,A.K.WERNIMONT,C.BOUNTRA,C.H.ARROWSMITH, JRNL AUTH 2 A.M.EDWARDS,J.MIN JRNL TITL CRYSTAL STRUCTURE MBD4 MBD DOMAIN IN COMPLEX WITH METHYLATED JRNL TITL 2 CPG DNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT BUSTER 2.10.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 5747 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) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.510 REMARK 3 FREE R VALUE TEST SET COUNT : 259 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.79 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.12 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1571 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2656 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1498 REMARK 3 BIN R VALUE (WORKING SET) : 0.2613 REMARK 3 BIN FREE R VALUE : 0.3506 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.65 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 73 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 484 REMARK 3 NUCLEIC ACID ATOMS : 488 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -18.62270 REMARK 3 B22 (A**2) : 8.81590 REMARK 3 B33 (A**2) : 9.80680 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.530 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.380 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1043 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1511 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 459 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 8 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 100 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1043 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 133 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 951 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.35 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.41 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 20.25 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 54.4874 24.7234 53.9133 REMARK 3 T TENSOR REMARK 3 T11: -0.1060 T22: -0.1517 REMARK 3 T33: 0.0199 T12: -0.0027 REMARK 3 T13: -0.0194 T23: -0.0022 REMARK 3 L TENSOR REMARK 3 L11: 3.0520 L22: 9.3350 REMARK 3 L33: 5.0540 L12: 1.4881 REMARK 3 L13: 0.2156 L23: 1.9713 REMARK 3 S TENSOR REMARK 3 S11: 0.0805 S12: -0.0798 S13: 0.0739 REMARK 3 S21: -0.0033 S22: -0.0382 S23: 0.2924 REMARK 3 S31: -0.1166 S32: -0.0920 S33: -0.0422 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): 58.3496 8.3352 51.5271 REMARK 3 T TENSOR REMARK 3 T11: -0.0587 T22: -0.0886 REMARK 3 T33: -0.1503 T12: 0.1014 REMARK 3 T13: 0.0615 T23: 0.0395 REMARK 3 L TENSOR REMARK 3 L11: 7.2073 L22: 5.0506 REMARK 3 L33: 11.9182 L12: 0.7329 REMARK 3 L13: 0.7155 L23: -0.9161 REMARK 3 S TENSOR REMARK 3 S11: -0.0176 S12: 0.4501 S13: 0.1713 REMARK 3 S21: -0.4478 S22: 0.3115 S23: 0.0485 REMARK 3 S31: 0.2557 S32: 0.4761 S33: -0.2939 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { C|* } REMARK 3 ORIGIN FOR THE GROUP (A): 59.5941 9.2740 51.2163 REMARK 3 T TENSOR REMARK 3 T11: 0.0835 T22: -0.2683 REMARK 3 T33: -0.1430 T12: 0.0807 REMARK 3 T13: 0.0558 T23: -0.0073 REMARK 3 L TENSOR REMARK 3 L11: 12.5544 L22: 3.2933 REMARK 3 L33: 9.2091 L12: 0.0931 REMARK 3 L13: 0.9302 L23: 0.1278 REMARK 3 S TENSOR REMARK 3 S11: 0.0917 S12: 0.3055 S13: -0.0473 REMARK 3 S21: -0.3113 S22: 0.1339 S23: -0.1046 REMARK 3 S31: 0.1766 S32: 0.1422 S33: -0.2256 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFMAC, PHENIX, COOT, MOLPROBITY SERVER REMARK 3 WERE ALSO USED DURING REFINEMENT. WE NOTE THE SMALL NUMBER OF REMARK 3 REFLECTIONS IN THE X-VALIDATION FREE SET AND A SIGNIFICANT REMARK 3 DISCREPANCY BETWEEN AVERAGE REFINED AND WILSON B-FACTORS. REMARK 4 REMARK 4 4LG7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-13. REMARK 100 THE DEPOSITION ID IS D_1000080589. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 FR-E 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 : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5780 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 41.746 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09000 REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.92100 REMARK 200 R SYM FOR SHELL (I) : 0.92100 REMARK 200 FOR SHELL : 0.900 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: PDB ENTRY 3VXX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG400, 5% MPD, 0.2 M SODIUM REMARK 280 CHLORIDE, 0.1 M HEPES. PROTEIN:DNA 1:1.2., PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z 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 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 24.68350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.10450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.68350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.10450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 GLY A 82 REMARK 465 LEU A 146 REMARK 465 SER A 147 REMARK 465 LYS A 148 REMARK 465 ARG A 149 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 84 CG CD CE NZ REMARK 470 LYS A 95 NZ REMARK 470 PHE A 99 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 114 CG CD OE1 NE2 REMARK 470 LYS A 117 CE NZ REMARK 470 LYS A 130 CG CD CE NZ REMARK 470 LYS A 137 NZ REMARK 470 GLU A 139 CG CD OE1 OE2 REMARK 470 THR A 144 OG1 CG2 REMARK 470 VAL A 145 CG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OG1 THR A 134 UNK UNX C 101 3758 2.09 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 DA B 4 O3' DA B 4 C3' 0.094 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 DC B 2 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC B 3 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DA B 4 C3' - O3' - P ANGL. DEV. = 12.7 DEGREES REMARK 500 DT B 9 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG B 11 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG C 1 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 DA C 4 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 DA C 4 C3' - O3' - P ANGL. DEV. = 10.7 DEGREES REMARK 500 DA C 5 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 5CM C 6 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 DG C 10 O4' - C1' - N9 ANGL. DEV. = -4.3 DEGREES REMARK 500 DG C 11 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DC C 12 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 4LG7 A 83 149 UNP O95243 MBD4_HUMAN 83 149 DBREF 4LG7 B 1 12 PDB 4LG7 4LG7 1 12 DBREF 4LG7 C 1 12 PDB 4LG7 4LG7 1 12 SEQADV 4LG7 GLY A 82 UNP O95243 EXPRESSION TAG SEQRES 1 A 68 GLY ARG LYS SER VAL PRO CYS GLY TRP GLU ARG VAL VAL SEQRES 2 A 68 LYS GLN ARG LEU PHE GLY LYS THR ALA GLY ARG PHE ASP SEQRES 3 A 68 VAL TYR PHE ILE SER PRO GLN GLY LEU LYS PHE ARG SER SEQRES 4 A 68 LYS SER SER LEU ALA ASN TYR LEU HIS LYS ASN GLY GLU SEQRES 5 A 68 THR SER LEU LYS PRO GLU ASP PHE ASP PHE THR VAL LEU SEQRES 6 A 68 SER LYS ARG SEQRES 1 B 12 DG DC DC DA DA 5CM DG DT DT DG DG DC SEQRES 1 C 12 DG DC DC DA DA 5CM DG DT DT DG DG DC MODRES 4LG7 5CM B 6 DC MODRES 4LG7 5CM C 6 DC HET 5CM B 6 20 HET 5CM C 6 20 HET UNX A 201 1 HET UNX A 202 1 HET UNX A 203 1 HET UNX B 101 1 HET UNX B 102 1 HET UNX B 103 1 HET UNX B 104 1 HET UNX C 101 1 HET UNX C 102 1 HET UNX C 103 1 HET UNX C 104 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM UNX UNKNOWN ATOM OR ION FORMUL 2 5CM 2(C10 H16 N3 O7 P) FORMUL 4 UNX 11(X) HELIX 1 1 SER A 120 ASN A 131 1 12 HELIX 2 2 LYS A 137 PHE A 141 5 5 SHEET 1 A 3 GLU A 91 GLN A 96 0 SHEET 2 A 3 PHE A 106 ILE A 111 -1 O TYR A 109 N VAL A 93 SHEET 3 A 3 LYS A 117 PHE A 118 -1 O PHE A 118 N PHE A 110 SSBOND 1 CYS A 88 CYS A 88 1555 2765 2.03 LINK O3' DA B 5 P 5CM B 6 1555 1555 1.60 LINK O3' 5CM B 6 P DG B 7 1555 1555 1.58 LINK O3' DA C 5 P 5CM C 6 1555 1555 1.58 LINK O3' 5CM C 6 P DG C 7 1555 1555 1.60 CRYST1 49.367 78.209 40.557 90.00 90.00 90.00 P 21 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 0.020256 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012786 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024657 0.00000