PDB Short entry for 4E9E HEADER HYDROLASE 21-MAR-12 4E9E TITLE STRUCTURE OF THE GLYCOSYLASE DOMAIN OF MBD4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GLYCOSYLASE DOMAIN OF MBD4 (RESIDUES 426-580); 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 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET29B KEYWDS HHH DNA GLYCOSYLASE SUPERFAMILY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.MORERA,A.VIGOUROUX REVDAT 3 13-SEP-23 4E9E 1 SEQADV REVDAT 2 07-NOV-12 4E9E 1 JRNL REVDAT 1 08-AUG-12 4E9E 0 JRNL AUTH S.MORERA,I.GRIN,A.VIGOUROUX,S.COUVE,V.HENRIOT,M.SAPARBAEV, JRNL AUTH 2 A.A.ISHCHENKO JRNL TITL BIOCHEMICAL AND STRUCTURAL CHARACTERIZATION OF THE JRNL TITL 2 GLYCOSYLASE DOMAIN OF MBD4 BOUND TO THYMINE AND JRNL TITL 3 5-HYDROXYMETHYURACIL-CONTAINING DNA. JRNL REF NUCLEIC ACIDS RES. V. 40 9917 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22848106 JRNL DOI 10.1093/NAR/GKS714 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 13467 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 674 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 : 7 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.05 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.81 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2164 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2466 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2056 REMARK 3 BIN R VALUE (WORKING SET) : 0.2468 REMARK 3 BIN FREE R VALUE : 0.2433 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.99 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 108 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 : 1197 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 75 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.08730 REMARK 3 B22 (A**2) : -7.08730 REMARK 3 B33 (A**2) : 14.17450 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) : 0.252 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) : 0.146 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 : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.899 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1240 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1686 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 420 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 27 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 172 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1240 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 149 ; 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 : 1472 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.93 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.91 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.83 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4E9E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000071334. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-11 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 : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13475 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 40.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.77000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 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 3IHO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 100 MM TRIS-HCL AND 0.2 REMARK 280 M MGCL2, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.48500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.37403 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.85333 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 40.48500 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 23.37403 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 24.85333 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 40.48500 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 23.37403 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 24.85333 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.74805 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 49.70667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 46.74805 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 49.70667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 46.74805 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 49.70667 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET 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 LEU A 577 REMARK 465 SER A 578 REMARK 465 LEU A 579 REMARK 465 SER A 580 REMARK 465 HIS A 581 REMARK 465 HIS A 582 REMARK 465 HIS A 583 REMARK 465 HIS A 584 REMARK 465 HIS A 585 REMARK 465 HIS A 586 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 GLN A 527 58.02 -99.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IHO RELATED DB: PDB REMARK 900 RELATED ID: 4E9F RELATED DB: PDB REMARK 900 RELATED ID: 4E9G RELATED DB: PDB REMARK 900 RELATED ID: 4E9H RELATED DB: PDB REMARK 900 RELATED ID: 4EA4 RELATED DB: PDB REMARK 900 RELATED ID: 4EAB RELATED DB: PDB DBREF 4E9E A 427 580 UNP O95243 MBD4_HUMAN 427 580 SEQADV 4E9E MET A 426 UNP O95243 EXPRESSION TAG SEQADV 4E9E HIS A 581 UNP O95243 EXPRESSION TAG SEQADV 4E9E HIS A 582 UNP O95243 EXPRESSION TAG SEQADV 4E9E HIS A 583 UNP O95243 EXPRESSION TAG SEQADV 4E9E HIS A 584 UNP O95243 EXPRESSION TAG SEQADV 4E9E HIS A 585 UNP O95243 EXPRESSION TAG SEQADV 4E9E HIS A 586 UNP O95243 EXPRESSION TAG SEQRES 1 A 161 MET LEU SER PRO PRO ARG ARG LYS ALA PHE LYS LYS TRP SEQRES 2 A 161 THR PRO PRO ARG SER PRO PHE ASN LEU VAL GLN GLU THR SEQRES 3 A 161 LEU PHE HIS ASP PRO TRP LYS LEU LEU ILE ALA THR ILE SEQRES 4 A 161 PHE LEU ASN ARG THR SER GLY LYS MET ALA ILE PRO VAL SEQRES 5 A 161 LEU TRP LYS PHE LEU GLU LYS TYR PRO SER ALA GLU VAL SEQRES 6 A 161 ALA ARG THR ALA ASP TRP ARG ASP VAL SER GLU LEU LEU SEQRES 7 A 161 LYS PRO LEU GLY LEU TYR ASP LEU ARG ALA LYS THR ILE SEQRES 8 A 161 VAL LYS PHE SER ASP GLU TYR LEU THR LYS GLN TRP LYS SEQRES 9 A 161 TYR PRO ILE GLU LEU HIS GLY ILE GLY LYS TYR GLY ASN SEQRES 10 A 161 ASP SER TYR ARG ILE PHE CYS VAL ASN GLU TRP LYS GLN SEQRES 11 A 161 VAL HIS PRO GLU ASP HIS LYS LEU ASN LYS TYR HIS ASP SEQRES 12 A 161 TRP LEU TRP GLU ASN HIS GLU LYS LEU SER LEU SER HIS SEQRES 13 A 161 HIS HIS HIS HIS HIS FORMUL 2 HOH *75(H2 O) HELIX 1 1 LEU A 447 PHE A 453 1 7 HELIX 2 2 ASP A 455 ASN A 467 1 13 HELIX 3 3 SER A 470 TYR A 485 1 16 HELIX 4 4 SER A 487 THR A 493 1 7 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 CISPEP 1 LYS A 504 PRO A 505 0 3.06 CRYST1 80.970 80.970 74.560 90.00 90.00 120.00 H 3 9 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 0.012350 0.007130 0.000000 0.00000 SCALE2 0.000000 0.014261 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013412 0.00000