HEADER SIGNALING PROTEIN/TRANSFERASE 28-DEC-16 5WVO TITLE CRYSTAL STRUCTURE OF DNMT1 RFTS DOMAIN IN COMPLEX WITH K18/K23 MONO- TITLE 2 UBIQUITYLATED HISTONE H3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (CYTOSINE-5)-METHYLTRANSFERASE 1; COMPND 8 CHAIN: C; COMPND 9 FRAGMENT: RFTS DOMAIN, UNP RESIDUES 351-600; COMPND 10 SYNONYM: DNMT1,CXXC-TYPE ZINC FINGER PROTEIN 9,DNA METHYLTRANSFERASE COMPND 11 HSAI,M.HSAI,MCMT; COMPND 12 EC: 2.1.1.37; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: HISTONE H3.1; COMPND 16 CHAIN: D; COMPND 17 FRAGMENT: UNP RESIDUES 2-37; COMPND 18 SYNONYM: HISTONE H3/A,HISTONE H3/B,HISTONE H3/C,HISTONE H3/D,HISTONE COMPND 19 H3/F,HISTONE H3/H,HISTONE H3/I,HISTONE H3/J,HISTONE H3/K,HISTONE COMPND 20 H3/L; COMPND 21 ENGINEERED: YES; COMPND 22 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RPS27A, UBA80, UBCEP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR SOURCE 7 PPPT4; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 1182041; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET22B; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 GENE: DNMT1, AIM, CXXC9, DNMT; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR SOURCE 18 PPPT4; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 1182041; SOURCE 20 EXPRESSION_SYSTEM_STRAIN: ROSETTA2 (DE3); SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: MODIFIED PGEX4T VECTOR; SOURCE 23 MOL_ID: 3; SOURCE 24 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 25 ORGANISM_COMMON: HUMAN; SOURCE 26 ORGANISM_TAXID: 9606; SOURCE 27 GENE: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, SOURCE 28 H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, SOURCE 29 H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ; SOURCE 30 EXPRESSION_SYSTEM: ESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR SOURCE 31 PPPT4; SOURCE 32 EXPRESSION_SYSTEM_TAXID: 1182041; SOURCE 33 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 34 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 35 EXPRESSION_SYSTEM_PLASMID: MODIFIED PGEX4T KEYWDS DNA METHYLATION, UBIQUITINATION, SIGNALING PROTEIN-TRANSFERASE KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.ISHIYAMA,A.NISHIYAMA,M.NAKANISHI,K.ARITA REVDAT 3 23-OCT-24 5WVO 1 REMARK REVDAT 2 22-NOV-23 5WVO 1 REMARK REVDAT 1 15-NOV-17 5WVO 0 JRNL AUTH S.ISHIYAMA,A.NISHIYAMA,Y.SAEKI,K.MORITSUGU,D.MORIMOTO, JRNL AUTH 2 L.YAMAGUCHI,N.ARAI,R.MATSUMURA,T.KAWAKAMI,Y.MISHIMA,H.HOJO, JRNL AUTH 3 S.SHIMAMURA,F.ISHIKAWA,S.TAJIMA,K.TANAKA,M.ARIYOSHI, JRNL AUTH 4 M.SHIRAKAWA,M.IKEGUCHI,A.KIDERA,I.SUETAKE,K.ARITA, JRNL AUTH 5 M.NAKANISHI JRNL TITL STRUCTURE OF THE DNMT1 READER MODULE COMPLEXED WITH A UNIQUE JRNL TITL 2 TWO-MONO-UBIQUITIN MARK ON HISTONE H3 REVEALS THE BASIS FOR JRNL TITL 3 DNA METHYLATION MAINTENANCE JRNL REF MOL. CELL V. 68 350 2017 JRNL REFN ISSN 1097-4164 JRNL PMID 29053958 JRNL DOI 10.1016/J.MOLCEL.2017.09.037 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 35890 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 1855 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 34.1860 - 4.6918 0.99 2773 153 0.1741 0.1889 REMARK 3 2 4.6918 - 3.7255 1.00 2692 124 0.1525 0.1874 REMARK 3 3 3.7255 - 3.2550 1.00 2642 141 0.1821 0.2276 REMARK 3 4 3.2550 - 2.9575 1.00 2641 131 0.2099 0.2481 REMARK 3 5 2.9575 - 2.7457 1.00 2634 151 0.2165 0.2823 REMARK 3 6 2.7457 - 2.5838 1.00 2612 147 0.2198 0.2452 REMARK 3 7 2.5838 - 2.4545 1.00 2597 137 0.2130 0.3036 REMARK 3 8 2.4545 - 2.3477 1.00 2585 172 0.2200 0.2814 REMARK 3 9 2.3477 - 2.2573 1.00 2606 143 0.2163 0.2199 REMARK 3 10 2.2573 - 2.1794 1.00 2598 136 0.2260 0.2982 REMARK 3 11 2.1794 - 2.1113 1.00 2598 128 0.2312 0.2896 REMARK 3 12 2.1113 - 2.0509 1.00 2580 154 0.2450 0.3164 REMARK 3 13 2.0509 - 1.9969 0.96 2477 138 0.2456 0.2723 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.019 3237 REMARK 3 ANGLE : 0.934 4378 REMARK 3 CHIRALITY : 0.063 496 REMARK 3 PLANARITY : 0.006 576 REMARK 3 DIHEDRAL : 17.912 1980 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5WVO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1300002411. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35892 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.997 REMARK 200 RESOLUTION RANGE LOW (A) : 34.181 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.70600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.600 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: 1UBQ, 3EPZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM BIS-TRIS (PH 6.0), 200MM LITHIUM REMARK 280 SULFATE MONOHYDRATE, 20% PEG 10000, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 38.45200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.45200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 34.18100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 99.38950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.18100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 99.38950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.45200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.18100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 99.38950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.45200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.18100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 99.38950 REMARK 290 SMTRY3 8 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: 6780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 PRO C 351 REMARK 465 LYS C 352 REMARK 465 GLN C 358 REMARK 465 TYR C 359 REMARK 465 LEU C 360 REMARK 465 ASP C 361 REMARK 465 ASP C 362 REMARK 465 PRO C 363 REMARK 465 ASP C 364 REMARK 465 LEU C 592 REMARK 465 GLY C 593 REMARK 465 GLN C 594 REMARK 465 ARG C 595 REMARK 465 ARG C 596 REMARK 465 ALA C 597 REMARK 465 GLN C 598 REMARK 465 ALA C 599 REMARK 465 ARG C 600 REMARK 465 ALA D 1 REMARK 465 ALA D 21 REMARK 465 THR D 22 REMARK 465 CYS D 23 REMARK 465 ALA D 24 REMARK 465 ALA D 25 REMARK 465 ARG D 26 REMARK 465 LYS D 27 REMARK 465 SER D 28 REMARK 465 ALA D 29 REMARK 465 PRO D 30 REMARK 465 ALA D 31 REMARK 465 THR D 32 REMARK 465 GLY D 33 REMARK 465 GLY D 34 REMARK 465 VAL D 35 REMARK 465 LYS D 36 REMARK 465 TRP D 37 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 63 CD CE NZ REMARK 470 ILE C 354 CG1 CD1 REMARK 470 LYS C 366 CD CE NZ REMARK 470 TYR C 367 CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS C 415 CD CE NZ REMARK 470 SER C 520 OG REMARK 470 ASP C 521 CG OD1 OD2 REMARK 470 SER C 522 OG REMARK 470 GLN C 573 CG CD OE1 NE2 REMARK 470 LEU D 20 CG CD1 CD2 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 O HOH C 852 O HOH C 883 2.00 REMARK 500 OD2 ASP C 548 NH1 ARG C 552 2.12 REMARK 500 O HOH A 127 O HOH A 153 2.13 REMARK 500 NH1 ARG A 54 O HOH A 101 2.17 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 GLN C 355 -62.82 -106.18 REMARK 500 CYS C 356 -88.98 -48.03 REMARK 500 LYS C 415 -6.20 -49.26 REMARK 500 HIS C 416 49.41 -152.56 REMARK 500 MET C 489 -107.71 -109.17 REMARK 500 ASN C 519 60.90 -150.84 REMARK 500 SER C 570 26.37 -65.85 REMARK 500 ASP C 571 17.25 -141.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS C 416 GLY C 417 148.15 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 ZN C 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 353 SG REMARK 620 2 CYS C 414 SG 104.3 REMARK 620 3 HIS C 418 ND1 115.6 83.4 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 701 DBREF 5WVO A 1 76 UNP P62979 RS27A_HUMAN 1 76 DBREF 5WVO B 1 76 UNP P62979 RS27A_HUMAN 1 76 DBREF 5WVO C 351 600 UNP P26358 DNMT1_HUMAN 351 600 DBREF 5WVO D 1 36 UNP P68431 H31_HUMAN 2 37 SEQADV 5WVO CYS A 76 UNP P62979 GLY 76 ENGINEERED MUTATION SEQADV 5WVO CYS B 76 UNP P62979 GLY 76 ENGINEERED MUTATION SEQADV 5WVO CYS D 18 UNP P68431 LYS 19 ENGINEERED MUTATION SEQADV 5WVO CYS D 23 UNP P68431 LYS 24 ENGINEERED MUTATION SEQADV 5WVO TRP D 37 UNP P68431 EXPRESSION TAG SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY CYS SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY CYS SEQRES 1 C 250 PRO LYS CYS ILE GLN CYS GLY GLN TYR LEU ASP ASP PRO SEQRES 2 C 250 ASP LEU LYS TYR GLY GLN HIS PRO PRO ASP ALA VAL ASP SEQRES 3 C 250 GLU PRO GLN MET LEU THR ASN GLU LYS LEU SER ILE PHE SEQRES 4 C 250 ASP ALA ASN GLU SER GLY PHE GLU SER TYR GLU ALA LEU SEQRES 5 C 250 PRO GLN HIS LYS LEU THR CYS PHE SER VAL TYR CYS LYS SEQRES 6 C 250 HIS GLY HIS LEU CYS PRO ILE ASP THR GLY LEU ILE GLU SEQRES 7 C 250 LYS ASN ILE GLU LEU PHE PHE SER GLY SER ALA LYS PRO SEQRES 8 C 250 ILE TYR ASP ASP ASP PRO SER LEU GLU GLY GLY VAL ASN SEQRES 9 C 250 GLY LYS ASN LEU GLY PRO ILE ASN GLU TRP TRP ILE THR SEQRES 10 C 250 GLY PHE ASP GLY GLY GLU LYS ALA LEU ILE GLY PHE SER SEQRES 11 C 250 THR SER PHE ALA GLU TYR ILE LEU MET ASP PRO SER PRO SEQRES 12 C 250 GLU TYR ALA PRO ILE PHE GLY LEU MET GLN GLU LYS ILE SEQRES 13 C 250 TYR ILE SER LYS ILE VAL VAL GLU PHE LEU GLN SER ASN SEQRES 14 C 250 SER ASP SER THR TYR GLU ASP LEU ILE ASN LYS ILE GLU SEQRES 15 C 250 THR THR VAL PRO PRO SER GLY LEU ASN LEU ASN ARG PHE SEQRES 16 C 250 THR GLU ASP SER LEU LEU ARG HIS ALA GLN PHE VAL VAL SEQRES 17 C 250 GLU GLN VAL GLU SER TYR ASP GLU ALA GLY ASP SER ASP SEQRES 18 C 250 GLU GLN PRO ILE PHE LEU THR PRO CYS MET ARG ASP LEU SEQRES 19 C 250 ILE LYS LEU ALA GLY VAL THR LEU GLY GLN ARG ARG ALA SEQRES 20 C 250 GLN ALA ARG SEQRES 1 D 37 ALA ARG THR LYS GLN THR ALA ARG LYS SER THR GLY GLY SEQRES 2 D 37 LYS ALA PRO ARG CYS GLN LEU ALA THR CYS ALA ALA ARG SEQRES 3 D 37 LYS SER ALA PRO ALA THR GLY GLY VAL LYS TRP HET ZN C 701 1 HETNAM ZN ZINC ION FORMUL 5 ZN ZN 2+ FORMUL 6 HOH *197(H2 O) HELIX 1 AA1 THR A 22 GLY A 35 1 14 HELIX 2 AA2 PRO A 37 ASP A 39 5 3 HELIX 3 AA3 THR A 55 ASN A 60 1 6 HELIX 4 AA4 THR B 22 GLY B 35 1 14 HELIX 5 AA5 PRO B 37 ASP B 39 5 3 HELIX 6 AA6 ASP C 376 THR C 382 1 7 HELIX 7 AA7 ASN C 383 SER C 387 5 5 HELIX 8 AA8 TYR C 495 ASN C 519 1 25 HELIX 9 AA9 THR C 523 THR C 534 1 12 HELIX 10 AB1 THR C 546 ARG C 552 1 7 HELIX 11 AB2 HIS C 553 ALA C 567 1 15 HELIX 12 AB3 THR C 578 GLY C 589 1 12 SHEET 1 AA1 5 THR A 12 GLU A 16 0 SHEET 2 AA1 5 GLN A 2 THR A 7 -1 N VAL A 5 O ILE A 13 SHEET 3 AA1 5 THR A 66 LEU A 71 1 O LEU A 67 N LYS A 6 SHEET 4 AA1 5 GLN A 41 PHE A 45 -1 N ARG A 42 O VAL A 70 SHEET 5 AA1 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 SHEET 1 AA2 5 THR B 12 GLU B 16 0 SHEET 2 AA2 5 GLN B 2 THR B 7 -1 N VAL B 5 O ILE B 13 SHEET 3 AA2 5 THR B 66 LEU B 71 1 O LEU B 67 N PHE B 4 SHEET 4 AA2 5 GLN B 41 PHE B 45 -1 N ARG B 42 O VAL B 70 SHEET 5 AA2 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 SHEET 1 AA3 7 VAL C 453 LEU C 458 0 SHEET 2 AA3 7 LEU C 433 LYS C 440 -1 N GLY C 437 O GLY C 455 SHEET 3 AA3 7 GLN C 404 CYS C 414 -1 N THR C 408 O SER C 438 SHEET 4 AA3 7 GLU C 485 LEU C 488 1 O ILE C 487 N HIS C 405 SHEET 5 AA3 7 LEU C 476 SER C 480 -1 N ILE C 477 O LEU C 488 SHEET 6 AA3 7 GLU C 463 THR C 467 -1 N GLU C 463 O SER C 480 SHEET 7 AA3 7 LYS D 9 LYS D 14 -1 O SER D 10 N ILE C 466 SSBOND 1 CYS B 76 CYS D 18 1555 1555 2.05 LINK SG CYS C 353 ZN ZN C 701 1555 1555 2.62 LINK SG CYS C 414 ZN ZN C 701 1555 1555 2.68 LINK ND1 HIS C 418 ZN ZN C 701 1555 1555 2.39 CISPEP 1 GLY C 459 PRO C 460 0 9.22 SITE 1 AC1 4 CYS C 353 CYS C 356 CYS C 414 HIS C 418 CRYST1 68.362 198.779 76.904 90.00 90.00 90.00 C 2 2 21 16 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 0.014628 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005031 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013003 0.00000