HEADER PROTEIN BINDING/TRANSFERASE 14-SEP-17 5YDR TITLE STRUCTURE OF DNMT1 RFTS DOMAIN IN COMPLEX WITH UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYUBIQUITIN-B; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: UNP RESIDUES 1-73; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (CYTOSINE-5)-METHYLTRANSFERASE 1; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: RFTS DOMAIN, UNP RESIDUES 351-599; 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UBB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: DNMT1, AIM, CXXC9, DNMT; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA METHYLATION, PROTEIN BINDING, PROTEIN BINDING-TRANSFERASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.QIAN REVDAT 3 22-NOV-23 5YDR 1 REMARK REVDAT 2 18-APR-18 5YDR 1 JRNL REVDAT 1 21-FEB-18 5YDR 0 JRNL AUTH T.LI,L.WANG,Y.DU,S.XIE,X.YANG,F.LIAN,Z.ZHOU,C.QIAN JRNL TITL STRUCTURAL AND MECHANISTIC INSIGHTS INTO UHRF1-MEDIATED JRNL TITL 2 DNMT1 ACTIVATION IN THE MAINTENANCE DNA METHYLATION. JRNL REF NUCLEIC ACIDS RES. V. 46 3218 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 29471350 JRNL DOI 10.1093/NAR/GKY104 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_2067 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) : 44.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 79112 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3874 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 44.7804 - 6.0779 0.99 2724 88 0.1690 0.1525 REMARK 3 2 6.0779 - 4.8260 1.00 2718 142 0.1759 0.2098 REMARK 3 3 4.8260 - 4.2165 1.00 2714 144 0.1440 0.1588 REMARK 3 4 4.2165 - 3.8312 1.00 2681 145 0.1619 0.2628 REMARK 3 5 3.8312 - 3.5567 0.99 2703 134 0.1832 0.2110 REMARK 3 6 3.5567 - 3.3471 1.00 2727 124 0.2011 0.2622 REMARK 3 7 3.3471 - 3.1795 1.00 2685 144 0.2122 0.2310 REMARK 3 8 3.1795 - 3.0411 1.00 2704 129 0.2293 0.2716 REMARK 3 9 3.0411 - 2.9241 1.00 2687 180 0.2297 0.2586 REMARK 3 10 2.9241 - 2.8232 1.00 2666 166 0.2296 0.2593 REMARK 3 11 2.8232 - 2.7349 0.99 2682 137 0.2285 0.2321 REMARK 3 12 2.7349 - 2.6568 1.00 2720 136 0.2231 0.2364 REMARK 3 13 2.6568 - 2.5868 0.99 2637 152 0.2150 0.2399 REMARK 3 14 2.5868 - 2.5237 0.99 2719 118 0.2286 0.2592 REMARK 3 15 2.5237 - 2.4664 1.00 2700 158 0.2273 0.2641 REMARK 3 16 2.4664 - 2.4139 0.99 2714 84 0.2273 0.3014 REMARK 3 17 2.4139 - 2.3656 1.00 2713 144 0.2186 0.2508 REMARK 3 18 2.3656 - 2.3210 0.98 2736 110 0.2270 0.2891 REMARK 3 19 2.3210 - 2.2795 1.00 2611 168 0.2177 0.2606 REMARK 3 20 2.2795 - 2.2409 0.98 2621 176 0.2194 0.2571 REMARK 3 21 2.2409 - 2.2047 1.00 2683 144 0.2247 0.2268 REMARK 3 22 2.2047 - 2.1708 0.99 2669 136 0.2089 0.2600 REMARK 3 23 2.1708 - 2.1389 0.98 2688 101 0.2184 0.2649 REMARK 3 24 2.1389 - 2.1088 1.00 2667 171 0.2213 0.2257 REMARK 3 25 2.1088 - 2.0803 0.97 2666 138 0.2284 0.2363 REMARK 3 26 2.0803 - 2.0532 1.00 2705 110 0.2372 0.2754 REMARK 3 27 2.0532 - 2.0276 0.99 2662 143 0.2552 0.2955 REMARK 3 28 2.0276 - 2.0032 0.97 2636 152 0.2549 0.3293 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) : 23.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.02 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 : 0.009 3165 REMARK 3 ANGLE : 1.415 4296 REMARK 3 CHIRALITY : 0.062 487 REMARK 3 PLANARITY : 0.010 562 REMARK 3 DIHEDRAL : 10.471 3064 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: THE STRUCTURE FACTOR FILE CONTAINS REMARK 3 FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 5YDR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1300005100. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 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 : 79146 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.7000 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) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.47800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHENIX REMARK 200 STARTING MODEL: 3AV4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM TRIS-HCL, 200MM SODIUM ACETATE, REMARK 280 25% PEG 4000, PH 8.0, EVAPORATION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 40.68333 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 20.34167 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 30.51250 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 10.17083 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 50.85417 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: 3560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 ALA D -1 REMARK 465 LEU D 73 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 48 CE NZ REMARK 470 LYS A 63 CD CE NZ REMARK 470 LYS B 366 CD CE NZ REMARK 470 GLU B 393 CG CD OE1 OE2 REMARK 470 GLU B 400 CG CD OE1 OE2 REMARK 470 GLU B 494 CD OE1 OE2 REMARK 470 GLU B 525 CD OE1 OE2 REMARK 470 LYS B 586 CD CE NZ REMARK 470 HIS D 0 CG ND1 CD2 CE1 NE2 REMARK 470 GLU D 16 CD OE1 OE2 REMARK 470 GLU D 24 CG CD OE1 OE2 REMARK 470 ASN D 25 CG OD1 ND2 REMARK 470 LYS D 29 CE NZ REMARK 470 THR D 55 CB OG1 CG2 REMARK 470 GLN D 62 OE1 NE2 REMARK 470 LYS D 63 CG CD CE NZ REMARK 470 ARG D 72 CG CD NE CZ NH1 NH2 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 PRO B 351 C - N - CA ANGL. DEV. = 10.8 DEGREES REMARK 500 TYR B 413 CB - CG - CD2 ANGL. DEV. = -9.3 DEGREES REMARK 500 TYR B 413 CB - CG - CD1 ANGL. DEV. = 4.0 DEGREES REMARK 500 PHE B 434 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 PHE B 435 CB - CG - CD2 ANGL. DEV. = -9.4 DEGREES REMARK 500 PHE B 435 CB - CG - CD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 TYR B 486 CB - CG - CD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 TYR B 507 CB - CG - CD2 ANGL. DEV. = -6.0 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 GLU B 393 8.84 -69.62 REMARK 500 PHE B 469 48.47 -92.23 REMARK 500 MET B 489 -106.68 -109.37 REMARK 500 ASP B 571 99.87 -52.80 REMARK 500 ILE B 575 -63.59 -124.12 REMARK 500 PHE B 576 -122.24 51.76 REMARK 500 LEU B 577 58.65 -110.24 REMARK 500 GLU D 64 4.75 56.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR B 413 0.09 SIDE CHAIN REMARK 500 PHE B 434 0.06 SIDE CHAIN REMARK 500 PHE B 435 0.09 SIDE CHAIN REMARK 500 TYR B 486 0.07 SIDE CHAIN REMARK 500 TYR B 507 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 902 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH B 903 DISTANCE = 6.44 ANGSTROMS 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 B 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 353 SG REMARK 620 2 CYS B 356 SG 106.2 REMARK 620 3 CYS B 414 SG 118.7 122.2 REMARK 620 4 HIS B 418 ND1 102.0 111.2 93.8 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 PO4 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 602 DBREF 5YDR A 1 73 UNP J3QS39 J3QS39_HUMAN 1 73 DBREF 5YDR B 351 599 UNP P26358 DNMT1_HUMAN 351 599 DBREF 5YDR D 1 73 UNP J3QS39 J3QS39_HUMAN 1 73 SEQADV 5YDR ALA A -1 UNP J3QS39 EXPRESSION TAG SEQADV 5YDR HIS A 0 UNP J3QS39 EXPRESSION TAG SEQADV 5YDR MET B 350 UNP P26358 EXPRESSION TAG SEQADV 5YDR ALA D -1 UNP J3QS39 EXPRESSION TAG SEQADV 5YDR HIS D 0 UNP J3QS39 EXPRESSION TAG SEQRES 1 A 75 ALA HIS MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS SEQRES 2 A 75 THR ILE THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU SEQRES 3 A 75 ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO SEQRES 4 A 75 PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU SEQRES 5 A 75 GLU ASP GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS SEQRES 6 A 75 GLU SER THR LEU HIS LEU VAL LEU ARG LEU SEQRES 1 B 250 MET PRO LYS CYS ILE GLN CYS GLY GLN TYR LEU ASP ASP SEQRES 2 B 250 PRO ASP LEU LYS TYR GLY GLN HIS PRO PRO ASP ALA VAL SEQRES 3 B 250 ASP GLU PRO GLN MET LEU THR ASN GLU LYS LEU SER ILE SEQRES 4 B 250 PHE ASP ALA ASN GLU SER GLY PHE GLU SER TYR GLU ALA SEQRES 5 B 250 LEU PRO GLN HIS LYS LEU THR CYS PHE SER VAL TYR CYS SEQRES 6 B 250 LYS HIS GLY HIS LEU CYS PRO ILE ASP THR GLY LEU ILE SEQRES 7 B 250 GLU LYS ASN ILE GLU LEU PHE PHE SER GLY SER ALA LYS SEQRES 8 B 250 PRO ILE TYR ASP ASP ASP PRO SER LEU GLU GLY GLY VAL SEQRES 9 B 250 ASN GLY LYS ASN LEU GLY PRO ILE ASN GLU TRP TRP ILE SEQRES 10 B 250 THR GLY PHE ASP GLY GLY GLU LYS ALA LEU ILE GLY PHE SEQRES 11 B 250 SER THR SER PHE ALA GLU TYR ILE LEU MET ASP PRO SER SEQRES 12 B 250 PRO GLU TYR ALA PRO ILE PHE GLY LEU MET GLN GLU LYS SEQRES 13 B 250 ILE TYR ILE SER LYS ILE VAL VAL GLU PHE LEU GLN SER SEQRES 14 B 250 ASN SER ASP SER THR TYR GLU ASP LEU ILE ASN LYS ILE SEQRES 15 B 250 GLU THR THR VAL PRO PRO SER GLY LEU ASN LEU ASN ARG SEQRES 16 B 250 PHE THR GLU ASP SER LEU LEU ARG HIS ALA GLN PHE VAL SEQRES 17 B 250 VAL GLU GLN VAL GLU SER TYR ASP GLU ALA GLY ASP SER SEQRES 18 B 250 ASP GLU GLN PRO ILE PHE LEU THR PRO CYS MET ARG ASP SEQRES 19 B 250 LEU ILE LYS LEU ALA GLY VAL THR LEU GLY GLN ARG ARG SEQRES 20 B 250 ALA GLN ALA SEQRES 1 D 75 ALA HIS MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS SEQRES 2 D 75 THR ILE THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU SEQRES 3 D 75 ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO SEQRES 4 D 75 PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU SEQRES 5 D 75 GLU ASP GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS SEQRES 6 D 75 GLU SER THR LEU HIS LEU VAL LEU ARG LEU HET PO4 A 101 5 HET ZN B 601 1 HET PO4 B 602 5 HETNAM PO4 PHOSPHATE ION HETNAM ZN ZINC ION FORMUL 4 PO4 2(O4 P 3-) FORMUL 5 ZN ZN 2+ FORMUL 7 HOH *235(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 ASP B 362 LYS B 366 5 5 HELIX 4 AA4 ASP B 376 THR B 382 1 7 HELIX 5 AA5 ASN B 383 SER B 387 5 5 HELIX 6 AA6 TYR B 495 MET B 502 1 8 HELIX 7 AA7 MET B 502 ASN B 519 1 18 HELIX 8 AA8 THR B 523 THR B 534 1 12 HELIX 9 AA9 THR B 546 HIS B 553 1 8 HELIX 10 AB1 HIS B 553 GLY B 568 1 16 HELIX 11 AB2 THR B 578 GLY B 589 1 12 HELIX 12 AB3 THR B 591 GLN B 598 1 8 HELIX 13 AB4 THR D 22 GLY D 35 1 14 HELIX 14 AB5 PRO D 37 ASP D 39 5 3 HELIX 15 AB6 THR D 55 ASN D 60 5 6 SHEET 1 AA1 5 THR A 12 VAL A 17 0 SHEET 2 AA1 5 MET A 1 LYS A 6 -1 N MET A 1 O VAL A 17 SHEET 3 AA1 5 THR A 66 LEU A 71 1 O LEU A 67 N PHE A 4 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 6 VAL B 453 LEU B 458 0 SHEET 2 AA2 6 LEU B 433 LYS B 440 -1 N PHE B 435 O LEU B 458 SHEET 3 AA2 6 GLN B 404 CYS B 414 -1 N TYR B 413 O PHE B 434 SHEET 4 AA2 6 GLU B 485 LEU B 488 1 O ILE B 487 N HIS B 405 SHEET 5 AA2 6 LEU B 476 SER B 480 -1 N PHE B 479 O TYR B 486 SHEET 6 AA2 6 GLU B 463 THR B 467 -1 N THR B 467 O LEU B 476 SHEET 1 AA3 5 THR D 12 VAL D 17 0 SHEET 2 AA3 5 MET D 1 THR D 7 -1 N MET D 1 O VAL D 17 SHEET 3 AA3 5 THR D 66 LEU D 71 1 O LEU D 67 N PHE D 4 SHEET 4 AA3 5 GLN D 41 PHE D 45 -1 N ARG D 42 O VAL D 70 SHEET 5 AA3 5 LYS D 48 GLN D 49 -1 O LYS D 48 N PHE D 45 LINK SG CYS B 353 ZN ZN B 601 1555 1555 2.39 LINK SG CYS B 356 ZN ZN B 601 1555 1555 2.26 LINK SG CYS B 414 ZN ZN B 601 1555 1555 2.30 LINK ND1 HIS B 418 ZN ZN B 601 1555 1555 2.13 CISPEP 1 GLY B 459 PRO B 460 0 5.90 SITE 1 AC1 3 ALA A -1 HIS A 0 LYS B 415 SITE 1 AC2 4 CYS B 353 CYS B 356 CYS B 414 HIS B 418 SITE 1 AC3 2 HIS B 370 ASN B 457 CRYST1 131.760 131.760 61.025 90.00 90.00 120.00 P 65 12 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 0.007590 0.004382 0.000000 0.00000 SCALE2 0.000000 0.008764 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016387 0.00000