HEADER TRANSFERASE/TRANSFERASE REGULATOR 31-JUL-14 4U7P TITLE CRYSTAL STRUCTURE OF DNMT3A-DNMT3L COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (CYTOSINE-5)-METHYLTRANSFERASE 3A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 455-912; COMPND 5 SYNONYM: DNA METHYLTRANSFERASES DNMT3A; COMPND 6 EC: 2.1.1.37; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (CYTOSINE-5)-METHYLTRANSFERASE 3-LIKE; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 178-379; COMPND 12 SYNONYM: DNA METHYLTRANSFERASES DNMT3L; 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: DNMT3A; 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: DNMT3L; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA METHYLTRANSFERASE, AUTOINHIBITORY FORM, TRANSFERASE-TRANSFERASE KEYWDS 2 REGULATOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.WANG,X.GUO,J.LI,J.XIAO,X.YIN,S.HE,J.WANG,Y.XU REVDAT 3 04-FEB-15 4U7P 1 JRNL REVDAT 2 17-DEC-14 4U7P 1 JRNL REVDAT 1 12-NOV-14 4U7P 0 JRNL AUTH X.GUO,L.WANG,J.LI,Z.DING,J.XIAO,X.YIN,S.HE,P.SHI,L.DONG, JRNL AUTH 2 G.LI,C.TIAN,J.WANG,Y.CONG,Y.XU JRNL TITL STRUCTURAL INSIGHT INTO AUTOINHIBITION AND HISTONE JRNL TITL 2 H3-INDUCED ACTIVATION OF DNMT3A JRNL REF NATURE V. 517 640 2015 JRNL REFN ISSN 0028-0836 JRNL PMID 25383530 JRNL DOI 10.1038/NATURE13899 REMARK 2 REMARK 2 RESOLUTION. 3.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 79.2 REMARK 3 NUMBER OF REFLECTIONS : 13977 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1392 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 42.0077 - 9.3907 0.99 1540 171 0.2032 0.2412 REMARK 3 2 9.3907 - 7.4674 1.00 1567 177 0.2051 0.2253 REMARK 3 3 7.4674 - 6.5274 1.00 1597 136 0.2169 0.2477 REMARK 3 4 6.5274 - 5.9324 1.00 1562 168 0.2082 0.2411 REMARK 3 5 5.9324 - 5.5082 1.00 1551 185 0.1918 0.2509 REMARK 3 6 5.5082 - 5.1841 1.00 1561 169 0.1960 0.2697 REMARK 3 7 5.1841 - 4.9249 0.99 1554 151 0.1939 0.2431 REMARK 3 8 4.9249 - 4.7108 0.97 1498 167 0.2001 0.2229 REMARK 3 9 4.7108 - 4.5296 0.80 1224 160 0.2253 0.2927 REMARK 3 10 4.5296 - 4.3735 0.56 885 98 0.2471 0.3362 REMARK 3 11 4.3735 - 4.2369 0.54 817 99 0.2589 0.2981 REMARK 3 12 4.2369 - 4.1159 0.53 829 96 0.2748 0.3589 REMARK 3 13 4.1159 - 4.0076 0.53 817 92 0.3009 0.3499 REMARK 3 14 4.0076 - 3.9099 0.52 802 102 0.3167 0.3183 REMARK 3 15 3.9099 - 3.8211 0.45 720 65 0.3248 0.3406 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.450 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.31 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 78.33 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 : 0.006 5218 REMARK 3 ANGLE : 0.977 7072 REMARK 3 CHIRALITY : 0.036 744 REMARK 3 PLANARITY : 0.005 916 REMARK 3 DIHEDRAL : 14.243 1944 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 4U7P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000202950. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6-6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2816 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) 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 : 14153 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.820 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.87000 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: PHASER REMARK 200 STARTING MODEL: 2QRV, 3A1A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M BIS-TRIS, 0.1M SODIUM MALONATE, REMARK 280 8% PEG3350, PH 5.6, VAPOR DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 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,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.66800 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 37.66800 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 37.66800 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 37.66800 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 37.66800 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 37.66800 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLY A 447 REMARK 465 PRO A 448 REMARK 465 LEU A 449 REMARK 465 GLY A 450 REMARK 465 SER A 451 REMARK 465 PRO A 452 REMARK 465 GLU A 453 REMARK 465 PHE A 454 REMARK 465 LYS A 455 REMARK 465 LYS A 456 REMARK 465 PRO A 457 REMARK 465 ARG A 458 REMARK 465 LYS A 459 REMARK 465 SER A 460 REMARK 465 THR A 461 REMARK 465 ALA A 462 REMARK 465 GLU A 463 REMARK 465 LYS A 464 REMARK 465 PRO A 465 REMARK 465 LYS A 466 REMARK 465 VAL A 467 REMARK 465 LYS A 468 REMARK 465 GLU A 469 REMARK 465 ILE A 470 REMARK 465 ILE A 471 REMARK 465 ASP A 472 REMARK 465 GLU A 473 REMARK 465 ILE A 833 REMARK 465 THR A 834 REMARK 465 THR A 835 REMARK 465 ARG A 836 REMARK 465 SER A 837 REMARK 465 ASN A 838 REMARK 465 SER A 839 REMARK 465 ILE A 840 REMARK 465 LYS A 841 REMARK 465 GLN A 842 REMARK 465 GLY A 843 REMARK 465 LYS A 844 REMARK 465 ASP A 845 REMARK 465 GLY B 171 REMARK 465 PRO B 172 REMARK 465 LEU B 173 REMARK 465 GLY B 174 REMARK 465 SER B 175 REMARK 465 GLU B 176 REMARK 465 PHE B 177 REMARK 465 MET B 178 REMARK 465 LYS B 354 REMARK 465 LEU B 355 REMARK 465 ALA B 356 REMARK 465 SER B 379 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 TYR A 528 OG SER A 535 2.04 REMARK 500 NZ LYS B 376 O PHE B 378 2.13 REMARK 500 OE2 GLU A 733 NH1 ARG A 736 2.19 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 SER A 496 -72.90 -84.64 REMARK 500 SER A 535 -23.65 64.03 REMARK 500 TYR A 536 -134.56 40.54 REMARK 500 CYS A 541 19.43 58.90 REMARK 500 ARG A 544 -72.52 -110.85 REMARK 500 CYS A 554 -71.20 -119.71 REMARK 500 LYS A 577 -4.58 82.09 REMARK 500 ASP A 618 79.76 52.26 REMARK 500 PHE A 640 71.89 53.42 REMARK 500 ALA A 644 59.80 -63.12 REMARK 500 VAL A 665 -62.04 -105.14 REMARK 500 CYS A 666 105.93 -45.01 REMARK 500 HIS A 677 10.76 -142.38 REMARK 500 CYS A 710 -76.93 -88.54 REMARK 500 ASN A 711 -108.93 50.11 REMARK 500 ASP A 712 -6.41 -57.63 REMARK 500 ARG A 729 -38.38 -35.20 REMARK 500 VAL A 785 -14.12 -144.26 REMARK 500 ARG A 831 -66.22 -130.79 REMARK 500 HIS A 847 -73.72 -76.74 REMARK 500 SER A 878 -150.62 57.13 REMARK 500 PRO B 183 153.18 -49.72 REMARK 500 ARG B 186 -6.54 -146.23 REMARK 500 PHE B 196 -31.65 63.90 REMARK 500 GLU B 210 -77.90 -82.26 REMARK 500 SER B 211 176.47 174.10 REMARK 500 SER B 213 -62.57 -139.28 REMARK 500 PRO B 215 63.86 -100.46 REMARK 500 VAL B 224 31.44 -95.43 REMARK 500 ASP B 226 63.36 -114.62 REMARK 500 TRP B 235 23.86 -75.13 REMARK 500 THR B 251 -141.30 48.02 REMARK 500 CYS B 252 -64.25 -132.63 REMARK 500 ASP B 253 -114.87 57.10 REMARK 500 ASN B 287 55.09 -101.93 REMARK 500 LEU B 317 87.62 -64.75 REMARK 500 ILE B 330 -55.59 -135.07 REMARK 500 ARG B 333 -88.60 -121.08 REMARK 500 HIS B 334 -21.58 57.74 REMARK 500 TRP B 335 -156.89 43.71 REMARK 500 ALA B 336 -63.17 -145.96 REMARK 500 GLN B 351 -74.47 -121.34 REMARK 500 PRO B 370 9.25 -69.14 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 A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 494 SG REMARK 620 2 CYS A 497 SG 119.6 REMARK 620 3 CYS A 514 SG 116.3 118.8 REMARK 620 4 CYS A 517 SG 101.3 98.2 93.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 537 SG REMARK 620 2 CYS A 540 SG 106.1 REMARK 620 3 CYS A 559 SG 96.8 135.2 REMARK 620 4 CYS A 562 SG 118.5 109.7 91.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1003 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 549 SG REMARK 620 2 CYS A 554 SG 115.7 REMARK 620 3 CYS A 583 SG 111.0 112.6 REMARK 620 4 CYS A 586 SG 107.0 86.4 122.4 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 ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAH A 1004 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4U7T RELATED DB: PDB DBREF 4U7P A 455 912 UNP Q9Y6K1 DNM3A_HUMAN 455 912 DBREF 4U7P B 178 379 UNP Q9UJW3 DNM3L_HUMAN 178 379 SEQADV 4U7P GLY A 447 UNP Q9Y6K1 EXPRESSION TAG SEQADV 4U7P PRO A 448 UNP Q9Y6K1 EXPRESSION TAG SEQADV 4U7P LEU A 449 UNP Q9Y6K1 EXPRESSION TAG SEQADV 4U7P GLY A 450 UNP Q9Y6K1 EXPRESSION TAG SEQADV 4U7P SER A 451 UNP Q9Y6K1 EXPRESSION TAG SEQADV 4U7P PRO A 452 UNP Q9Y6K1 EXPRESSION TAG SEQADV 4U7P GLU A 453 UNP Q9Y6K1 EXPRESSION TAG SEQADV 4U7P PHE A 454 UNP Q9Y6K1 EXPRESSION TAG SEQADV 4U7P GLY B 171 UNP Q9UJW3 EXPRESSION TAG SEQADV 4U7P PRO B 172 UNP Q9UJW3 EXPRESSION TAG SEQADV 4U7P LEU B 173 UNP Q9UJW3 EXPRESSION TAG SEQADV 4U7P GLY B 174 UNP Q9UJW3 EXPRESSION TAG SEQADV 4U7P SER B 175 UNP Q9UJW3 EXPRESSION TAG SEQADV 4U7P GLU B 176 UNP Q9UJW3 EXPRESSION TAG SEQADV 4U7P PHE B 177 UNP Q9UJW3 EXPRESSION TAG SEQRES 1 A 466 GLY PRO LEU GLY SER PRO GLU PHE LYS LYS PRO ARG LYS SEQRES 2 A 466 SER THR ALA GLU LYS PRO LYS VAL LYS GLU ILE ILE ASP SEQRES 3 A 466 GLU ARG THR ARG GLU ARG LEU VAL TYR GLU VAL ARG GLN SEQRES 4 A 466 LYS CYS ARG ASN ILE GLU ASP ILE CYS ILE SER CYS GLY SEQRES 5 A 466 SER LEU ASN VAL THR LEU GLU HIS PRO LEU PHE VAL GLY SEQRES 6 A 466 GLY MET CYS GLN ASN CYS LYS ASN CYS PHE LEU GLU CYS SEQRES 7 A 466 ALA TYR GLN TYR ASP ASP ASP GLY TYR GLN SER TYR CYS SEQRES 8 A 466 THR ILE CYS CYS GLY GLY ARG GLU VAL LEU MET CYS GLY SEQRES 9 A 466 ASN ASN ASN CYS CYS ARG CYS PHE CYS VAL GLU CYS VAL SEQRES 10 A 466 ASP LEU LEU VAL GLY PRO GLY ALA ALA GLN ALA ALA ILE SEQRES 11 A 466 LYS GLU ASP PRO TRP ASN CYS TYR MET CYS GLY HIS LYS SEQRES 12 A 466 GLY THR TYR GLY LEU LEU ARG ARG ARG GLU ASP TRP PRO SEQRES 13 A 466 SER ARG LEU GLN MET PHE PHE ALA ASN ASN HIS ASP GLN SEQRES 14 A 466 GLU PHE ASP PRO PRO LYS VAL TYR PRO PRO VAL PRO ALA SEQRES 15 A 466 GLU LYS ARG LYS PRO ILE ARG VAL LEU SER LEU PHE ASP SEQRES 16 A 466 GLY ILE ALA THR GLY LEU LEU VAL LEU LYS ASP LEU GLY SEQRES 17 A 466 ILE GLN VAL ASP ARG TYR ILE ALA SER GLU VAL CYS GLU SEQRES 18 A 466 ASP SER ILE THR VAL GLY MET VAL ARG HIS GLN GLY LYS SEQRES 19 A 466 ILE MET TYR VAL GLY ASP VAL ARG SER VAL THR GLN LYS SEQRES 20 A 466 HIS ILE GLN GLU TRP GLY PRO PHE ASP LEU VAL ILE GLY SEQRES 21 A 466 GLY SER PRO CYS ASN ASP LEU SER ILE VAL ASN PRO ALA SEQRES 22 A 466 ARG LYS GLY LEU TYR GLU GLY THR GLY ARG LEU PHE PHE SEQRES 23 A 466 GLU PHE TYR ARG LEU LEU HIS ASP ALA ARG PRO LYS GLU SEQRES 24 A 466 GLY ASP ASP ARG PRO PHE PHE TRP LEU PHE GLU ASN VAL SEQRES 25 A 466 VAL ALA MET GLY VAL SER ASP LYS ARG ASP ILE SER ARG SEQRES 26 A 466 PHE LEU GLU SER ASN PRO VAL MET ILE ASP ALA LYS GLU SEQRES 27 A 466 VAL SER ALA ALA HIS ARG ALA ARG TYR PHE TRP GLY ASN SEQRES 28 A 466 LEU PRO GLY MET ASN ARG PRO LEU ALA SER THR VAL ASN SEQRES 29 A 466 ASP LYS LEU GLU LEU GLN GLU CYS LEU GLU HIS GLY ARG SEQRES 30 A 466 ILE ALA LYS PHE SER LYS VAL ARG THR ILE THR THR ARG SEQRES 31 A 466 SER ASN SER ILE LYS GLN GLY LYS ASP GLN HIS PHE PRO SEQRES 32 A 466 VAL PHE MET ASN GLU LYS GLU ASP ILE LEU TRP CYS THR SEQRES 33 A 466 GLU MET GLU ARG VAL PHE GLY PHE PRO VAL HIS TYR THR SEQRES 34 A 466 ASP VAL SER ASN MET SER ARG LEU ALA ARG GLN ARG LEU SEQRES 35 A 466 LEU GLY ARG SER TRP SER VAL PRO VAL ILE ARG HIS LEU SEQRES 36 A 466 PHE ALA PRO LEU LYS GLU TYR PHE ALA CYS VAL SEQRES 1 B 209 GLY PRO LEU GLY SER GLU PHE MET PHE GLU THR VAL PRO SEQRES 2 B 209 VAL TRP ARG ARG GLN PRO VAL ARG VAL LEU SER LEU PHE SEQRES 3 B 209 GLU ASP ILE LYS LYS GLU LEU THR SER LEU GLY PHE LEU SEQRES 4 B 209 GLU SER GLY SER ASP PRO GLY GLN LEU LYS HIS VAL VAL SEQRES 5 B 209 ASP VAL THR ASP THR VAL ARG LYS ASP VAL GLU GLU TRP SEQRES 6 B 209 GLY PRO PHE ASP LEU VAL TYR GLY ALA THR PRO PRO LEU SEQRES 7 B 209 GLY HIS THR CYS ASP ARG PRO PRO SER TRP TYR LEU PHE SEQRES 8 B 209 GLN PHE HIS ARG LEU LEU GLN TYR ALA ARG PRO LYS PRO SEQRES 9 B 209 GLY SER PRO ARG PRO PHE PHE TRP MET PHE VAL ASP ASN SEQRES 10 B 209 LEU VAL LEU ASN LYS GLU ASP LEU ASP VAL ALA SER ARG SEQRES 11 B 209 PHE LEU GLU MET GLU PRO VAL THR ILE PRO ASP VAL HIS SEQRES 12 B 209 GLY GLY SER LEU GLN ASN ALA VAL ARG VAL TRP SER ASN SEQRES 13 B 209 ILE PRO ALA ILE ARG SER ARG HIS TRP ALA LEU VAL SER SEQRES 14 B 209 GLU GLU GLU LEU SER LEU LEU ALA GLN ASN LYS GLN SER SEQRES 15 B 209 SER LYS LEU ALA ALA LYS TRP PRO THR LYS LEU VAL LYS SEQRES 16 B 209 ASN CYS PHE LEU PRO LEU ARG GLU TYR PHE LYS TYR PHE SEQRES 17 B 209 SER HET ZN A1001 1 HET ZN A1002 1 HET ZN A1003 1 HET SAH A1004 26 HETNAM ZN ZINC ION HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 3 ZN 3(ZN 2+) FORMUL 6 SAH C14 H20 N6 O5 S HELIX 1 AA1 ARG A 474 GLN A 485 1 12 HELIX 2 AA2 ASN A 489 ILE A 493 5 5 HELIX 3 AA3 CYS A 514 TYR A 528 1 15 HELIX 4 AA4 VAL A 560 VAL A 567 1 8 HELIX 5 AA5 GLY A 570 ILE A 576 1 7 HELIX 6 AA6 ASP A 600 PHE A 609 1 10 HELIX 7 AA7 ALA A 644 GLY A 654 1 11 HELIX 8 AA8 CYS A 666 HIS A 677 1 12 HELIX 9 AA9 THR A 691 TRP A 698 1 8 HELIX 10 AB1 CYS A 710 SER A 714 5 5 HELIX 11 AB2 ARG A 729 ASP A 740 1 12 HELIX 12 AB3 GLY A 762 GLU A 774 1 13 HELIX 13 AB4 LYS A 783 VAL A 785 5 3 HELIX 14 AB5 GLU A 814 CYS A 818 5 5 HELIX 15 AB6 TRP A 860 GLY A 869 1 10 HELIX 16 AB7 SER A 881 ARG A 891 1 11 HELIX 17 AB8 SER A 894 PHE A 902 1 9 HELIX 18 AB9 ALA A 903 LYS A 906 5 4 HELIX 19 AC1 PRO B 183 ARG B 187 5 5 HELIX 20 AC2 ILE B 199 LEU B 206 1 8 HELIX 21 AC3 ASP B 223 THR B 227 5 5 HELIX 22 AC4 VAL B 228 TRP B 235 1 8 HELIX 23 AC5 PRO B 255 ARG B 271 1 17 HELIX 24 AC6 ASN B 291 LEU B 302 1 12 HELIX 25 AC7 SER B 339 LYS B 350 1 12 HELIX 26 AC8 THR B 361 ASN B 366 1 6 HELIX 27 AC9 CYS B 367 TYR B 374 5 8 SHEET 1 AA1 2 LEU A 504 GLU A 505 0 SHEET 2 AA1 2 GLY A 512 MET A 513 -1 O MET A 513 N LEU A 504 SHEET 1 AA2 2 VAL A 546 MET A 548 0 SHEET 2 AA2 2 CYS A 557 CYS A 559 -1 O PHE A 558 N LEU A 547 SHEET 1 AA3 2 THR A 591 TYR A 592 0 SHEET 2 AA3 2 LEU A 595 ARG A 596 -1 O LEU A 595 N TYR A 592 SHEET 1 AA4 7 ILE A 681 VAL A 684 0 SHEET 2 AA4 7 VAL A 657 SER A 663 1 N TYR A 660 O MET A 682 SHEET 3 AA4 7 ILE A 634 LEU A 639 1 N SER A 638 O SER A 663 SHEET 4 AA4 7 LEU A 703 GLY A 707 1 O LEU A 703 N LEU A 637 SHEET 5 AA4 7 PHE A 752 VAL A 758 1 O PHE A 752 N VAL A 704 SHEET 6 AA4 7 ALA A 791 GLY A 796 -1 O TRP A 795 N PHE A 755 SHEET 7 AA4 7 VAL A 778 ASP A 781 -1 N ILE A 780 O ARG A 792 SHEET 1 AA5 3 ILE A 824 ALA A 825 0 SHEET 2 AA5 3 VAL A 850 PHE A 851 -1 O PHE A 851 N ILE A 824 SHEET 3 AA5 3 GLU A 856 ASP A 857 -1 O ASP A 857 N VAL A 850 SHEET 1 AA6 6 LEU B 218 VAL B 221 0 SHEET 2 AA6 6 VAL B 192 LEU B 195 1 N VAL B 192 O LYS B 219 SHEET 3 AA6 6 LEU B 240 ALA B 244 1 O TYR B 242 N LEU B 195 SHEET 4 AA6 6 PHE B 281 ASP B 286 1 O MET B 283 N VAL B 241 SHEET 5 AA6 6 LEU B 317 SER B 325 -1 O TRP B 324 N PHE B 284 SHEET 6 AA6 6 VAL B 307 VAL B 312 -1 N VAL B 307 O VAL B 323 LINK SG CYS A 494 ZN ZN A1002 1555 1555 2.37 LINK SG CYS A 497 ZN ZN A1002 1555 1555 2.35 LINK SG CYS A 514 ZN ZN A1002 1555 1555 2.26 LINK SG CYS A 517 ZN ZN A1002 1555 1555 2.17 LINK SG CYS A 537 ZN ZN A1001 1555 1555 2.39 LINK SG CYS A 540 ZN ZN A1001 1555 1555 2.22 LINK SG CYS A 549 ZN ZN A1003 1555 1555 2.44 LINK SG CYS A 554 ZN ZN A1003 1555 1555 2.36 LINK SG CYS A 559 ZN ZN A1001 1555 1555 2.32 LINK SG CYS A 562 ZN ZN A1001 1555 1555 2.38 LINK SG CYS A 583 ZN ZN A1003 1555 1555 2.27 LINK SG CYS A 586 ZN ZN A1003 1555 1555 2.28 CISPEP 1 TYR A 536 CYS A 537 0 -3.92 CISPEP 2 GLU A 629 LYS A 630 0 -0.50 CISPEP 3 SER B 213 ASP B 214 0 11.08 CISPEP 4 PRO B 215 GLY B 216 0 -7.18 SITE 1 AC1 4 CYS A 537 CYS A 540 CYS A 559 CYS A 562 SITE 1 AC2 4 CYS A 494 CYS A 497 CYS A 514 CYS A 517 SITE 1 AC3 4 CYS A 549 CYS A 554 CYS A 583 CYS A 586 SITE 1 AC4 15 PHE A 640 ASP A 641 ILE A 643 THR A 645 SITE 2 AC4 15 GLU A 664 VAL A 665 CYS A 666 ASP A 686 SITE 3 AC4 15 VAL A 687 GLY A 707 PRO A 709 LEU A 730 SITE 4 AC4 15 ARG A 891 SER A 892 TRP A 893 CRYST1 252.031 252.031 75.336 90.00 90.00 120.00 P 63 2 2 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 0.003968 0.002291 0.000000 0.00000 SCALE2 0.000000 0.004582 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013274 0.00000 MASTER 421 0 4 27 22 0 7 6 0 0 0 53 END