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 4 08-NOV-23 4U7P 1 SOURCE REMARK 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 PDBJ 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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