HEADER TRANSFERASE/TRANSFERASE INHIBITOR 28-JAN-14 4ONQ TITLE CRYSTAL STRUCTURE OF NTDRM E283S/R309S/F310S/Y590S/D591S MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA METHYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN (UNP RESIDUES 255-608); COMPND 5 SYNONYM: NTDRM; COMPND 6 EC: 2.1.1.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NICOTIANA TABACUM; SOURCE 3 ORGANISM_COMMON: TOBACCO; SOURCE 4 ORGANISM_TAXID: 4097; SOURCE 5 GENE: DRM, NTDRM1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-SUMO KEYWDS DNA METHYLTRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.DU,D.J.PATEL REVDAT 2 20-SEP-23 4ONQ 1 REMARK SEQADV REVDAT 1 04-JUN-14 4ONQ 0 JRNL AUTH X.ZHONG,J.DU,C.J.HALE,J.GALLEGO-BARTOLOME,S.FENG, JRNL AUTH 2 A.A.VASHISHT,J.CHORY,J.A.WOHLSCHLEGEL,D.J.PATEL,S.E.JACOBSEN JRNL TITL MOLECULAR MECHANISM OF ACTION OF PLANT DRM DE NOVO DNA JRNL TITL 2 METHYLTRANSFERASES. JRNL REF CELL(CAMBRIDGE,MASS.) V. 157 1050 2014 JRNL REFN ISSN 0092-8674 JRNL PMID 24855943 JRNL DOI 10.1016/J.CELL.2014.03.056 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 30026 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1524 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 32.8788 - 5.5558 1.00 2661 128 0.1753 0.2223 REMARK 3 2 5.5558 - 4.4132 1.00 2601 140 0.1522 0.1755 REMARK 3 3 4.4132 - 3.8563 1.00 2579 153 0.1508 0.1804 REMARK 3 4 3.8563 - 3.5042 1.00 2616 139 0.1801 0.2859 REMARK 3 5 3.5042 - 3.2532 1.00 2574 148 0.2035 0.2315 REMARK 3 6 3.2532 - 3.0616 1.00 2558 139 0.2129 0.2643 REMARK 3 7 3.0616 - 2.9083 1.00 2609 133 0.2375 0.2559 REMARK 3 8 2.9083 - 2.7818 1.00 2577 135 0.2348 0.3063 REMARK 3 9 2.7818 - 2.6748 1.00 2546 144 0.2381 0.3145 REMARK 3 10 2.6748 - 2.5825 1.00 2605 129 0.2379 0.3372 REMARK 3 11 2.5825 - 2.5020 0.99 2576 136 0.2418 0.2668 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.640 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 : 0.015 5328 REMARK 3 ANGLE : 1.410 7241 REMARK 3 CHIRALITY : 0.096 786 REMARK 3 PLANARITY : 0.011 931 REMARK 3 DIHEDRAL : 15.556 1981 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 258 THROUGH 335 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.7962 39.7805 5.8900 REMARK 3 T TENSOR REMARK 3 T11: 0.6896 T22: 0.6505 REMARK 3 T33: 0.4087 T12: -0.0298 REMARK 3 T13: 0.1175 T23: -0.0286 REMARK 3 L TENSOR REMARK 3 L11: 3.6755 L22: 1.3323 REMARK 3 L33: 2.1031 L12: -0.6877 REMARK 3 L13: 1.1953 L23: -0.6300 REMARK 3 S TENSOR REMARK 3 S11: -0.1140 S12: -1.0112 S13: 0.0705 REMARK 3 S21: 0.5049 S22: -0.0367 S23: 0.0924 REMARK 3 S31: -0.0975 S32: -0.4866 S33: 0.1597 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 336 THROUGH 382 ) REMARK 3 ORIGIN FOR THE GROUP (A): -36.9487 44.0434 -12.2801 REMARK 3 T TENSOR REMARK 3 T11: 0.5398 T22: 0.3779 REMARK 3 T33: 0.4691 T12: 0.0016 REMARK 3 T13: 0.1632 T23: -0.0819 REMARK 3 L TENSOR REMARK 3 L11: 2.7214 L22: 1.8499 REMARK 3 L33: 0.9430 L12: 0.1348 REMARK 3 L13: 1.5308 L23: 0.2972 REMARK 3 S TENSOR REMARK 3 S11: 0.0004 S12: -0.5324 S13: 0.3779 REMARK 3 S21: 0.1055 S22: -0.2090 S23: 0.1815 REMARK 3 S31: -0.0262 S32: -0.3496 S33: 0.1756 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 383 THROUGH 429 ) REMARK 3 ORIGIN FOR THE GROUP (A): -49.5382 31.7713 -21.2740 REMARK 3 T TENSOR REMARK 3 T11: 0.3721 T22: 0.3515 REMARK 3 T33: 0.3917 T12: -0.0034 REMARK 3 T13: 0.0811 T23: -0.0367 REMARK 3 L TENSOR REMARK 3 L11: 5.2426 L22: 3.2165 REMARK 3 L33: 5.1319 L12: 1.5494 REMARK 3 L13: -1.7418 L23: 0.6838 REMARK 3 S TENSOR REMARK 3 S11: 0.1830 S12: -0.1890 S13: -0.0872 REMARK 3 S21: -0.0261 S22: -0.2468 S23: 0.3509 REMARK 3 S31: 0.2658 S32: -0.7222 S33: 0.0414 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 430 THROUGH 544 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.5611 38.6799 -11.7718 REMARK 3 T TENSOR REMARK 3 T11: 0.3792 T22: 0.2618 REMARK 3 T33: 0.4936 T12: -0.0278 REMARK 3 T13: 0.0449 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 2.9976 L22: 0.8455 REMARK 3 L33: 2.2573 L12: 0.5566 REMARK 3 L13: 0.8684 L23: 0.1213 REMARK 3 S TENSOR REMARK 3 S11: 0.0179 S12: 0.0525 S13: 0.0126 REMARK 3 S21: 0.1166 S22: -0.0349 S23: -0.3136 REMARK 3 S31: 0.0167 S32: 0.2260 S33: -0.0027 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 545 THROUGH 604 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.6491 33.1026 2.6524 REMARK 3 T TENSOR REMARK 3 T11: 0.7056 T22: 0.5251 REMARK 3 T33: 0.5834 T12: 0.0007 REMARK 3 T13: -0.1065 T23: 0.1253 REMARK 3 L TENSOR REMARK 3 L11: 4.9590 L22: 4.5690 REMARK 3 L33: 3.2864 L12: 1.1623 REMARK 3 L13: -0.8087 L23: -0.6916 REMARK 3 S TENSOR REMARK 3 S11: -0.1034 S12: -0.6080 S13: -0.6225 REMARK 3 S21: 0.8131 S22: -0.0533 S23: -0.4835 REMARK 3 S31: 0.1943 S32: 0.3514 S33: 0.0938 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 258 THROUGH 289 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.5902 72.7885 -20.0495 REMARK 3 T TENSOR REMARK 3 T11: 1.3958 T22: 1.0682 REMARK 3 T33: 0.6954 T12: 0.4847 REMARK 3 T13: -0.2687 T23: -0.3272 REMARK 3 L TENSOR REMARK 3 L11: 1.2496 L22: 1.3180 REMARK 3 L33: 2.1651 L12: -1.0553 REMARK 3 L13: 0.3466 L23: -0.3725 REMARK 3 S TENSOR REMARK 3 S11: 0.7828 S12: 0.7532 S13: -0.3387 REMARK 3 S21: -1.0156 S22: -0.1723 S23: 0.4541 REMARK 3 S31: -0.0599 S32: 0.0535 S33: -0.1411 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 290 THROUGH 382 ) REMARK 3 ORIGIN FOR THE GROUP (A): -35.9517 75.0405 -7.2639 REMARK 3 T TENSOR REMARK 3 T11: 1.0890 T22: 0.6181 REMARK 3 T33: 0.5194 T12: 0.2203 REMARK 3 T13: -0.3080 T23: -0.1366 REMARK 3 L TENSOR REMARK 3 L11: 2.3751 L22: 1.5557 REMARK 3 L33: 2.0745 L12: -0.5138 REMARK 3 L13: -1.1591 L23: 0.1085 REMARK 3 S TENSOR REMARK 3 S11: 0.7271 S12: 0.7386 S13: -0.0929 REMARK 3 S21: -0.9065 S22: -0.2407 S23: 0.4708 REMARK 3 S31: 0.4539 S32: -0.5171 S33: 0.2985 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 383 THROUGH 429 ) REMARK 3 ORIGIN FOR THE GROUP (A): -53.8626 81.3185 10.0834 REMARK 3 T TENSOR REMARK 3 T11: 0.5234 T22: 0.7236 REMARK 3 T33: 0.6715 T12: 0.0340 REMARK 3 T13: -0.1737 T23: 0.1481 REMARK 3 L TENSOR REMARK 3 L11: 6.0074 L22: 4.8072 REMARK 3 L33: 3.8680 L12: -1.8905 REMARK 3 L13: 0.7675 L23: 0.9987 REMARK 3 S TENSOR REMARK 3 S11: 0.2112 S12: 0.5060 S13: 0.0524 REMARK 3 S21: -0.1543 S22: 0.0880 S23: 0.9259 REMARK 3 S31: -0.2535 S32: -1.2216 S33: -0.2187 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 430 THROUGH 603 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.5048 79.2123 -2.8530 REMARK 3 T TENSOR REMARK 3 T11: 0.6984 T22: 0.4266 REMARK 3 T33: 0.4585 T12: 0.1578 REMARK 3 T13: -0.0024 T23: -0.0117 REMARK 3 L TENSOR REMARK 3 L11: 1.8357 L22: 2.0607 REMARK 3 L33: 2.8453 L12: -0.9106 REMARK 3 L13: -0.1267 L23: 1.3062 REMARK 3 S TENSOR REMARK 3 S11: 0.4033 S12: 0.3127 S13: 0.0297 REMARK 3 S21: -0.7099 S22: -0.1965 S23: -0.2953 REMARK 3 S31: -0.1582 S32: 0.3869 S33: -0.1312 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 4ONQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084723. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : CRYOGENICALLY-COOLED SINGLE REMARK 200 CRYSTAL SI(220) SIDE BOUNCE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31550 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : 0.07100 REMARK 200 FOR THE DATA SET : 45.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.20 REMARK 200 R MERGE FOR SHELL (I) : 0.69400 REMARK 200 R SYM FOR SHELL (I) : 0.69400 REMARK 200 FOR SHELL : 3.700 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: PDB ENTRY 4ONJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM NITRATE, 20% PEG3350, 0.1 REMARK 280 M BIS-TRIS PROPANE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 58.78667 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 29.39333 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 44.09000 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 14.69667 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 73.48333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 SER A 252 REMARK 465 GLU A 253 REMARK 465 PHE A 254 REMARK 465 GLU A 255 REMARK 465 THR A 256 REMARK 465 ILE A 257 REMARK 465 CYS A 567 REMARK 465 ASN A 568 REMARK 465 ASN A 569 REMARK 465 LEU A 570 REMARK 465 ALA A 571 REMARK 465 GLY A 572 REMARK 465 SER A 573 REMARK 465 ASN A 574 REMARK 465 ARG A 575 REMARK 465 VAL A 576 REMARK 465 SER A 577 REMARK 465 ARG A 578 REMARK 465 ASP A 579 REMARK 465 GLY A 580 REMARK 465 LEU A 581 REMARK 465 GLU A 582 REMARK 465 GLY A 583 REMARK 465 LYS A 584 REMARK 465 GLU A 585 REMARK 465 SER A 586 REMARK 465 ARG A 605 REMARK 465 HIS A 606 REMARK 465 LYS A 607 REMARK 465 HIS A 608 REMARK 465 SER B 252 REMARK 465 GLU B 253 REMARK 465 PHE B 254 REMARK 465 GLU B 255 REMARK 465 THR B 256 REMARK 465 ILE B 257 REMARK 465 PRO B 272 REMARK 465 LEU B 273 REMARK 465 PRO B 274 REMARK 465 ALA B 275 REMARK 465 MET B 276 REMARK 465 VAL B 277 REMARK 465 ARG B 278 REMARK 465 PRO B 566 REMARK 465 CYS B 567 REMARK 465 ASN B 568 REMARK 465 ASN B 569 REMARK 465 LEU B 570 REMARK 465 ALA B 571 REMARK 465 GLY B 572 REMARK 465 SER B 573 REMARK 465 ASN B 574 REMARK 465 ARG B 575 REMARK 465 VAL B 576 REMARK 465 SER B 577 REMARK 465 ARG B 578 REMARK 465 ASP B 579 REMARK 465 GLY B 580 REMARK 465 LEU B 581 REMARK 465 GLU B 582 REMARK 465 GLY B 583 REMARK 465 LYS B 584 REMARK 465 GLU B 585 REMARK 465 SER B 586 REMARK 465 SER B 587 REMARK 465 SER B 604 REMARK 465 ARG B 605 REMARK 465 HIS B 606 REMARK 465 LYS B 607 REMARK 465 HIS B 608 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 A 260 C - N - CD ANGL. DEV. = -14.2 DEGREES REMARK 500 PRO B 260 C - N - CA ANGL. DEV. = 10.8 DEGREES REMARK 500 PRO B 365 C - N - CD ANGL. DEV. = -14.0 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 VAL A 286 -157.21 -85.73 REMARK 500 LEU A 311 59.66 -111.37 REMARK 500 LEU B 259 98.18 73.43 REMARK 500 PRO B 260 162.28 -42.17 REMARK 500 PRO B 282 -176.73 -60.96 REMARK 500 LEU B 311 68.55 -106.03 REMARK 500 ASP B 395 31.87 -98.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SFG A 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SFG B 700 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ONJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF NTDRM DBREF 4ONQ A 255 608 UNP Q76KU6 Q76KU6_TOBAC 255 608 DBREF 4ONQ B 255 608 UNP Q76KU6 Q76KU6_TOBAC 255 608 SEQADV 4ONQ SER A 252 UNP Q76KU6 EXPRESSION TAG SEQADV 4ONQ GLU A 253 UNP Q76KU6 EXPRESSION TAG SEQADV 4ONQ PHE A 254 UNP Q76KU6 EXPRESSION TAG SEQADV 4ONQ SER A 283 UNP Q76KU6 GLU 283 ENGINEERED MUTATION SEQADV 4ONQ SER A 309 UNP Q76KU6 ARG 309 ENGINEERED MUTATION SEQADV 4ONQ SER A 310 UNP Q76KU6 PHE 310 ENGINEERED MUTATION SEQADV 4ONQ SER A 590 UNP Q76KU6 TYR 590 ENGINEERED MUTATION SEQADV 4ONQ SER A 591 UNP Q76KU6 ASP 591 ENGINEERED MUTATION SEQADV 4ONQ SER B 252 UNP Q76KU6 EXPRESSION TAG SEQADV 4ONQ GLU B 253 UNP Q76KU6 EXPRESSION TAG SEQADV 4ONQ PHE B 254 UNP Q76KU6 EXPRESSION TAG SEQADV 4ONQ SER B 283 UNP Q76KU6 GLU 283 ENGINEERED MUTATION SEQADV 4ONQ SER B 309 UNP Q76KU6 ARG 309 ENGINEERED MUTATION SEQADV 4ONQ SER B 310 UNP Q76KU6 PHE 310 ENGINEERED MUTATION SEQADV 4ONQ SER B 590 UNP Q76KU6 TYR 590 ENGINEERED MUTATION SEQADV 4ONQ SER B 591 UNP Q76KU6 ASP 591 ENGINEERED MUTATION SEQRES 1 A 357 SER GLU PHE GLU THR ILE ARG LEU PRO LYS PRO MET ILE SEQRES 2 A 357 GLY PHE GLY VAL PRO THR GLU PRO LEU PRO ALA MET VAL SEQRES 3 A 357 ARG ARG THR LEU PRO SER GLN ALA VAL GLY PRO PRO PHE SEQRES 4 A 357 PHE TYR TYR GLU ASN VAL ALA LEU ALA PRO LYS GLY VAL SEQRES 5 A 357 TRP ASP THR ILE SER SER SER LEU TYR ASP ILE GLU PRO SEQRES 6 A 357 GLU PHE VAL ASP SER LYS TYR PHE CYS ALA ALA ALA ARG SEQRES 7 A 357 LYS ARG GLY TYR ILE HIS ASN LEU PRO VAL GLU ASN ARG SEQRES 8 A 357 PHE PRO LEU PHE PRO LEU ALA PRO ARG THR ILE HIS GLU SEQRES 9 A 357 ALA LEU PRO LEU SER LYS LYS TRP TRP PRO SER TRP ASP SEQRES 10 A 357 PRO ARG THR LYS LEU ASN CYS LEU GLN THR ALA ILE GLY SEQRES 11 A 357 SER ALA GLN LEU THR ASN ARG ILE ARG LYS ALA VAL GLU SEQRES 12 A 357 ASP PHE ASP GLY GLU PRO PRO MET ARG VAL GLN LYS PHE SEQRES 13 A 357 VAL LEU ASP GLN CYS ARG LYS TRP ASN LEU VAL TRP VAL SEQRES 14 A 357 GLY ARG ASN LYS VAL ALA PRO LEU GLU PRO ASP GLU VAL SEQRES 15 A 357 GLU MET LEU LEU GLY PHE PRO LYS ASN HIS THR ARG GLY SEQRES 16 A 357 GLY GLY ILE SER ARG THR ASP ARG TYR LYS SER LEU GLY SEQRES 17 A 357 ASN SER PHE GLN VAL ASP THR VAL ALA TYR HIS LEU SER SEQRES 18 A 357 VAL LEU LYS ASP LEU PHE PRO GLY GLY ILE ASN VAL LEU SEQRES 19 A 357 SER LEU PHE SER GLY ILE GLY GLY GLY GLU VAL ALA LEU SEQRES 20 A 357 TYR ARG LEU GLY ILE PRO LEU ASN THR VAL VAL SER VAL SEQRES 21 A 357 GLU LYS SER GLU VAL ASN ARG ASP ILE VAL ARG SER TRP SEQRES 22 A 357 TRP GLU GLN THR ASN GLN ARG GLY ASN LEU ILE HIS PHE SEQRES 23 A 357 ASN ASP VAL GLN GLN LEU ASN GLY ASP ARG LEU GLU GLN SEQRES 24 A 357 LEU ILE GLU SER PHE GLY GLY PHE ASP LEU VAL ILE GLY SEQRES 25 A 357 GLY SER PRO CYS ASN ASN LEU ALA GLY SER ASN ARG VAL SEQRES 26 A 357 SER ARG ASP GLY LEU GLU GLY LYS GLU SER SER LEU PHE SEQRES 27 A 357 SER SER TYR VAL ARG ILE LEU ASP LEU VAL LYS SER ILE SEQRES 28 A 357 MET SER ARG HIS LYS HIS SEQRES 1 B 357 SER GLU PHE GLU THR ILE ARG LEU PRO LYS PRO MET ILE SEQRES 2 B 357 GLY PHE GLY VAL PRO THR GLU PRO LEU PRO ALA MET VAL SEQRES 3 B 357 ARG ARG THR LEU PRO SER GLN ALA VAL GLY PRO PRO PHE SEQRES 4 B 357 PHE TYR TYR GLU ASN VAL ALA LEU ALA PRO LYS GLY VAL SEQRES 5 B 357 TRP ASP THR ILE SER SER SER LEU TYR ASP ILE GLU PRO SEQRES 6 B 357 GLU PHE VAL ASP SER LYS TYR PHE CYS ALA ALA ALA ARG SEQRES 7 B 357 LYS ARG GLY TYR ILE HIS ASN LEU PRO VAL GLU ASN ARG SEQRES 8 B 357 PHE PRO LEU PHE PRO LEU ALA PRO ARG THR ILE HIS GLU SEQRES 9 B 357 ALA LEU PRO LEU SER LYS LYS TRP TRP PRO SER TRP ASP SEQRES 10 B 357 PRO ARG THR LYS LEU ASN CYS LEU GLN THR ALA ILE GLY SEQRES 11 B 357 SER ALA GLN LEU THR ASN ARG ILE ARG LYS ALA VAL GLU SEQRES 12 B 357 ASP PHE ASP GLY GLU PRO PRO MET ARG VAL GLN LYS PHE SEQRES 13 B 357 VAL LEU ASP GLN CYS ARG LYS TRP ASN LEU VAL TRP VAL SEQRES 14 B 357 GLY ARG ASN LYS VAL ALA PRO LEU GLU PRO ASP GLU VAL SEQRES 15 B 357 GLU MET LEU LEU GLY PHE PRO LYS ASN HIS THR ARG GLY SEQRES 16 B 357 GLY GLY ILE SER ARG THR ASP ARG TYR LYS SER LEU GLY SEQRES 17 B 357 ASN SER PHE GLN VAL ASP THR VAL ALA TYR HIS LEU SER SEQRES 18 B 357 VAL LEU LYS ASP LEU PHE PRO GLY GLY ILE ASN VAL LEU SEQRES 19 B 357 SER LEU PHE SER GLY ILE GLY GLY GLY GLU VAL ALA LEU SEQRES 20 B 357 TYR ARG LEU GLY ILE PRO LEU ASN THR VAL VAL SER VAL SEQRES 21 B 357 GLU LYS SER GLU VAL ASN ARG ASP ILE VAL ARG SER TRP SEQRES 22 B 357 TRP GLU GLN THR ASN GLN ARG GLY ASN LEU ILE HIS PHE SEQRES 23 B 357 ASN ASP VAL GLN GLN LEU ASN GLY ASP ARG LEU GLU GLN SEQRES 24 B 357 LEU ILE GLU SER PHE GLY GLY PHE ASP LEU VAL ILE GLY SEQRES 25 B 357 GLY SER PRO CYS ASN ASN LEU ALA GLY SER ASN ARG VAL SEQRES 26 B 357 SER ARG ASP GLY LEU GLU GLY LYS GLU SER SER LEU PHE SEQRES 27 B 357 SER SER TYR VAL ARG ILE LEU ASP LEU VAL LYS SER ILE SEQRES 28 B 357 MET SER ARG HIS LYS HIS HET SFG A 700 27 HET SFG B 700 27 HETNAM SFG SINEFUNGIN HETSYN SFG ADENOSYL-ORNITHINE FORMUL 3 SFG 2(C15 H23 N7 O5) FORMUL 5 HOH *113(H2 O) HELIX 1 1 PRO A 282 VAL A 286 5 5 HELIX 2 2 PRO A 300 LEU A 311 1 12 HELIX 3 3 LYS A 322 PHE A 324 5 3 HELIX 4 4 THR A 352 LEU A 357 1 6 HELIX 5 5 LEU A 357 LYS A 362 1 6 HELIX 6 6 SER A 382 ASP A 395 1 14 HELIX 7 7 PRO A 401 ASN A 416 1 16 HELIX 8 8 GLU A 429 GLY A 438 1 10 HELIX 9 9 SER A 450 ASN A 460 1 11 HELIX 10 10 GLN A 463 SER A 472 1 10 HELIX 11 11 VAL A 473 LYS A 475 5 3 HELIX 12 12 GLY A 492 LEU A 501 1 10 HELIX 13 13 SER A 514 THR A 528 1 15 HELIX 14 14 ASP A 539 LEU A 543 5 5 HELIX 15 15 ASN A 544 GLY A 556 1 13 HELIX 16 16 LEU A 588 SER A 604 1 17 HELIX 17 17 PRO B 300 LEU B 311 1 12 HELIX 18 18 LYS B 322 PHE B 324 5 3 HELIX 19 19 THR B 352 LEU B 357 1 6 HELIX 20 20 LEU B 357 LYS B 362 1 6 HELIX 21 21 SER B 382 ASP B 395 1 14 HELIX 22 22 PRO B 401 ASN B 416 1 16 HELIX 23 23 GLU B 429 LEU B 437 1 9 HELIX 24 24 SER B 450 ASN B 460 1 11 HELIX 25 25 GLN B 463 SER B 472 1 10 HELIX 26 26 VAL B 473 PHE B 478 1 6 HELIX 27 27 GLY B 492 GLY B 502 1 11 HELIX 28 28 SER B 514 THR B 528 1 15 HELIX 29 29 ASP B 539 LEU B 543 5 5 HELIX 30 30 ASN B 544 GLY B 556 1 13 HELIX 31 31 PHE B 589 MET B 603 1 15 SHEET 1 A 7 GLU A 317 ASP A 320 0 SHEET 2 A 7 LYS A 330 HIS A 335 -1 O TYR A 333 N GLU A 317 SHEET 3 A 7 PHE A 290 VAL A 296 -1 N ASN A 295 O GLY A 332 SHEET 4 A 7 LEU A 560 GLY A 563 1 O VAL A 561 N PHE A 290 SHEET 5 A 7 ILE A 482 LEU A 487 1 N LEU A 485 O LEU A 560 SHEET 6 A 7 LEU A 505 VAL A 511 1 O VAL A 509 N VAL A 484 SHEET 7 A 7 ASN A 533 PHE A 537 1 O ILE A 535 N SER A 510 SHEET 1 B 2 LEU A 417 GLY A 421 0 SHEET 2 B 2 LYS A 424 PRO A 427 -1 O LYS A 424 N VAL A 420 SHEET 1 C 7 GLU B 317 ASP B 320 0 SHEET 2 C 7 LYS B 330 HIS B 335 -1 O TYR B 333 N GLU B 317 SHEET 3 C 7 PHE B 290 VAL B 296 -1 N ASN B 295 O GLY B 332 SHEET 4 C 7 LEU B 560 GLY B 563 1 O GLY B 563 N TYR B 292 SHEET 5 C 7 ILE B 482 LEU B 487 1 N LEU B 487 O ILE B 562 SHEET 6 C 7 LEU B 505 VAL B 511 1 O VAL B 509 N SER B 486 SHEET 7 C 7 ASN B 533 PHE B 537 1 O ILE B 535 N VAL B 508 SHEET 1 D 2 VAL B 418 GLY B 421 0 SHEET 2 D 2 LYS B 424 ALA B 426 -1 O LYS B 424 N VAL B 420 CISPEP 1 PRO A 288 PRO A 289 0 3.72 CISPEP 2 PHE A 346 PRO A 347 0 0.27 CISPEP 3 GLY A 398 GLU A 399 0 7.65 CISPEP 4 PRO B 288 PRO B 289 0 -0.59 CISPEP 5 PHE B 346 PRO B 347 0 2.25 SITE 1 AC1 14 ASN A 460 SER A 461 PHE A 462 PHE A 488 SITE 2 AC1 14 SER A 489 GLY A 490 ILE A 491 GLY A 493 SITE 3 AC1 14 GLU A 512 LYS A 513 ASN A 517 VAL A 540 SITE 4 AC1 14 SER A 565 LEU A 588 SITE 1 AC2 18 ASN B 460 SER B 461 PHE B 462 PHE B 488 SITE 2 AC2 18 SER B 489 GLY B 490 ILE B 491 GLY B 492 SITE 3 AC2 18 GLY B 493 VAL B 511 GLU B 512 LYS B 513 SITE 4 AC2 18 ASN B 538 ASP B 539 VAL B 540 SER B 565 SITE 5 AC2 18 LEU B 588 HOH B 827 CRYST1 131.504 131.504 88.180 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 0.007604 0.004390 0.000000 0.00000 SCALE2 0.000000 0.008781 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011340 0.00000