HEADER TRANSCRIPTION/DNA 17-MAY-14 4QEN TITLE CRYSTAL STRUCTURE OF KRYPTONITE IN COMPLEX WITH MCHH DNA AND SAH COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC COMPND 3 SUVH4; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: FUNCTIONAL FRAGMENT; COMPND 6 SYNONYM: HISTONE H3-K9 METHYLTRANSFERASE 4, H3-K9-HMTASE 4, PROTEIN COMPND 7 KRYPTONITE, PROTEIN SET DOMAIN GROUP 33, SUPPRESSOR OF VARIEGATION 3- COMPND 8 9 HOMOLOG PROTEIN 4, SU(VAR)3-9 HOMOLOG PROTEIN 4; COMPND 9 EC: 2.1.1.43; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: DNA (5'-D(*GP*GP*TP*AP*CP*TP*(5CM) COMPND 13 P*AP*TP*CP*AP*GP*TP*AP*T)-3'); COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 3; COMPND 17 MOLECULE: DNA (5'-D(*AP*CP*TP*GP*AP*TP*GP*AP*GP*TP*AP*CP*CP*AP*T)- COMPND 18 3'); COMPND 19 CHAIN: D; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS,THALE-CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: SUVH4, KYP, SDG33, SET33, AT5G13960, MAC12.7; 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; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS SRA, SET, HISTONE METHYLATION, METHYLATED DNA, TRANSCRIPTION-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.DU,S.LI,D.J.PATEL REVDAT 3 28-FEB-24 4QEN 1 REMARK SEQADV LINK REVDAT 2 20-AUG-14 4QEN 1 JRNL REVDAT 1 30-JUL-14 4QEN 0 JRNL AUTH J.DU,L.M.JOHNSON,M.GROTH,S.FENG,C.J.HALE,S.LI,A.A.VASHISHT, JRNL AUTH 2 J.GALLEGO-BARTOLOME,J.A.WOHLSCHLEGEL,D.J.PATEL,S.E.JACOBSEN JRNL TITL MECHANISM OF DNA METHYLATION-DIRECTED HISTONE METHYLATION BY JRNL TITL 2 KRYPTONITE. JRNL REF MOL.CELL V. 55 495 2014 JRNL REFN ISSN 1097-2765 JRNL PMID 25018018 JRNL DOI 10.1016/J.MOLCEL.2014.06.009 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 44884 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2261 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 40.6919 - 6.2137 0.99 2691 125 0.2019 0.2202 REMARK 3 2 6.2137 - 4.9348 1.00 2693 148 0.1713 0.2005 REMARK 3 3 4.9348 - 4.3118 1.00 2683 139 0.1424 0.1764 REMARK 3 4 4.3118 - 3.9179 1.00 2689 136 0.1479 0.1761 REMARK 3 5 3.9179 - 3.6373 1.00 2680 157 0.1584 0.1902 REMARK 3 6 3.6373 - 3.4229 1.00 2719 136 0.1643 0.1794 REMARK 3 7 3.4229 - 3.2516 1.00 2727 126 0.1653 0.2111 REMARK 3 8 3.2516 - 3.1101 1.00 2710 148 0.1793 0.2087 REMARK 3 9 3.1101 - 2.9904 1.00 2656 164 0.1776 0.2138 REMARK 3 10 2.9904 - 2.8872 1.00 2694 147 0.1843 0.2246 REMARK 3 11 2.8872 - 2.7970 1.00 2691 141 0.1836 0.2422 REMARK 3 12 2.7970 - 2.7171 1.00 2715 126 0.1857 0.1707 REMARK 3 13 2.7171 - 2.6455 1.00 2735 148 0.1832 0.2501 REMARK 3 14 2.6455 - 2.5810 1.00 2669 130 0.1858 0.2448 REMARK 3 15 2.5810 - 2.5223 1.00 2738 139 0.1807 0.2246 REMARK 3 16 2.5223 - 2.4687 1.00 2681 172 0.1797 0.2305 REMARK 3 17 2.4687 - 2.4193 1.00 2735 131 0.1804 0.2274 REMARK 3 18 2.4193 - 2.3736 1.00 2626 151 0.1843 0.2115 REMARK 3 19 2.3736 - 2.3313 1.00 2721 156 0.1866 0.2023 REMARK 3 20 2.3313 - 2.2917 1.00 2703 129 0.1827 0.2586 REMARK 3 21 2.2917 - 2.2548 1.00 2701 167 0.1853 0.2233 REMARK 3 22 2.2548 - 2.2201 1.00 2691 125 0.1912 0.2691 REMARK 3 23 2.2201 - 2.1874 1.00 2688 120 0.1901 0.2059 REMARK 3 24 2.1874 - 2.1566 1.00 2706 136 0.1887 0.2639 REMARK 3 25 2.1566 - 2.1275 1.00 2743 134 0.1910 0.2258 REMARK 3 26 2.1275 - 2.0999 1.00 2661 146 0.2058 0.2669 REMARK 3 27 2.0999 - 2.0736 1.00 2651 190 0.2161 0.2835 REMARK 3 28 2.0736 - 2.0486 1.00 2756 131 0.2182 0.2408 REMARK 3 29 2.0486 - 2.0248 1.00 2687 154 0.2343 0.2782 REMARK 3 30 2.0248 - 2.0021 0.99 2633 136 0.2458 0.2571 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.100 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 : 0.008 4377 REMARK 3 ANGLE : 1.410 6011 REMARK 3 CHIRALITY : 0.099 654 REMARK 3 PLANARITY : 0.005 689 REMARK 3 DIHEDRAL : 18.268 1666 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 99 THROUGH 186 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.3681 22.0365 25.1445 REMARK 3 T TENSOR REMARK 3 T11: 0.2612 T22: 0.2665 REMARK 3 T33: 0.1976 T12: 0.0486 REMARK 3 T13: -0.0313 T23: -0.0014 REMARK 3 L TENSOR REMARK 3 L11: 1.2101 L22: 1.2382 REMARK 3 L33: 3.2760 L12: -0.2056 REMARK 3 L13: 0.5473 L23: -1.1205 REMARK 3 S TENSOR REMARK 3 S11: -0.1616 S12: -0.2655 S13: 0.0796 REMARK 3 S21: 0.1465 S22: 0.1278 S23: 0.0113 REMARK 3 S31: -0.3502 S32: -0.1647 S33: 0.1200 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 187 THROUGH 302 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.9878 17.1507 6.2399 REMARK 3 T TENSOR REMARK 3 T11: 0.2182 T22: 0.1658 REMARK 3 T33: 0.1885 T12: -0.0063 REMARK 3 T13: 0.0109 T23: 0.0016 REMARK 3 L TENSOR REMARK 3 L11: 1.6513 L22: 1.4138 REMARK 3 L33: 2.7042 L12: -0.3481 REMARK 3 L13: 0.4883 L23: -0.2424 REMARK 3 S TENSOR REMARK 3 S11: -0.0356 S12: 0.0256 S13: -0.0740 REMARK 3 S21: 0.0434 S22: 0.0091 S23: 0.0845 REMARK 3 S31: 0.0818 S32: -0.0809 S33: -0.0130 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 303 THROUGH 368 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.6574 -2.4157 30.8512 REMARK 3 T TENSOR REMARK 3 T11: 0.4273 T22: 0.4358 REMARK 3 T33: 0.4003 T12: 0.1008 REMARK 3 T13: 0.0483 T23: 0.0663 REMARK 3 L TENSOR REMARK 3 L11: 0.1182 L22: 1.5390 REMARK 3 L33: 2.1880 L12: -0.2972 REMARK 3 L13: 0.5644 L23: -1.3475 REMARK 3 S TENSOR REMARK 3 S11: 0.0699 S12: 0.1764 S13: -0.0702 REMARK 3 S21: -0.5023 S22: -0.2533 S23: -0.3239 REMARK 3 S31: 0.8714 S32: 0.5704 S33: 0.1637 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 369 THROUGH 624 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.1408 7.8797 46.1133 REMARK 3 T TENSOR REMARK 3 T11: 0.2220 T22: 0.1950 REMARK 3 T33: 0.2750 T12: -0.0103 REMARK 3 T13: -0.0467 T23: 0.0595 REMARK 3 L TENSOR REMARK 3 L11: 1.3855 L22: 2.0041 REMARK 3 L33: 2.6710 L12: -0.4719 REMARK 3 L13: 0.1417 L23: -1.1081 REMARK 3 S TENSOR REMARK 3 S11: -0.0405 S12: 0.0549 S13: 0.1639 REMARK 3 S21: 0.1602 S22: -0.0662 S23: -0.2918 REMARK 3 S31: -0.1749 S32: 0.1312 S33: 0.0966 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): -31.5501 18.3260 18.3796 REMARK 3 T TENSOR REMARK 3 T11: 0.2756 T22: 0.3887 REMARK 3 T33: 0.3344 T12: -0.0232 REMARK 3 T13: 0.0244 T23: 0.0458 REMARK 3 L TENSOR REMARK 3 L11: 3.5866 L22: 2.3607 REMARK 3 L33: 4.2315 L12: -0.7774 REMARK 3 L13: 0.1728 L23: 0.2686 REMARK 3 S TENSOR REMARK 3 S11: 0.0282 S12: -0.7427 S13: -0.3919 REMARK 3 S21: 0.2014 S22: 0.1601 S23: 0.7068 REMARK 3 S31: 0.0897 S32: -0.7429 S33: -0.2566 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 3 THROUGH 7 ) REMARK 3 ORIGIN FOR THE GROUP (A): -34.5878 8.0115 21.1245 REMARK 3 T TENSOR REMARK 3 T11: 0.4526 T22: 0.6825 REMARK 3 T33: 0.6117 T12: -0.1759 REMARK 3 T13: 0.0438 T23: -0.0181 REMARK 3 L TENSOR REMARK 3 L11: 3.9070 L22: 6.7484 REMARK 3 L33: 2.6129 L12: -3.8835 REMARK 3 L13: -0.9737 L23: -1.4179 REMARK 3 S TENSOR REMARK 3 S11: -0.2483 S12: 0.3520 S13: -1.1088 REMARK 3 S21: -0.4905 S22: -0.2328 S23: 0.7623 REMARK 3 S31: 0.8544 S32: -1.0813 S33: -0.2126 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 8 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): -33.3561 30.3679 15.8184 REMARK 3 T TENSOR REMARK 3 T11: 0.4572 T22: 0.4881 REMARK 3 T33: 0.4222 T12: 0.1479 REMARK 3 T13: -0.1110 T23: 0.0374 REMARK 3 L TENSOR REMARK 3 L11: 0.7158 L22: 1.9118 REMARK 3 L33: 1.7759 L12: 0.9028 REMARK 3 L13: -0.7164 L23: -0.0640 REMARK 3 S TENSOR REMARK 3 S11: -0.4453 S12: 0.1005 S13: 0.3290 REMARK 3 S21: 0.2301 S22: 0.1972 S23: 0.6676 REMARK 3 S31: -0.8043 S32: -0.7334 S33: -0.0248 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 4QEN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000085958. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2830 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMETER 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 : 44950 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.60 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : 0.06700 REMARK 200 FOR THE DATA SET : 48.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.70 REMARK 200 R MERGE FOR SHELL (I) : 0.61000 REMARK 200 R SYM FOR SHELL (I) : 0.61000 REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG200, 5% PEG3000, AND 0.1 M MES, REMARK 280 PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 27.19750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.29050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.00450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.29050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.19750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.00450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 92 REMARK 465 ASN A 93 REMARK 465 GLY A 94 REMARK 465 LYS A 95 REMARK 465 ASP A 96 REMARK 465 VAL A 97 REMARK 465 ASN A 98 REMARK 465 GLN A 313 REMARK 465 VAL A 314 REMARK 465 ASN A 315 REMARK 465 PHE A 316 REMARK 465 VAL A 317 REMARK 465 ALA A 318 REMARK 465 GLY A 319 REMARK 465 ARG A 320 REMARK 465 ILE A 321 REMARK 465 PRO A 322 REMARK 465 THR A 323 REMARK 465 SER A 324 REMARK 465 THR A 325 REMARK 465 SER A 326 REMARK 465 GLU A 327 REMARK 465 ASP A 486 REMARK 465 THR A 487 REMARK 465 ILE A 488 REMARK 465 SER A 489 REMARK 465 ASP A 490 REMARK 465 GLN A 500 REMARK 465 GLN A 501 REMARK 465 THR A 502 REMARK 465 MET A 503 REMARK 465 GLN A 504 REMARK 465 GLY A 505 REMARK 465 LEU A 506 REMARK 465 GLY A 507 REMARK 465 GLY A 508 REMARK 465 ARG A 509 REMARK 465 GLN A 510 REMARK 465 ARG A 511 REMARK 465 ARG A 512 REMARK 465 LEU A 513 REMARK 465 ARG A 514 REMARK 465 ASP A 515 REMARK 465 VAL A 516 REMARK 465 ALA A 517 REMARK 465 VAL A 518 REMARK 465 PRO A 519 REMARK 465 MET A 520 REMARK 465 ASN A 521 REMARK 465 ASN A 522 REMARK 465 GLY A 523 REMARK 465 VAL A 524 REMARK 465 SER A 525 REMARK 465 GLN A 526 REMARK 465 SER A 527 REMARK 465 SER A 528 REMARK 465 GLU A 529 REMARK 465 ASP A 530 REMARK 465 GLU A 531 REMARK 465 ASN A 532 REMARK 465 ALA A 533 REMARK 465 DG C 12 REMARK 465 DT C 13 REMARK 465 DA C 14 REMARK 465 DT C 15 REMARK 465 DA D 1 REMARK 465 DC D 2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DC D 12 O3' DC D 12 C3' -0.039 REMARK 500 REMARK 500 REMARK: NULL 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 DA C 8 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 DA C 11 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC D 12 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT D 15 O4' - C1' - N1 ANGL. DEV. = 2.1 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 TYR A 190 61.13 -117.51 REMARK 500 ALA A 214 -96.76 65.94 REMARK 500 ARG A 241 -128.52 51.37 REMARK 500 ASP A 353 62.08 -114.64 REMARK 500 SER A 565 -51.69 -144.60 REMARK 500 MET A 586 -0.46 80.20 REMARK 500 ASP A 604 -120.02 -165.54 REMARK 500 ASN A 618 40.08 -99.43 REMARK 500 ARG A 620 -22.36 63.45 REMARK 500 LYS A 621 2.30 82.00 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 A 802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 383 SG REMARK 620 2 CYS A 397 SG 115.5 REMARK 620 3 CYS A 425 SG 114.1 109.8 REMARK 620 4 CYS A 429 SG 104.3 99.4 112.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 804 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 383 SG REMARK 620 2 CYS A 385 SG 110.1 REMARK 620 3 CYS A 389 SG 98.1 103.0 REMARK 620 4 CYS A 395 SG 114.4 109.9 120.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 803 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 389 SG REMARK 620 2 CYS A 425 SG 103.3 REMARK 620 3 CYS A 431 SG 109.9 107.7 REMARK 620 4 CYS A 435 SG 102.6 116.3 116.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 805 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 554 SG REMARK 620 2 CYS A 612 SG 109.0 REMARK 620 3 CYS A 614 SG 107.1 107.5 REMARK 620 4 CYS A 619 SG 115.9 107.3 109.8 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 SAH A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 805 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QEO RELATED DB: PDB REMARK 900 RELATED ID: 4QEP RELATED DB: PDB DBREF 4QEN A 93 624 UNP Q8GZB6 SUVH4_ARATH 93 624 DBREF 4QEN C 1 15 PDB 4QEN 4QEN 1 15 DBREF 4QEN D 1 15 PDB 4QEN 4QEN 1 15 SEQADV 4QEN SER A 92 UNP Q8GZB6 EXPRESSION TAG SEQRES 1 A 533 SER ASN GLY LYS ASP VAL ASN LEU GLU PRO HIS LEU LYS SEQRES 2 A 533 VAL THR LYS CYS LEU ARG LEU PHE ASN LYS GLN TYR LEU SEQRES 3 A 533 LEU CYS VAL GLN ALA LYS LEU SER ARG PRO ASP LEU LYS SEQRES 4 A 533 GLY VAL THR GLU MET ILE LYS ALA LYS ALA ILE LEU TYR SEQRES 5 A 533 PRO ARG LYS ILE ILE GLY ASP LEU PRO GLY ILE ASP VAL SEQRES 6 A 533 GLY HIS ARG PHE PHE SER ARG ALA GLU MET CYS ALA VAL SEQRES 7 A 533 GLY PHE HIS ASN HIS TRP LEU ASN GLY ILE ASP TYR MET SEQRES 8 A 533 SER MET GLU TYR GLU LYS GLU TYR SER ASN TYR LYS LEU SEQRES 9 A 533 PRO LEU ALA VAL SER ILE VAL MET SER GLY GLN TYR GLU SEQRES 10 A 533 ASP ASP LEU ASP ASN ALA ASP THR VAL THR TYR THR GLY SEQRES 11 A 533 GLN GLY GLY HIS ASN LEU THR GLY ASN LYS ARG GLN ILE SEQRES 12 A 533 LYS ASP GLN LEU LEU GLU ARG GLY ASN LEU ALA LEU LYS SEQRES 13 A 533 HIS CYS CYS GLU TYR ASN VAL PRO VAL ARG VAL THR ARG SEQRES 14 A 533 GLY HIS ASN CYS LYS SER SER TYR THR LYS ARG VAL TYR SEQRES 15 A 533 THR TYR ASP GLY LEU TYR LYS VAL GLU LYS PHE TRP ALA SEQRES 16 A 533 GLN LYS GLY VAL SER GLY PHE THR VAL TYR LYS TYR ARG SEQRES 17 A 533 LEU LYS ARG LEU GLU GLY GLN PRO GLU LEU THR THR ASP SEQRES 18 A 533 GLN VAL ASN PHE VAL ALA GLY ARG ILE PRO THR SER THR SEQRES 19 A 533 SER GLU ILE GLU GLY LEU VAL CYS GLU ASP ILE SER GLY SEQRES 20 A 533 GLY LEU GLU PHE LYS GLY ILE PRO ALA THR ASN ARG VAL SEQRES 21 A 533 ASP ASP SER PRO VAL SER PRO THR SER GLY PHE THR TYR SEQRES 22 A 533 ILE LYS SER LEU ILE ILE GLU PRO ASN VAL ILE ILE PRO SEQRES 23 A 533 LYS SER SER THR GLY CYS ASN CYS ARG GLY SER CYS THR SEQRES 24 A 533 ASP SER LYS LYS CYS ALA CYS ALA LYS LEU ASN GLY GLY SEQRES 25 A 533 ASN PHE PRO TYR VAL ASP LEU ASN ASP GLY ARG LEU ILE SEQRES 26 A 533 GLU SER ARG ASP VAL VAL PHE GLU CYS GLY PRO HIS CYS SEQRES 27 A 533 GLY CYS GLY PRO LYS CYS VAL ASN ARG THR SER GLN LYS SEQRES 28 A 533 ARG LEU ARG PHE ASN LEU GLU VAL PHE ARG SER ALA LYS SEQRES 29 A 533 LYS GLY TRP ALA VAL ARG SER TRP GLU TYR ILE PRO ALA SEQRES 30 A 533 GLY SER PRO VAL CYS GLU TYR ILE GLY VAL VAL ARG ARG SEQRES 31 A 533 THR ALA ASP VAL ASP THR ILE SER ASP ASN GLU TYR ILE SEQRES 32 A 533 PHE GLU ILE ASP CYS GLN GLN THR MET GLN GLY LEU GLY SEQRES 33 A 533 GLY ARG GLN ARG ARG LEU ARG ASP VAL ALA VAL PRO MET SEQRES 34 A 533 ASN ASN GLY VAL SER GLN SER SER GLU ASP GLU ASN ALA SEQRES 35 A 533 PRO GLU PHE CYS ILE ASP ALA GLY SER THR GLY ASN PHE SEQRES 36 A 533 ALA ARG PHE ILE ASN HIS SER CYS GLU PRO ASN LEU PHE SEQRES 37 A 533 VAL GLN CYS VAL LEU SER SER HIS GLN ASP ILE ARG LEU SEQRES 38 A 533 ALA ARG VAL VAL LEU PHE ALA ALA ASP ASN ILE SER PRO SEQRES 39 A 533 MET GLN GLU LEU THR TYR ASP TYR GLY TYR ALA LEU ASP SEQRES 40 A 533 SER VAL HIS GLY PRO ASP GLY LYS VAL LYS GLN LEU ALA SEQRES 41 A 533 CYS TYR CYS GLY ALA LEU ASN CYS ARG LYS ARG LEU TYR SEQRES 1 C 15 DG DG DT DA DC DT 5CM DA DT DC DA DG DT SEQRES 2 C 15 DA DT SEQRES 1 D 15 DA DC DT DG DA DT DG DA DG DT DA DC DC SEQRES 2 D 15 DA DT MODRES 4QEN 5CM C 7 DC HET 5CM C 7 20 HET SAH A 801 26 HET ZN A 802 1 HET ZN A 803 1 HET ZN A 804 1 HET ZN A 805 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM ZN ZINC ION FORMUL 2 5CM C10 H16 N3 O7 P FORMUL 4 SAH C14 H20 N6 O5 S FORMUL 5 ZN 4(ZN 2+) FORMUL 9 HOH *383(H2 O) HELIX 1 1 GLU A 100 ALA A 122 1 23 HELIX 2 2 ARG A 126 ALA A 138 1 13 HELIX 3 3 SER A 162 GLY A 170 1 9 HELIX 4 4 SER A 183 GLU A 187 5 5 HELIX 5 5 ARG A 241 ASN A 253 1 13 HELIX 6 6 CYS A 395 ASN A 401 1 7 HELIX 7 7 CYS A 435 LYS A 442 5 8 HELIX 8 8 ALA A 483 VAL A 485 5 3 HELIX 9 9 ASN A 545 ILE A 550 5 6 HELIX 10 10 ASP A 569 ALA A 573 5 5 SHEET 1 A 5 ARG A 159 PHE A 160 0 SHEET 2 A 5 ARG A 271 LYS A 288 -1 O TYR A 273 N PHE A 160 SHEET 3 A 5 VAL A 256 ASN A 263 -1 N HIS A 262 O VAL A 272 SHEET 4 A 5 LEU A 197 MET A 203 1 N MET A 203 O THR A 259 SHEET 5 A 5 ILE A 179 MET A 182 -1 N ASP A 180 O SER A 200 SHEET 1 B 5 ARG A 159 PHE A 160 0 SHEET 2 B 5 ARG A 271 LYS A 288 -1 O TYR A 273 N PHE A 160 SHEET 3 B 5 THR A 294 ARG A 302 -1 O VAL A 295 N GLN A 287 SHEET 4 B 5 THR A 216 THR A 220 -1 N VAL A 217 O LEU A 300 SHEET 5 B 5 LEU A 211 ASN A 213 -1 N LEU A 211 O THR A 218 SHEET 1 C 4 LEU A 331 CYS A 333 0 SHEET 2 C 4 ALA A 347 THR A 348 -1 O ALA A 347 N VAL A 332 SHEET 3 C 4 LEU A 448 ARG A 452 1 O VAL A 450 N THR A 348 SHEET 4 C 4 TRP A 458 SER A 462 -1 O ARG A 461 N GLU A 449 SHEET 1 D 2 THR A 363 TYR A 364 0 SHEET 2 D 2 THR A 543 GLY A 544 1 O GLY A 544 N THR A 363 SHEET 1 E 4 ILE A 369 ILE A 370 0 SHEET 2 E 4 VAL A 478 ARG A 481 1 O VAL A 479 N ILE A 369 SHEET 3 E 4 PHE A 536 ASP A 539 -1 O ASP A 539 N VAL A 478 SHEET 4 E 4 ILE A 494 GLU A 496 -1 N PHE A 495 O ILE A 538 SHEET 1 F 2 TYR A 407 VAL A 408 0 SHEET 2 F 2 ARG A 414 LEU A 415 -1 O ARG A 414 N VAL A 408 SHEET 1 G 4 VAL A 422 PHE A 423 0 SHEET 2 G 4 LEU A 558 LEU A 564 1 O LEU A 564 N VAL A 422 SHEET 3 G 4 ARG A 574 ALA A 579 -1 O ARG A 574 N VAL A 563 SHEET 4 G 4 PRO A 471 GLU A 474 -1 N VAL A 472 O LEU A 577 SHEET 1 H 2 ASN A 551 HIS A 552 0 SHEET 2 H 2 THR A 590 TYR A 591 1 O TYR A 591 N ASN A 551 LINK O3' DT C 6 P 5CM C 7 1555 1555 1.61 LINK O3' 5CM C 7 P DA C 8 1555 1555 1.61 LINK SG CYS A 383 ZN ZN A 802 1555 1555 2.33 LINK SG CYS A 383 ZN ZN A 804 1555 1555 2.41 LINK SG CYS A 385 ZN ZN A 804 1555 1555 2.40 LINK SG CYS A 389 ZN ZN A 803 1555 1555 2.43 LINK SG CYS A 389 ZN ZN A 804 1555 1555 2.30 LINK SG CYS A 395 ZN ZN A 804 1555 1555 2.39 LINK SG CYS A 397 ZN ZN A 802 1555 1555 2.25 LINK SG CYS A 425 ZN ZN A 802 1555 1555 2.42 LINK SG CYS A 425 ZN ZN A 803 1555 1555 2.35 LINK SG CYS A 429 ZN ZN A 802 1555 1555 2.45 LINK SG CYS A 431 ZN ZN A 803 1555 1555 2.31 LINK SG CYS A 435 ZN ZN A 803 1555 1555 2.40 LINK SG CYS A 554 ZN ZN A 805 1555 1555 2.43 LINK SG CYS A 612 ZN ZN A 805 1555 1555 2.31 LINK SG CYS A 614 ZN ZN A 805 1555 1555 2.36 LINK SG CYS A 619 ZN ZN A 805 1555 1555 2.36 CISPEP 1 LEU A 195 PRO A 196 0 1.82 SITE 1 AC1 15 LYS A 456 GLY A 457 TRP A 458 GLU A 492 SITE 2 AC1 15 TYR A 493 ARG A 548 ASN A 551 HIS A 552 SITE 3 AC1 15 TYR A 593 ALA A 611 CYS A 612 TYR A 613 SITE 4 AC1 15 LEU A 623 HOH A 993 HOH A1174 SITE 1 AC2 4 CYS A 383 CYS A 397 CYS A 425 CYS A 429 SITE 1 AC3 4 CYS A 389 CYS A 425 CYS A 431 CYS A 435 SITE 1 AC4 4 CYS A 383 CYS A 385 CYS A 389 CYS A 395 SITE 1 AC5 4 CYS A 554 CYS A 612 CYS A 614 CYS A 619 CRYST1 54.395 98.009 122.581 90.00 90.00 90.00 P 21 21 21 4 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 0.018384 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010203 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008158 0.00000