HEADER GENE REGULATION/DNA 24-JUN-18 6A5N TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA SUVH6 IN COMPLEX WITH TITLE 2 METHYLATED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC COMPND 3 SUVH6; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: HISTONE H3-K9 METHYLTRANSFERASE 6,H3-K9-HMTASE 6,PROTEIN SET COMPND 6 DOMAIN GROUP 23,SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG PROTEIN 6, COMPND 7 SU(VAR)3-9 HOMOLOG PROTEIN 6; COMPND 8 EC: 2.1.1.43; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: DNA (5'-D(*GP*AP*GP*TP*AP*CP*TP*(5CM)P*AP*GP*CP*AP*GP*T)- COMPND 13 3'); COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: METHYLATED DNA; COMPND 17 MOL_ID: 3; COMPND 18 MOLECULE: DNA (5'-D(*CP*AP*CP*TP*GP*CP*TP*GP*AP*GP*TP*AP*CP*T)-3'); COMPND 19 CHAIN: D; COMPND 20 ENGINEERED: YES; COMPND 21 OTHER_DETAILS: COMPLEMENTARY DNA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: SUVH6, SDG23, SET23, AT2G22740, T9I22.18; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: 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 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS SRA, SET, HISTONE METHYLTRANSFERASE, DNA METHYLATION, GENE KEYWDS 2 REGULATION, GENE REGULATION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.LI,J.DU REVDAT 4 22-NOV-23 6A5N 1 LINK REVDAT 3 26-SEP-18 6A5N 1 JRNL REVDAT 2 19-SEP-18 6A5N 1 JRNL REVDAT 1 29-AUG-18 6A5N 0 JRNL AUTH X.LI,C.J.HARRIS,Z.ZHONG,W.CHEN,R.LIU,B.JIA,Z.WANG,S.LI, JRNL AUTH 2 S.E.JACOBSEN,J.DU JRNL TITL MECHANISTIC INSIGHTS INTO PLANT SUVH FAMILY H3K9 JRNL TITL 2 METHYLTRANSFERASES AND THEIR BINDING TO CONTEXT-BIASED JRNL TITL 3 NON-CG DNA METHYLATION. JRNL REF PROC. NATL. ACAD. SCI. V. 115 E8793 2018 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 30150382 JRNL DOI 10.1073/PNAS.1809841115 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 24873 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1267 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 33.5949 - 4.9876 0.96 2735 139 0.1873 0.2277 REMARK 3 2 4.9876 - 3.9608 0.97 2632 166 0.1811 0.2270 REMARK 3 3 3.9608 - 3.4607 0.90 2434 126 0.2346 0.2946 REMARK 3 4 3.4607 - 3.1445 0.99 2674 160 0.2532 0.3078 REMARK 3 5 3.1445 - 2.9193 1.00 2641 142 0.2729 0.3158 REMARK 3 6 2.9193 - 2.7473 1.00 2640 152 0.2864 0.3504 REMARK 3 7 2.7473 - 2.6097 0.96 2602 129 0.3838 0.4755 REMARK 3 8 2.6097 - 2.4962 1.00 2633 136 0.3178 0.3879 REMARK 3 9 2.4962 - 2.4001 0.99 2615 117 0.3129 0.3753 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.830 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 : 0.009 4615 REMARK 3 ANGLE : 1.314 6331 REMARK 3 CHIRALITY : 0.077 678 REMARK 3 PLANARITY : 0.005 737 REMARK 3 DIHEDRAL : 22.034 1784 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 266 THROUGH 469 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.9449 -1.4330 104.8948 REMARK 3 T TENSOR REMARK 3 T11: 0.3304 T22: 0.3812 REMARK 3 T33: 0.3914 T12: -0.0174 REMARK 3 T13: 0.0388 T23: 0.0990 REMARK 3 L TENSOR REMARK 3 L11: 6.0180 L22: 1.4121 REMARK 3 L33: 1.2209 L12: -2.2509 REMARK 3 L13: 0.0408 L23: 0.4829 REMARK 3 S TENSOR REMARK 3 S11: -0.0460 S12: -0.1152 S13: -0.4590 REMARK 3 S21: 0.1012 S22: 0.0635 S23: 0.1634 REMARK 3 S31: 0.1304 S32: -0.1417 S33: -0.0006 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 470 THROUGH 518 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.7228 -6.8370 124.8953 REMARK 3 T TENSOR REMARK 3 T11: 0.7108 T22: 0.5914 REMARK 3 T33: 0.6337 T12: 0.1376 REMARK 3 T13: 0.0344 T23: 0.1198 REMARK 3 L TENSOR REMARK 3 L11: 5.1903 L22: 0.8296 REMARK 3 L33: 2.8406 L12: -2.2419 REMARK 3 L13: -3.6521 L23: 1.5910 REMARK 3 S TENSOR REMARK 3 S11: -0.6438 S12: -0.6115 S13: -0.5331 REMARK 3 S21: 0.6726 S22: 0.2150 S23: 0.1852 REMARK 3 S31: 0.7806 S32: 0.0881 S33: 0.4792 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 519 THROUGH 780 ) REMARK 3 ORIGIN FOR THE GROUP (A): -51.2210 14.4849 123.4487 REMARK 3 T TENSOR REMARK 3 T11: 0.3363 T22: 0.6223 REMARK 3 T33: 0.5026 T12: 0.0419 REMARK 3 T13: 0.0645 T23: -0.0091 REMARK 3 L TENSOR REMARK 3 L11: 1.6902 L22: 1.9706 REMARK 3 L33: 1.7011 L12: -0.5545 REMARK 3 L13: 0.0865 L23: -0.3234 REMARK 3 S TENSOR REMARK 3 S11: -0.1245 S12: -0.3849 S13: 0.2533 REMARK 3 S21: 0.1637 S22: 0.0488 S23: 0.1655 REMARK 3 S31: -0.1628 S32: -0.0577 S33: 0.0681 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 2 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): -36.3662 -9.4074 93.1175 REMARK 3 T TENSOR REMARK 3 T11: 0.5315 T22: 0.4251 REMARK 3 T33: 0.7180 T12: 0.0360 REMARK 3 T13: -0.0050 T23: 0.0930 REMARK 3 L TENSOR REMARK 3 L11: 8.6676 L22: 5.8746 REMARK 3 L33: 5.8863 L12: 0.8839 REMARK 3 L13: -0.9363 L23: 0.0275 REMARK 3 S TENSOR REMARK 3 S11: 0.1088 S12: 0.9968 S13: 0.2007 REMARK 3 S21: -0.7590 S22: -0.0566 S23: 0.3916 REMARK 3 S31: 0.4391 S32: -1.0897 S33: -0.0987 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 2 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): -41.7594 -16.6493 97.4900 REMARK 3 T TENSOR REMARK 3 T11: 1.3401 T22: 0.7509 REMARK 3 T33: 0.9317 T12: -0.0012 REMARK 3 T13: 0.2750 T23: 0.0370 REMARK 3 L TENSOR REMARK 3 L11: 8.8885 L22: 4.6020 REMARK 3 L33: 4.4422 L12: 5.4794 REMARK 3 L13: -5.3934 L23: -4.4715 REMARK 3 S TENSOR REMARK 3 S11: -0.6721 S12: 0.2138 S13: -2.1893 REMARK 3 S21: -1.9563 S22: -0.1656 S23: -0.5157 REMARK 3 S31: 1.8001 S32: 1.7004 S33: 0.9358 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 9 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.6718 -1.4973 89.0387 REMARK 3 T TENSOR REMARK 3 T11: 1.0677 T22: 1.0834 REMARK 3 T33: 0.7921 T12: 0.1615 REMARK 3 T13: 0.3115 T23: 0.1680 REMARK 3 L TENSOR REMARK 3 L11: 4.5970 L22: 9.3564 REMARK 3 L33: 3.8933 L12: 5.4843 REMARK 3 L13: 2.4726 L23: 0.3619 REMARK 3 S TENSOR REMARK 3 S11: 0.1545 S12: 1.1694 S13: -0.4136 REMARK 3 S21: 1.1864 S22: 0.7337 S23: 0.2324 REMARK 3 S31: 0.1303 S32: 0.7509 S33: -0.4365 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 6A5N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1300008194. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25062 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 97.9 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.71500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 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: 6A5K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% ETHANOL, 10% W/V GLYCEROL, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 37.06850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.92250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.72150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.92250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.06850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.72150 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: 4050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 264 REMARK 465 SER A 265 REMARK 465 VAL A 399 REMARK 465 MET A 400 REMARK 465 GLN A 401 REMARK 465 VAL A 402 REMARK 465 LYS A 403 REMARK 465 LYS A 404 REMARK 465 LYS A 405 REMARK 465 GLY A 406 REMARK 465 GLU A 407 REMARK 465 GLU A 408 REMARK 465 LEU A 409 REMARK 465 LYS A 410 REMARK 465 GLU A 411 REMARK 465 GLY A 781 REMARK 465 ALA A 782 REMARK 465 ALA A 783 REMARK 465 VAL A 784 REMARK 465 CYS A 785 REMARK 465 ARG A 786 REMARK 465 ARG A 787 REMARK 465 ARG A 788 REMARK 465 LEU A 789 REMARK 465 TYR A 790 REMARK 465 DG C 1 REMARK 465 DC D 1 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 2 O4' - C1' - N9 ANGL. DEV. = 2.2 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 THR A 419 -114.00 39.97 REMARK 500 ASP A 446 60.57 37.65 REMARK 500 LYS A 500 -51.83 70.26 REMARK 500 VAL A 609 -57.71 -131.22 REMARK 500 ILE A 642 -72.71 -89.63 REMARK 500 ARG A 658 -11.39 87.35 REMARK 500 ASP A 662 -48.77 72.83 REMARK 500 ASN A 711 -154.75 -104.80 REMARK 500 ASP A 732 -44.87 71.53 REMARK 500 ASP A 735 109.79 -55.02 REMARK 500 LEU A 752 -12.72 72.51 REMARK 500 TYR A 761 165.11 83.19 REMARK 500 LEU A 763 -10.10 80.75 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 801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 553 SG REMARK 620 2 CYS A 569 SG 127.1 REMARK 620 3 CYS A 595 SG 95.6 107.6 REMARK 620 4 CYS A 599 SG 111.2 103.8 110.9 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 553 SG REMARK 620 2 CYS A 555 SG 117.5 REMARK 620 3 CYS A 559 SG 87.3 104.2 REMARK 620 4 CYS A 567 SG 110.6 122.1 108.3 REMARK 620 N 1 2 3 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 559 SG REMARK 620 2 CYS A 595 SG 113.0 REMARK 620 3 CYS A 601 SG 123.0 102.4 REMARK 620 4 CYS A 605 SG 100.8 108.5 108.7 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 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 DBREF 6A5N A 264 790 UNP Q8VZ17 SUVH6_ARATH 264 790 DBREF 6A5N C 1 14 PDB 6A5N 6A5N 1 14 DBREF 6A5N D 1 14 PDB 6A5N 6A5N 1 14 SEQADV 6A5N LEU A 777 UNP Q8VZ17 PRO 777 ENGINEERED MUTATION SEQRES 1 A 527 SER SER GLY ASP SER SER ARG ASN LYS VAL LYS GLU THR SEQRES 2 A 527 LEU ARG LEU PHE HIS GLY VAL CYS ARG LYS ILE LEU GLN SEQRES 3 A 527 GLU ASP GLU ALA LYS PRO GLU ASP GLN ARG ARG LYS GLY SEQRES 4 A 527 LYS GLY LEU ARG ILE ASP PHE GLU ALA SER THR ILE LEU SEQRES 5 A 527 LYS ARG ASN GLY LYS PHE LEU ASN SER GLY VAL HIS ILE SEQRES 6 A 527 LEU GLY GLU VAL PRO GLY VAL GLU VAL GLY ASP GLU PHE SEQRES 7 A 527 GLN TYR ARG MET GLU LEU ASN ILE LEU GLY ILE HIS LYS SEQRES 8 A 527 PRO SER GLN ALA GLY ILE ASP TYR MET LYS TYR GLY LYS SEQRES 9 A 527 ALA LYS VAL ALA THR SER ILE VAL ALA SER GLY GLY TYR SEQRES 10 A 527 ASP ASP HIS LEU ASP ASN SER ASP VAL LEU THR TYR THR SEQRES 11 A 527 GLY GLN GLY GLY ASN VAL MET GLN VAL LYS LYS LYS GLY SEQRES 12 A 527 GLU GLU LEU LYS GLU PRO GLU ASP GLN LYS LEU ILE THR SEQRES 13 A 527 GLY ASN LEU ALA LEU ALA THR SER ILE GLU LYS GLN THR SEQRES 14 A 527 PRO VAL ARG VAL ILE ARG GLY LYS HIS LYS SER THR HIS SEQRES 15 A 527 ASP LYS SER LYS GLY GLY ASN TYR VAL TYR ASP GLY LEU SEQRES 16 A 527 TYR LEU VAL GLU LYS TYR TRP GLN GLN VAL GLY SER HIS SEQRES 17 A 527 GLY MET ASN VAL PHE LYS PHE GLN LEU ARG ARG ILE PRO SEQRES 18 A 527 GLY GLN PRO GLU LEU SER TRP VAL GLU VAL LYS LYS SER SEQRES 19 A 527 LYS SER LYS TYR ARG GLU GLY LEU CYS LYS LEU ASP ILE SEQRES 20 A 527 SER GLU GLY LYS GLU GLN SER PRO ILE SER ALA VAL ASN SEQRES 21 A 527 GLU ILE ASP ASP GLU LYS PRO PRO LEU PHE THR TYR THR SEQRES 22 A 527 VAL LYS LEU ILE TYR PRO ASP TRP CYS ARG PRO VAL PRO SEQRES 23 A 527 PRO LYS SER CYS CYS CYS THR THR ARG CYS THR GLU ALA SEQRES 24 A 527 GLU ALA ARG VAL CYS ALA CYS VAL GLU LYS ASN GLY GLY SEQRES 25 A 527 GLU ILE PRO TYR ASN PHE ASP GLY ALA ILE VAL GLY ALA SEQRES 26 A 527 LYS PRO THR ILE TYR GLU CYS GLY PRO LEU CYS LYS CYS SEQRES 27 A 527 PRO SER SER CYS TYR LEU ARG VAL THR GLN HIS GLY ILE SEQRES 28 A 527 LYS LEU PRO LEU GLU ILE PHE LYS THR LYS SER ARG GLY SEQRES 29 A 527 TRP GLY VAL ARG CYS LEU LYS SER ILE PRO ILE GLY SER SEQRES 30 A 527 PHE ILE CYS GLU TYR VAL GLY GLU LEU LEU GLU ASP SER SEQRES 31 A 527 GLU ALA GLU ARG ARG ILE GLY ASN ASP GLU TYR LEU PHE SEQRES 32 A 527 ASP ILE GLY ASN ARG TYR ASP ASN SER LEU ALA GLN GLY SEQRES 33 A 527 MET SER GLU LEU MET LEU GLY THR GLN ALA GLY ARG SER SEQRES 34 A 527 MET ALA GLU GLY ASP GLU SER SER GLY PHE THR ILE ASP SEQRES 35 A 527 ALA ALA SER LYS GLY ASN VAL GLY ARG PHE ILE ASN HIS SEQRES 36 A 527 SER CYS SER PRO ASN LEU TYR ALA GLN ASN VAL LEU TYR SEQRES 37 A 527 ASP HIS GLU ASP SER ARG ILE PRO HIS VAL MET PHE PHE SEQRES 38 A 527 ALA GLN ASP ASN ILE PRO PRO LEU GLN GLU LEU CYS TYR SEQRES 39 A 527 ASP TYR ASN TYR ALA LEU ASP GLN VAL ARG ASP SER LYS SEQRES 40 A 527 GLY ASN ILE LYS GLN LYS LEU CYS PHE CYS GLY ALA ALA SEQRES 41 A 527 VAL CYS ARG ARG ARG LEU TYR SEQRES 1 C 14 DG DA DG DT DA DC DT 5CM DA DG DC DA DG SEQRES 2 C 14 DT SEQRES 1 D 14 DC DA DC DT DG DC DT DG DA DG DT DA DC SEQRES 2 D 14 DT HET 5CM C 8 20 HET ZN A 801 1 HET ZN A 802 1 HET ZN A 803 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION FORMUL 2 5CM C10 H16 N3 O7 P FORMUL 4 ZN 3(ZN 2+) FORMUL 7 HOH *40(H2 O) HELIX 1 AA1 GLY A 266 LYS A 294 1 29 HELIX 2 AA2 PRO A 295 ARG A 299 5 5 HELIX 3 AA3 ARG A 306 ASN A 318 1 13 HELIX 4 AA4 TYR A 343 GLY A 351 1 9 HELIX 5 AA5 ILE A 418 GLN A 431 1 14 HELIX 6 AA6 SER A 490 SER A 499 1 10 HELIX 7 AA7 CYS A 567 ASN A 573 1 7 HELIX 8 AA8 ASN A 674 LEU A 685 1 12 HELIX 9 AA9 ASN A 711 ILE A 716 5 6 SHEET 1 AA1 5 GLU A 340 PHE A 341 0 SHEET 2 AA1 5 TYR A 453 VAL A 468 -1 O TYR A 453 N PHE A 341 SHEET 3 AA1 5 VAL A 434 GLY A 439 -1 N VAL A 436 O ASP A 456 SHEET 4 AA1 5 ALA A 368 ALA A 376 1 N ILE A 374 O ARG A 435 SHEET 5 AA1 5 ILE A 360 TYR A 365 -1 N ASP A 361 O SER A 373 SHEET 1 AA2 4 GLU A 340 PHE A 341 0 SHEET 2 AA2 4 TYR A 453 VAL A 468 -1 O TYR A 453 N PHE A 341 SHEET 3 AA2 4 ASN A 474 ARG A 482 -1 O VAL A 475 N GLN A 467 SHEET 4 AA2 4 VAL A 389 THR A 393 -1 N LEU A 390 O LEU A 480 SHEET 1 AA3 4 LEU A 505 LYS A 507 0 SHEET 2 AA3 4 SER A 520 VAL A 522 -1 O ALA A 521 N CYS A 506 SHEET 3 AA3 4 LEU A 618 THR A 623 1 O ILE A 620 N VAL A 522 SHEET 4 AA3 4 GLY A 627 CYS A 632 -1 O ARG A 631 N GLU A 619 SHEET 1 AA4 2 THR A 534 TYR A 535 0 SHEET 2 AA4 2 LYS A 709 GLY A 710 1 O GLY A 710 N THR A 534 SHEET 1 AA5 4 ILE A 592 TYR A 593 0 SHEET 2 AA5 4 LEU A 724 LEU A 730 1 O LEU A 730 N ILE A 592 SHEET 3 AA5 4 HIS A 740 ALA A 745 -1 O MET A 742 N GLN A 727 SHEET 4 AA5 4 PHE A 641 GLU A 644 -1 N ILE A 642 O PHE A 743 SHEET 1 AA6 3 GLU A 648 GLU A 651 0 SHEET 2 AA6 3 PHE A 702 ASP A 705 -1 O ASP A 705 N GLU A 648 SHEET 3 AA6 3 LEU A 665 ASP A 667 -1 N PHE A 666 O ILE A 704 SHEET 1 AA7 2 TYR A 672 ASP A 673 0 SHEET 2 AA7 2 MET A 693 ALA A 694 -1 O ALA A 694 N TYR A 672 SHEET 1 AA8 2 ASN A 717 HIS A 718 0 SHEET 2 AA8 2 CYS A 756 TYR A 757 1 O TYR A 757 N ASN A 717 SHEET 1 AA9 2 GLN A 765 ARG A 767 0 SHEET 2 AA9 2 ILE A 773 GLN A 775 -1 O LYS A 774 N VAL A 766 LINK O3' DT C 7 P 5CM C 8 1555 1555 1.60 LINK O3' 5CM C 8 P DA C 9 1555 1555 1.62 LINK SG CYS A 553 ZN ZN A 801 1555 1555 2.42 LINK SG CYS A 553 ZN ZN A 803 1555 1555 2.57 LINK SG CYS A 555 ZN ZN A 803 1555 1555 2.46 LINK SG CYS A 559 ZN ZN A 802 1555 1555 2.18 LINK SG CYS A 559 ZN ZN A 803 1555 1555 2.46 LINK SG CYS A 567 ZN ZN A 803 1555 1555 2.29 LINK SG CYS A 569 ZN ZN A 801 1555 1555 2.17 LINK SG CYS A 595 ZN ZN A 801 1555 1555 2.62 LINK SG CYS A 595 ZN ZN A 802 1555 1555 2.11 LINK SG CYS A 599 ZN ZN A 801 1555 1555 2.41 LINK SG CYS A 601 ZN ZN A 802 1555 1555 2.44 LINK SG CYS A 605 ZN ZN A 802 1555 1555 2.65 SITE 1 AC1 4 CYS A 553 CYS A 569 CYS A 595 CYS A 599 SITE 1 AC2 4 CYS A 559 CYS A 595 CYS A 601 CYS A 605 SITE 1 AC3 4 CYS A 553 CYS A 555 CYS A 559 CYS A 567 CRYST1 74.137 79.443 107.845 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 0.013489 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012588 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009273 0.00000