HEADER DNA BINDING PROTEIN/DNA 21-JAN-25 9LNK TITLE CRYSTAL STRUCTURE OF VANC21 IN COMPLEX WITH ITS TARGET DNA (NATIVE). COMPND MOL_ID: 1; COMPND 2 MOLECULE: VANC21; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: VANC21 BINDING DNA FRAGMENT (MOTIF STRAND); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: VANC21 BINDING DNA FRAGMENT (COMPLEMENTARY STRAND); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 10 ORGANISM_TAXID: 3702; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 14 ORGANISM_TAXID: 3702 KEYWDS PROTEIN-DNA COMPLEX, TRANSPOSON, VANDAL, DNA BINDING PROTEIN, DNA KEYWDS 2 BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.TANAKA,W.SHIHOYA,H.HIRANO,Y.ITOH,T.KAKUTANI,O.NUREKI REVDAT 1 10-DEC-25 9LNK 0 JRNL AUTH Y.TANAKA,A.OSAKABE,W.SHIHOYA,H.HIRANO,Y.ITOH,T.KAKUTANI, JRNL AUTH 2 O.NUREKI JRNL TITL STRUCTURE AND EVOLUTION OF THE SEQUENCE-SPECIFIC JRNL TITL 2 ANTI-SILENCING FACTOR VANC21 AND ITS TARGET DNA. JRNL REF GENES GENET SYST 2025 JRNL REFN ISSN 1880-5779 JRNL PMID 41260640 JRNL DOI 10.1266/GGS.25-00096 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 28674 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1434 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 48.3500 - 5.4900 0.99 2900 153 0.2041 0.2380 REMARK 3 2 5.4900 - 4.3600 1.00 2755 144 0.1936 0.2375 REMARK 3 3 4.3600 - 3.8100 1.00 2739 145 0.1929 0.2255 REMARK 3 4 3.8100 - 3.4600 1.00 2710 143 0.2300 0.2556 REMARK 3 5 3.4600 - 3.2100 1.00 2742 144 0.2357 0.2659 REMARK 3 6 3.2100 - 3.0200 1.00 2687 141 0.2524 0.2831 REMARK 3 7 3.0200 - 2.8700 1.00 2687 142 0.2857 0.3232 REMARK 3 8 2.8700 - 2.7500 1.00 2664 140 0.2897 0.3043 REMARK 3 9 2.7500 - 2.6400 1.00 2680 142 0.2863 0.3082 REMARK 3 10 2.6400 - 2.5500 1.00 2676 140 0.3343 0.3912 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 69.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 74.52 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 : 0.010 3718 REMARK 3 ANGLE : 1.090 5152 REMARK 3 CHIRALITY : 0.056 553 REMARK 3 PLANARITY : 0.009 567 REMARK 3 DIHEDRAL : 20.994 731 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 275 THROUGH 313 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.4998 24.9261 -21.6363 REMARK 3 T TENSOR REMARK 3 T11: 0.4130 T22: 0.3902 REMARK 3 T33: 0.4558 T12: -0.0270 REMARK 3 T13: -0.0552 T23: -0.0179 REMARK 3 L TENSOR REMARK 3 L11: 3.9838 L22: 1.5616 REMARK 3 L33: 2.6860 L12: -0.2084 REMARK 3 L13: -0.7088 L23: -0.0767 REMARK 3 S TENSOR REMARK 3 S11: 0.1414 S12: -0.3127 S13: 0.3376 REMARK 3 S21: 0.1026 S22: 0.0445 S23: -0.1673 REMARK 3 S31: -0.3911 S32: -0.4142 S33: -0.1554 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 314 THROUGH 396 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.9437 25.7355 -25.9328 REMARK 3 T TENSOR REMARK 3 T11: 0.4639 T22: 0.4291 REMARK 3 T33: 0.4737 T12: -0.0200 REMARK 3 T13: -0.0657 T23: 0.0691 REMARK 3 L TENSOR REMARK 3 L11: 4.2702 L22: 1.1254 REMARK 3 L33: 3.6117 L12: 0.3157 REMARK 3 L13: -1.6485 L23: 0.0519 REMARK 3 S TENSOR REMARK 3 S11: -0.1460 S12: -0.0660 S13: 0.0102 REMARK 3 S21: -0.0447 S22: 0.0158 S23: -0.2313 REMARK 3 S31: -0.1864 S32: 0.2891 S33: 0.1364 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 397 THROUGH 433 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.8302 36.8160 -47.4053 REMARK 3 T TENSOR REMARK 3 T11: 0.7461 T22: 0.8866 REMARK 3 T33: 0.8229 T12: -0.1720 REMARK 3 T13: -0.0492 T23: 0.3324 REMARK 3 L TENSOR REMARK 3 L11: 6.6294 L22: 5.2667 REMARK 3 L33: 5.6926 L12: 1.2321 REMARK 3 L13: -0.9170 L23: -0.4436 REMARK 3 S TENSOR REMARK 3 S11: -0.0904 S12: 1.5690 S13: 0.9291 REMARK 3 S21: -0.4735 S22: 0.1347 S23: -0.5569 REMARK 3 S31: -0.9511 S32: 0.1244 S33: -0.0524 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 434 THROUGH 526 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.4268 31.4518 -32.4914 REMARK 3 T TENSOR REMARK 3 T11: 0.5094 T22: 0.4295 REMARK 3 T33: 0.5069 T12: -0.0657 REMARK 3 T13: -0.0517 T23: 0.0408 REMARK 3 L TENSOR REMARK 3 L11: 3.2780 L22: 2.0282 REMARK 3 L33: 3.3354 L12: 0.2798 REMARK 3 L13: -1.1486 L23: -0.5933 REMARK 3 S TENSOR REMARK 3 S11: -0.0782 S12: 0.1905 S13: 0.5580 REMARK 3 S21: -0.0507 S22: 0.0199 S23: -0.1750 REMARK 3 S31: -0.5173 S32: 0.1201 S33: 0.0502 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 527 THROUGH 583 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.1947 12.4682 -19.0333 REMARK 3 T TENSOR REMARK 3 T11: 0.6593 T22: 0.4571 REMARK 3 T33: 0.5766 T12: 0.0392 REMARK 3 T13: 0.0366 T23: 0.0148 REMARK 3 L TENSOR REMARK 3 L11: 6.7012 L22: 1.9721 REMARK 3 L33: 3.4547 L12: -0.2480 REMARK 3 L13: 0.2755 L23: -1.2675 REMARK 3 S TENSOR REMARK 3 S11: -0.1006 S12: -0.3288 S13: -0.5833 REMARK 3 S21: 0.0784 S22: -0.0123 S23: -0.0634 REMARK 3 S31: 0.5278 S32: 0.1931 S33: 0.0877 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 584 THROUGH 604 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.6543 31.7847 -13.9069 REMARK 3 T TENSOR REMARK 3 T11: 0.6937 T22: 1.0194 REMARK 3 T33: 0.8311 T12: -0.0863 REMARK 3 T13: -0.1846 T23: -0.0268 REMARK 3 L TENSOR REMARK 3 L11: 5.3704 L22: 6.5577 REMARK 3 L33: 4.8600 L12: -4.8934 REMARK 3 L13: -2.4212 L23: 3.0489 REMARK 3 S TENSOR REMARK 3 S11: -0.4507 S12: -1.0031 S13: 0.8017 REMARK 3 S21: 0.4826 S22: 0.3532 S23: -0.8906 REMARK 3 S31: -0.7493 S32: 1.2100 S33: 0.1574 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 605 THROUGH 636 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.0376 23.4589 -4.0783 REMARK 3 T TENSOR REMARK 3 T11: 0.6152 T22: 0.8330 REMARK 3 T33: 0.4554 T12: 0.0822 REMARK 3 T13: 0.0325 T23: -0.0909 REMARK 3 L TENSOR REMARK 3 L11: 7.3081 L22: 4.8066 REMARK 3 L33: 5.1595 L12: 4.1715 REMARK 3 L13: 4.4714 L23: 2.3910 REMARK 3 S TENSOR REMARK 3 S11: 0.2327 S12: -1.4131 S13: 0.1515 REMARK 3 S21: 0.3760 S22: -0.4907 S23: 0.0742 REMARK 3 S31: 0.1830 S32: -0.5068 S33: 0.3132 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.4796 26.6542 -40.1751 REMARK 3 T TENSOR REMARK 3 T11: 0.6432 T22: 0.5437 REMARK 3 T33: 0.5964 T12: -0.1023 REMARK 3 T13: -0.0699 T23: 0.0518 REMARK 3 L TENSOR REMARK 3 L11: 5.4936 L22: 8.1003 REMARK 3 L33: 4.6548 L12: -6.6512 REMARK 3 L13: 0.7831 L23: -1.7303 REMARK 3 S TENSOR REMARK 3 S11: 0.3313 S12: 0.4743 S13: 0.2284 REMARK 3 S21: -0.4863 S22: -0.3897 S23: 0.2049 REMARK 3 S31: -0.2893 S32: -0.1710 S33: 0.0727 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 2 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.2286 17.9081 -39.7554 REMARK 3 T TENSOR REMARK 3 T11: 0.6483 T22: 0.5353 REMARK 3 T33: 0.5547 T12: -0.0823 REMARK 3 T13: -0.0401 T23: 0.0033 REMARK 3 L TENSOR REMARK 3 L11: 5.7661 L22: 7.0102 REMARK 3 L33: 6.1403 L12: -1.8791 REMARK 3 L13: 0.6537 L23: -0.4791 REMARK 3 S TENSOR REMARK 3 S11: 0.1778 S12: 0.7538 S13: -0.4367 REMARK 3 S21: -0.2326 S22: -0.5079 S23: -0.2878 REMARK 3 S31: 0.5855 S32: 0.1805 S33: 0.3084 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 9LNK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1300055925. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28722 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 48.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 9.260 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 8.82 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.510 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9% PEG 3350, 75MM HEPES-KOH, PH 8.0, REMARK 280 50MM SUCCINIC ACID, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 26.32000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 83.69500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.42500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 83.69500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.32000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.42500 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: 4270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 MET A 256 REMARK 465 GLY A 257 REMARK 465 HIS A 258 REMARK 465 HIS A 259 REMARK 465 HIS A 260 REMARK 465 HIS A 261 REMARK 465 HIS A 262 REMARK 465 HIS A 263 REMARK 465 HIS A 264 REMARK 465 HIS A 265 REMARK 465 HIS A 266 REMARK 465 HIS A 267 REMARK 465 SER A 268 REMARK 465 SER A 269 REMARK 465 GLY A 270 REMARK 465 GLU A 271 REMARK 465 ASN A 272 REMARK 465 LEU A 273 REMARK 465 TYR A 274 REMARK 465 PRO A 637 REMARK 465 ASN A 638 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 GLN A 276 40.09 -83.93 REMARK 500 CYS A 303 83.63 -160.98 REMARK 500 LYS A 433 37.78 -89.54 REMARK 500 ILE A 447 -30.34 -133.23 REMARK 500 PRO A 546 -176.66 -62.53 REMARK 500 ARG A 621 107.92 -169.76 REMARK 500 GLU A 635 -50.53 -134.56 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 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 335 ND1 REMARK 620 2 HIS A 338 ND1 98.9 REMARK 620 3 CYS A 545 SG 114.0 103.4 REMARK 620 4 CYS A 549 SG 104.7 115.0 119.2 REMARK 620 N 1 2 3 DBREF 9LNK A 280 638 UNP O80464 O80464_ARATH 280 638 DBREF 9LNK B 1 15 PDB 9LNK 9LNK 1 15 DBREF 9LNK C 1 15 PDB 9LNK 9LNK 1 15 SEQADV 9LNK MET A 256 UNP O80464 INITIATING METHIONINE SEQADV 9LNK GLY A 257 UNP O80464 EXPRESSION TAG SEQADV 9LNK HIS A 258 UNP O80464 EXPRESSION TAG SEQADV 9LNK HIS A 259 UNP O80464 EXPRESSION TAG SEQADV 9LNK HIS A 260 UNP O80464 EXPRESSION TAG SEQADV 9LNK HIS A 261 UNP O80464 EXPRESSION TAG SEQADV 9LNK HIS A 262 UNP O80464 EXPRESSION TAG SEQADV 9LNK HIS A 263 UNP O80464 EXPRESSION TAG SEQADV 9LNK HIS A 264 UNP O80464 EXPRESSION TAG SEQADV 9LNK HIS A 265 UNP O80464 EXPRESSION TAG SEQADV 9LNK HIS A 266 UNP O80464 EXPRESSION TAG SEQADV 9LNK HIS A 267 UNP O80464 EXPRESSION TAG SEQADV 9LNK SER A 268 UNP O80464 EXPRESSION TAG SEQADV 9LNK SER A 269 UNP O80464 EXPRESSION TAG SEQADV 9LNK GLY A 270 UNP O80464 EXPRESSION TAG SEQADV 9LNK GLU A 271 UNP O80464 EXPRESSION TAG SEQADV 9LNK ASN A 272 UNP O80464 EXPRESSION TAG SEQADV 9LNK LEU A 273 UNP O80464 EXPRESSION TAG SEQADV 9LNK TYR A 274 UNP O80464 EXPRESSION TAG SEQADV 9LNK PHE A 275 UNP O80464 EXPRESSION TAG SEQADV 9LNK GLN A 276 UNP O80464 EXPRESSION TAG SEQADV 9LNK GLY A 277 UNP O80464 EXPRESSION TAG SEQADV 9LNK SER A 278 UNP O80464 EXPRESSION TAG SEQADV 9LNK HIS A 279 UNP O80464 EXPRESSION TAG SEQRES 1 A 383 MET GLY HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS SER SEQRES 2 A 383 SER GLY GLU ASN LEU TYR PHE GLN GLY SER HIS ALA MET SEQRES 3 A 383 GLN PRO LEU GLY MET TYR PHE PRO ALA SER GLU TYR THR SEQRES 4 A 383 LYS LYS MET LYS LEU ALA THR ARG CYS TYR ILE SER GLU SEQRES 5 A 383 VAL LEU LYS THR PHE ALA ASP LEU GLU HIS PRO LEU THR SEQRES 6 A 383 ASN VAL GLU LYS ASN TYR PHE MET GLU HIS PRO SER PHE SEQRES 7 A 383 LYS HIS ILE TYR HIS LEU PRO SER GLY TYR THR HIS LYS SEQRES 8 A 383 LEU MET GLY MET TRP MET LEU PHE LEU ARG THR ALA SER SEQRES 9 A 383 ILE GLU LYS LYS LYS GLU VAL TRP PHE VAL VAL ASN GLY SEQRES 10 A 383 VAL PRO ILE ARG TYR GLY ILE ARG GLU HIS ALA LEU ILE SEQRES 11 A 383 SER GLY PHE ASN CYS LYS ALA TYR PRO ALA ASN TYR GLN SEQRES 12 A 383 SER ALA GLY ASN MET ASN PHE ALA ASN ARG TYR PHE LYS SEQRES 13 A 383 THR GLY VAL ILE ARG ARG GLU ASP VAL LYS THR LYS LEU SEQRES 14 A 383 MET GLU MET GLU PRO ALA ARG SER LYS ASP ARG LEU ARG SEQRES 15 A 383 MET ALA VAL LEU TYR PHE LEU THR SER ILE ILE ALA VAL SEQRES 16 A 383 PRO THR LYS THR GLY GLU ARG ALA SER PRO ILE ASP ASP SEQRES 17 A 383 PHE CYS VAL ARG ALA ALA SER ASP LEU THR PHE CYS LYS SEQRES 18 A 383 THR PHE PRO TRP GLY ARG TYR SER PHE GLU TYR MET LEU SEQRES 19 A 383 LYS SER ILE SER HIS THR LEU ASP HIS PHE ASN GLY VAL SEQRES 20 A 383 VAL PRO ASN THR GLN SER PRO TRP PRO VAL PRO GLY PHE SEQRES 21 A 383 CYS VAL PRO LEU GLU PHE LEU ALA PHE GLU ALA ILE PRO SEQRES 22 A 383 SER LEU ARG GLU ARG PHE ILE GLU GLU LYS GLU GLY SER SEQRES 23 A 383 HIS ALA GLY CYS PRO ARG MET CYS LYS VAL SER PHE LYS SEQRES 24 A 383 ARG THR GLU MET LYS GLY PHE THR LEU GLU GLN ILE ASN SEQRES 25 A 383 HIS VAL LEU GLY THR THR GLU VAL ILE GLU SER ILE ILE SEQRES 26 A 383 ARG GLU LYS ALA GLU GLU VAL PRO LEU LEU ALA GLU ILE SEQRES 27 A 383 THR GLY VAL GLU ASP ASP VAL ASP LYS HIS ASP VAL VAL SEQRES 28 A 383 VAL ASP SER TRP MET LYS ARG LEU GLY GLN GLY ARG GLU SEQRES 29 A 383 ILE ARG PHE GLU GLU VAL TYR ASN GLU ASP VAL HIS ALA SEQRES 30 A 383 ARG MET GLU ALA PRO ASN SEQRES 1 B 15 3D1 DC DC DA DG DT DA DT DT DA DC DT DT SEQRES 2 B 15 DT DT SEQRES 1 C 15 3D1 DA DG DT DA DA DT DA DC DT DG DG DT SEQRES 2 C 15 DA DA HET 3D1 B 1 18 HET 3D1 C 1 36 HET ZN A 701 1 HETNAM 3D1 (2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-YL)-TETRAHYDRO-2- HETNAM 2 3D1 (HYDROXYMETHYL)FURAN-3-OL HETNAM ZN ZINC ION HETSYN 3D1 2'-DEOXYADENOSINE FORMUL 2 3D1 2(C10 H13 N5 O3) FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *54(H2 O) HELIX 1 AA1 PRO A 289 TYR A 293 5 5 HELIX 2 AA2 TYR A 304 ASP A 314 1 11 HELIX 3 AA3 THR A 320 GLU A 329 1 10 HELIX 4 AA4 SER A 332 HIS A 338 5 7 HELIX 5 AA5 LEU A 347 LEU A 355 1 9 HELIX 6 AA6 GLY A 378 GLY A 387 1 10 HELIX 7 AA7 ASN A 396 ALA A 400 5 5 HELIX 8 AA8 MET A 403 ARG A 408 1 6 HELIX 9 AA9 ARG A 416 MET A 427 1 12 HELIX 10 AB1 LYS A 433 ILE A 448 1 16 HELIX 11 AB2 THR A 454 ALA A 458 5 5 HELIX 12 AB3 ASP A 462 ALA A 469 1 8 HELIX 13 AB4 ASP A 471 PHE A 478 1 8 HELIX 14 AB5 PRO A 479 ASN A 500 1 22 HELIX 15 AB6 CYS A 516 ILE A 527 1 12 HELIX 16 AB7 ILE A 527 PHE A 534 1 8 HELIX 17 AB8 PRO A 546 LYS A 550 1 5 HELIX 18 AB9 THR A 562 GLY A 571 1 10 HELIX 19 AC1 LYS A 583 GLU A 585 5 3 HELIX 20 AC2 GLU A 586 THR A 594 1 9 HELIX 21 AC3 ASP A 604 GLY A 615 1 12 HELIX 22 AC4 PHE A 622 GLU A 635 1 14 SHEET 1 AA1 2 GLY A 285 MET A 286 0 SHEET 2 AA1 2 ALA A 358 SER A 359 -1 O SER A 359 N GLY A 285 SHEET 1 AA2 2 LEU A 299 ARG A 302 0 SHEET 2 AA2 2 TRP A 510 PRO A 513 1 O VAL A 512 N ALA A 300 SHEET 1 AA3 2 VAL A 366 VAL A 370 0 SHEET 2 AA3 2 VAL A 373 TYR A 377 -1 O TYR A 377 N VAL A 366 SHEET 1 AA4 2 ILE A 535 GLU A 537 0 SHEET 2 AA4 2 VAL A 551 PHE A 553 -1 O SER A 552 N GLU A 536 LINK O3' 3D1 B 1 P DC B 2 1555 1555 1.60 LINK O3'A3D1 C 1 P DA C 2 1555 1555 1.62 LINK O3'B3D1 C 1 P DA C 2 1555 1555 1.61 LINK ND1 HIS A 335 ZN ZN A 701 1555 1555 2.17 LINK ND1 HIS A 338 ZN ZN A 701 1555 1555 2.21 LINK SG CYS A 545 ZN ZN A 701 1555 1555 2.31 LINK SG CYS A 549 ZN ZN A 701 1555 1555 2.25 CRYST1 52.640 96.850 167.390 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 0.018997 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010325 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005974 0.00000 CONECT 500 3568 CONECT 530 3568 CONECT 2199 3568 CONECT 2231 3568 CONECT 2939 2940 CONECT 2940 2939 2941 CONECT 2941 2940 2942 2955 CONECT 2942 2941 2943 CONECT 2943 2942 2944 2954 CONECT 2944 2943 2945 2953 CONECT 2945 2944 2946 2951 CONECT 2946 2945 2947 CONECT 2947 2946 2948 CONECT 2948 2947 2949 CONECT 2949 2948 2950 2951 CONECT 2950 2949 CONECT 2951 2945 2949 2952 CONECT 2952 2951 2953 CONECT 2953 2944 2952 CONECT 2954 2943 2955 CONECT 2955 2941 2954 2956 CONECT 2956 2955 2957 CONECT 2957 2956 CONECT 3240 3242 CONECT 3241 3243 CONECT 3242 3240 3244 CONECT 3243 3241 3245 CONECT 3244 3242 3246 3272 CONECT 3245 3243 3247 3273 CONECT 3246 3244 3248 CONECT 3247 3245 3249 CONECT 3248 3246 3250 3270 CONECT 3249 3247 3251 3271 CONECT 3250 3248 3252 3268 CONECT 3251 3249 3253 3269 CONECT 3252 3250 3254 3264 CONECT 3253 3251 3255 3265 CONECT 3254 3252 3256 CONECT 3255 3253 3257 CONECT 3256 3254 3258 CONECT 3257 3255 3259 CONECT 3258 3256 3260 CONECT 3259 3257 3261 CONECT 3260 3258 3262 3264 CONECT 3261 3259 3263 3265 CONECT 3262 3260 CONECT 3263 3261 CONECT 3264 3252 3260 3266 CONECT 3265 3253 3261 3267 CONECT 3266 3264 3268 CONECT 3267 3265 3269 CONECT 3268 3250 3266 CONECT 3269 3251 3267 CONECT 3270 3248 3272 CONECT 3271 3249 3273 CONECT 3272 3244 3270 3274 CONECT 3273 3245 3271 3275 CONECT 3274 3272 3276 CONECT 3275 3273 3276 CONECT 3276 3274 3275 CONECT 3568 500 530 2199 2231 MASTER 402 0 3 22 8 0 0 6 3601 3 61 34 END