HEADER DNA BINDING PROTEIN/DNA 21-JAN-25 9LNJ TITLE CRYSTAL STRUCTURE OF VANC21 IN COMPLEX WITH ITS TARGET DNA (5- TITLE 2 BROMOURIDINE SUBSTITUTED). 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 9LNJ 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 31748 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 : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1603 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 40.2600 - 4.4500 1.00 2808 146 0.1701 0.2146 REMARK 3 2 4.4500 - 3.5300 1.00 2756 147 0.1603 0.1618 REMARK 3 3 3.5300 - 3.0800 1.00 2731 138 0.1684 0.2060 REMARK 3 4 3.0800 - 2.8000 1.00 2738 151 0.1862 0.2211 REMARK 3 5 2.8000 - 2.6000 1.00 2734 145 0.1803 0.2232 REMARK 3 6 2.6000 - 2.4500 1.00 2753 142 0.1780 0.2283 REMARK 3 7 2.4500 - 2.3300 1.00 2714 145 0.1743 0.1930 REMARK 3 8 2.3300 - 2.2200 1.00 2752 143 0.1813 0.2374 REMARK 3 9 2.2200 - 2.1400 1.00 2711 153 0.1992 0.2533 REMARK 3 10 2.1400 - 2.0600 1.00 2713 144 0.2050 0.2352 REMARK 3 11 2.0600 - 2.0000 1.00 2735 149 0.2339 0.2563 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.93 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 3631 REMARK 3 ANGLE : 1.132 5019 REMARK 3 CHIRALITY : 0.063 538 REMARK 3 PLANARITY : 0.009 574 REMARK 3 DIHEDRAL : 17.418 704 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 275 THROUGH 408 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.7196 -1.8272 41.3858 REMARK 3 T TENSOR REMARK 3 T11: 0.1699 T22: 0.2606 REMARK 3 T33: 0.1847 T12: -0.0047 REMARK 3 T13: 0.0182 T23: -0.0075 REMARK 3 L TENSOR REMARK 3 L11: 1.2492 L22: 1.0183 REMARK 3 L33: 2.3048 L12: 0.1167 REMARK 3 L13: 0.1016 L23: -0.2474 REMARK 3 S TENSOR REMARK 3 S11: -0.0297 S12: 0.1529 S13: 0.0641 REMARK 3 S21: -0.1394 S22: 0.0071 S23: -0.1385 REMARK 3 S31: 0.0813 S32: 0.1623 S33: -0.0005 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 409 THROUGH 447 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.7321 -9.0756 61.6272 REMARK 3 T TENSOR REMARK 3 T11: 0.2016 T22: 0.4624 REMARK 3 T33: 0.2679 T12: 0.0547 REMARK 3 T13: -0.0435 T23: 0.0473 REMARK 3 L TENSOR REMARK 3 L11: 4.6535 L22: 2.8192 REMARK 3 L33: 1.1269 L12: -0.9260 REMARK 3 L13: 1.0203 L23: -0.3013 REMARK 3 S TENSOR REMARK 3 S11: -0.0827 S12: -0.8818 S13: -0.2200 REMARK 3 S21: 0.4350 S22: 0.0718 S23: -0.2186 REMARK 3 S31: 0.1811 S32: 0.1760 S33: 0.0048 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 448 THROUGH 526 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.4704 -6.8319 45.7543 REMARK 3 T TENSOR REMARK 3 T11: 0.1524 T22: 0.2292 REMARK 3 T33: 0.1405 T12: 0.0094 REMARK 3 T13: -0.0001 T23: -0.0291 REMARK 3 L TENSOR REMARK 3 L11: 1.9062 L22: 1.5549 REMARK 3 L33: 1.9887 L12: -0.2077 REMARK 3 L13: 0.3354 L23: -0.4737 REMARK 3 S TENSOR REMARK 3 S11: -0.0092 S12: 0.2122 S13: -0.1467 REMARK 3 S21: -0.1434 S22: 0.0171 S23: -0.1239 REMARK 3 S31: 0.1984 S32: 0.0831 S33: -0.0260 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 527 THROUGH 583 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.2319 13.3451 36.1099 REMARK 3 T TENSOR REMARK 3 T11: 0.3663 T22: 0.2966 REMARK 3 T33: 0.3622 T12: -0.0560 REMARK 3 T13: -0.0083 T23: 0.0522 REMARK 3 L TENSOR REMARK 3 L11: 3.7020 L22: 3.3388 REMARK 3 L33: 4.0302 L12: -0.6631 REMARK 3 L13: -0.6112 L23: -0.5962 REMARK 3 S TENSOR REMARK 3 S11: -0.0700 S12: 0.0944 S13: 0.6951 REMARK 3 S21: -0.1949 S22: 0.0101 S23: -0.4390 REMARK 3 S31: -0.6124 S32: 0.3145 S33: 0.0444 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 584 THROUGH 636 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.0192 0.6786 23.1850 REMARK 3 T TENSOR REMARK 3 T11: 0.4308 T22: 0.4784 REMARK 3 T33: 0.2161 T12: -0.0192 REMARK 3 T13: 0.0222 T23: 0.0293 REMARK 3 L TENSOR REMARK 3 L11: 1.5841 L22: 1.3083 REMARK 3 L33: 3.2394 L12: 0.7254 REMARK 3 L13: 0.3503 L23: 0.1451 REMARK 3 S TENSOR REMARK 3 S11: -0.0910 S12: 0.6952 S13: -0.0004 REMARK 3 S21: -0.4318 S22: 0.0942 S23: -0.0467 REMARK 3 S31: 0.0313 S32: -0.0214 S33: -0.0141 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.5727 3.2239 56.9939 REMARK 3 T TENSOR REMARK 3 T11: 0.1551 T22: 0.2196 REMARK 3 T33: 0.2484 T12: 0.0294 REMARK 3 T13: -0.0063 T23: 0.0042 REMARK 3 L TENSOR REMARK 3 L11: 1.7822 L22: 3.2830 REMARK 3 L33: 3.6077 L12: 1.0911 REMARK 3 L13: -0.7518 L23: -0.4282 REMARK 3 S TENSOR REMARK 3 S11: 0.1159 S12: -0.1655 S13: 0.1389 REMARK 3 S21: 0.0352 S22: -0.0474 S23: 0.3199 REMARK 3 S31: -0.1635 S32: -0.0720 S33: -0.0644 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 2 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.0074 0.6648 57.1770 REMARK 3 T TENSOR REMARK 3 T11: 0.1414 T22: 0.2315 REMARK 3 T33: 0.1832 T12: 0.0122 REMARK 3 T13: 0.0213 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 2.6131 L22: 5.8125 REMARK 3 L33: 2.1952 L12: 0.1988 REMARK 3 L13: 0.3838 L23: 0.2127 REMARK 3 S TENSOR REMARK 3 S11: 0.0684 S12: -0.0047 S13: 0.0372 REMARK 3 S21: -0.0668 S22: -0.2002 S23: 0.0225 REMARK 3 S31: -0.1498 S32: -0.1614 S33: 0.1230 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 9LNJ 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_1300055923. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 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) : 0.91 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 : 31782 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 46.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 48.59 REMARK 200 R MERGE (I) : 0.53500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 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 : 45.06 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 6000, 100MM HEPES-KOH, PH 7.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 38.58000 REMARK 290 SMTRY3 2 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: 5190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 870 O HOH A 937 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 B 3 O3' DC B 3 C3' -0.046 REMARK 500 DT C 4 O3' DT C 4 C3' -0.040 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. = 4.8 DEGREES REMARK 500 DT C 10 O4' - C1' - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG C 11 O4' - C1' - N9 ANGL. DEV. = 1.9 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 CYS A 303 80.13 -159.20 REMARK 500 ARG A 457 40.56 -106.66 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 105.1 REMARK 620 3 CYS A 545 SG 113.6 99.2 REMARK 620 4 CYS A 549 SG 106.2 117.0 115.5 REMARK 620 N 1 2 3 DBREF 9LNJ A 280 638 UNP O80464 O80464_ARATH 280 638 DBREF 9LNJ B 1 13 PDB 9LNJ 9LNJ 1 13 DBREF 9LNJ C 1 13 PDB 9LNJ 9LNJ 1 13 SEQADV 9LNJ MET A 256 UNP O80464 INITIATING METHIONINE SEQADV 9LNJ GLY A 257 UNP O80464 EXPRESSION TAG SEQADV 9LNJ HIS A 258 UNP O80464 EXPRESSION TAG SEQADV 9LNJ HIS A 259 UNP O80464 EXPRESSION TAG SEQADV 9LNJ HIS A 260 UNP O80464 EXPRESSION TAG SEQADV 9LNJ HIS A 261 UNP O80464 EXPRESSION TAG SEQADV 9LNJ HIS A 262 UNP O80464 EXPRESSION TAG SEQADV 9LNJ HIS A 263 UNP O80464 EXPRESSION TAG SEQADV 9LNJ HIS A 264 UNP O80464 EXPRESSION TAG SEQADV 9LNJ HIS A 265 UNP O80464 EXPRESSION TAG SEQADV 9LNJ HIS A 266 UNP O80464 EXPRESSION TAG SEQADV 9LNJ HIS A 267 UNP O80464 EXPRESSION TAG SEQADV 9LNJ SER A 268 UNP O80464 EXPRESSION TAG SEQADV 9LNJ SER A 269 UNP O80464 EXPRESSION TAG SEQADV 9LNJ GLY A 270 UNP O80464 EXPRESSION TAG SEQADV 9LNJ GLU A 271 UNP O80464 EXPRESSION TAG SEQADV 9LNJ ASN A 272 UNP O80464 EXPRESSION TAG SEQADV 9LNJ LEU A 273 UNP O80464 EXPRESSION TAG SEQADV 9LNJ TYR A 274 UNP O80464 EXPRESSION TAG SEQADV 9LNJ PHE A 275 UNP O80464 EXPRESSION TAG SEQADV 9LNJ GLN A 276 UNP O80464 EXPRESSION TAG SEQADV 9LNJ GLY A 277 UNP O80464 EXPRESSION TAG SEQADV 9LNJ SER A 278 UNP O80464 EXPRESSION TAG SEQADV 9LNJ 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 13 3D1 DC DC DA DG DT DA DT DT DA DC BRU BRU SEQRES 1 C 13 3D1 DA DG DT DA DA DT DA DC DT DG DG BRU HET 3D1 B 1 18 HET BRU B 12 20 HET BRU B 13 20 HET 3D1 C 1 18 HET BRU C 13 20 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 BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION HETSYN 3D1 2'-DEOXYADENOSINE FORMUL 2 3D1 2(C10 H13 N5 O3) FORMUL 2 BRU 3(C9 H12 BR N2 O8 P) FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *202(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 LEU A 339 5 8 HELIX 5 AA5 LEU A 347 ARG A 356 1 10 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 ASP A 462 ALA A 469 1 8 HELIX 12 AB3 ASP A 471 PHE A 478 1 8 HELIX 13 AB4 PRO A 479 ASN A 500 1 22 HELIX 14 AB5 CYS A 516 ILE A 527 1 12 HELIX 15 AB6 ILE A 527 PHE A 534 1 8 HELIX 16 AB7 PRO A 546 LYS A 550 1 5 HELIX 17 AB8 THR A 562 GLY A 571 1 10 HELIX 18 AB9 LYS A 583 GLU A 585 5 3 HELIX 19 AC1 GLU A 586 THR A 594 1 9 HELIX 20 AC2 ASP A 604 GLN A 616 1 13 HELIX 21 AC3 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 1.61 LINK O3' DC B 11 P BRU B 12 1555 1555 1.60 LINK O3' BRU B 12 P BRU B 13 1555 1555 1.61 LINK O3' 3D1 C 1 P DA C 2 1555 1555 1.60 LINK O3' DG C 12 P BRU C 13 1555 1555 1.61 LINK ND1 HIS A 335 ZN ZN A 701 1555 1555 2.27 LINK ND1 HIS A 338 ZN ZN A 701 1555 1555 1.98 LINK SG CYS A 545 ZN ZN A 701 1555 1555 2.46 LINK SG CYS A 549 ZN ZN A 701 1555 1555 2.27 CRYST1 52.350 77.160 59.000 90.00 93.30 90.00 P 1 21 1 2 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 0.019102 0.000000 0.001101 0.00000 SCALE2 0.000000 0.012960 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016977 0.00000 CONECT 500 3490 CONECT 530 3490 CONECT 2213 3490 CONECT 2245 3490 CONECT 2961 2962 CONECT 2962 2961 2963 CONECT 2963 2962 2964 2977 CONECT 2964 2963 2965 CONECT 2965 2964 2966 2976 CONECT 2966 2965 2967 2975 CONECT 2967 2966 2968 2973 CONECT 2968 2967 2969 CONECT 2969 2968 2970 CONECT 2970 2969 2971 CONECT 2971 2970 2972 2973 CONECT 2972 2971 CONECT 2973 2967 2971 2974 CONECT 2974 2973 2975 CONECT 2975 2966 2974 CONECT 2976 2965 2977 CONECT 2977 2963 2976 2978 CONECT 2978 2977 2979 CONECT 2979 2978 CONECT 3170 3198 CONECT 3181 3182 3186 3190 CONECT 3182 3181 3183 3187 CONECT 3183 3182 3184 CONECT 3184 3183 3185 3188 CONECT 3185 3184 3186 3189 CONECT 3186 3181 3185 CONECT 3187 3182 CONECT 3188 3184 CONECT 3189 3185 CONECT 3190 3181 3191 3195 CONECT 3191 3190 3192 CONECT 3192 3191 3193 3194 CONECT 3193 3192 3195 3196 CONECT 3194 3192 3218 CONECT 3195 3190 3193 CONECT 3196 3193 3197 CONECT 3197 3196 3198 CONECT 3198 3170 3197 3199 3200 CONECT 3199 3198 CONECT 3200 3198 CONECT 3201 3202 3206 3210 CONECT 3202 3201 3203 3207 CONECT 3203 3202 3204 CONECT 3204 3203 3205 3208 CONECT 3205 3204 3206 3209 CONECT 3206 3201 3205 CONECT 3207 3202 CONECT 3208 3204 CONECT 3209 3205 CONECT 3210 3201 3211 3215 CONECT 3211 3210 3212 CONECT 3212 3211 3213 3214 CONECT 3213 3212 3215 3216 CONECT 3214 3212 CONECT 3215 3210 3213 CONECT 3216 3213 3217 CONECT 3217 3216 3218 CONECT 3218 3194 3217 3219 3220 CONECT 3219 3218 CONECT 3220 3218 CONECT 3222 3223 CONECT 3223 3222 3224 CONECT 3224 3223 3225 3238 CONECT 3225 3224 3226 CONECT 3226 3225 3227 3237 CONECT 3227 3226 3228 3236 CONECT 3228 3227 3229 3234 CONECT 3229 3228 3230 CONECT 3230 3229 3231 CONECT 3231 3230 3232 CONECT 3232 3231 3233 3234 CONECT 3233 3232 CONECT 3234 3228 3232 3235 CONECT 3235 3234 3236 CONECT 3236 3227 3235 CONECT 3237 3226 3238 CONECT 3238 3224 3237 3239 CONECT 3239 3238 3240 CONECT 3240 3239 CONECT 3455 3486 CONECT 3469 3470 3474 3478 CONECT 3470 3469 3471 3475 CONECT 3471 3470 3472 CONECT 3472 3471 3473 3476 CONECT 3473 3472 3474 3477 CONECT 3474 3469 3473 CONECT 3475 3470 CONECT 3476 3472 CONECT 3477 3473 CONECT 3478 3469 3479 3483 CONECT 3479 3478 3480 CONECT 3480 3479 3481 3482 CONECT 3481 3480 3483 3484 CONECT 3482 3480 CONECT 3483 3478 3481 CONECT 3484 3481 3485 CONECT 3485 3484 3486 CONECT 3486 3455 3485 3487 3488 CONECT 3487 3486 CONECT 3488 3486 CONECT 3490 500 530 2213 2245 MASTER 410 0 6 21 8 0 0 6 3667 3 105 32 END