HEADER NUCLEIC ACID BINDING PROTEIN/DNA/RNA 21-JUN-09 3HXM TITLE STRUCTURE OF AN ARGONAUTE COMPLEXED WITH GUIDE DNA AND TARGET RNA TITLE 2 DUPLEX CONTAINING TWO MISMATCHES. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARGONAUTE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'- COMPND 7 D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)- COMPND 8 3'); COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: RNA (5'- COMPND 13 R(*UP*AP*UP*AP*CP*AP*AP*CP*UP*CP*AP*CP*UP*AP*CP*CP*UP*CP*GP*U)-3'); COMPND 14 CHAIN: Y; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 262724; SOURCE 4 STRAIN: HB27; SOURCE 5 GENE: TT_P0026; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2 (DE3)PLYSS; 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 ARGONAUTE, PROTEIN-DNA-RNA COMPLEX, NUCLEIC ACID BINDING PROTEIN-DNA- KEYWDS 2 RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.WANG,H.LI,G.SHENG,D.J.PATEL REVDAT 4 06-SEP-23 3HXM 1 REMARK REVDAT 3 13-JUL-11 3HXM 1 VERSN REVDAT 2 20-OCT-09 3HXM 1 JRNL REVDAT 1 06-OCT-09 3HXM 0 JRNL AUTH Y.WANG,S.JURANEK,H.LI,G.SHENG,G.S.WARDLE,T.TUSCHL,D.J.PATEL JRNL TITL NUCLEATION, PROPAGATION AND CLEAVAGE OF TARGET RNAS IN AGO JRNL TITL 2 SILENCING COMPLEXES. JRNL REF NATURE V. 461 754 2009 JRNL REFN ISSN 0028-0836 JRNL PMID 19812667 JRNL DOI 10.1038/NATURE08434 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 13142 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.600 REMARK 3 FREE R VALUE TEST SET COUNT : 922 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4779 REMARK 3 NUCLEIC ACID ATOMS : 445 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 72.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 17.04900 REMARK 3 B22 (A**2) : -3.90300 REMARK 3 B33 (A**2) : -13.14500 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 23.20400 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 42.78 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3HXM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000053707. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27365 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.12600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.53700 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3F73 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5, VAPOR DIFFUSION, TEMPERATURE REMARK 280 308 K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 60.91950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.43350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 60.91950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 59.43350 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: 4240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, Y 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 1 REMARK 465 ASN A 2 REMARK 465 HIS A 3 REMARK 465 LEU A 4 REMARK 465 LYS A 213 REMARK 465 GLU A 214 REMARK 465 LEU A 215 REMARK 465 PRO A 216 REMARK 465 LEU A 217 REMARK 465 PRO A 218 REMARK 465 GLY A 219 REMARK 465 GLY A 220 REMARK 465 LEU A 221 REMARK 465 LEU A 233 REMARK 465 GLN A 234 REMARK 465 GLY A 235 REMARK 465 ARG A 236 REMARK 465 GLU A 237 REMARK 465 GLY A 238 REMARK 465 GLY A 239 REMARK 465 ARG A 240 REMARK 465 VAL A 241 REMARK 465 ALA A 242 REMARK 465 TRP A 243 REMARK 465 VAL A 244 REMARK 465 ALA A 245 REMARK 465 ASP A 246 REMARK 465 PRO A 247 REMARK 465 LYS A 248 REMARK 465 ASP A 249 REMARK 465 PRO A 250 REMARK 465 ARG A 251 REMARK 465 LYS A 252 REMARK 465 PRO A 253 REMARK 465 ILE A 254 REMARK 465 PRO A 255 REMARK 465 HIS A 256 REMARK 465 LEU A 257 REMARK 465 THR A 258 REMARK 465 GLY A 259 REMARK 465 LEU A 260 REMARK 465 LEU A 261 REMARK 465 GLU A 273 REMARK 465 GLU A 274 REMARK 465 GLY A 275 REMARK 465 SER A 276 REMARK 465 LEU A 277 REMARK 465 ASP A 497 REMARK 465 DT C 22 REMARK 465 DG C 23 REMARK 465 DT C 24 REMARK 465 DA C 25 REMARK 465 DT C 26 REMARK 465 DA C 27 REMARK 465 DG C 28 REMARK 465 DT C 29 REMARK 465 U Y 1 REMARK 465 A Y 2 REMARK 465 U Y 3 REMARK 465 A Y 4 REMARK 465 C Y 5 REMARK 465 A Y 6 REMARK 465 A Y 7 REMARK 465 C Y 8 REMARK 465 U Y 9 REMARK 465 C Y 10 REMARK 465 U Y 20 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 6 CG CD CE NZ REMARK 470 ARG A 39 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 40 CG CD OE1 OE2 REMARK 470 GLU A 41 CG CD OE1 OE2 REMARK 470 ARG A 81 CG CD NE CZ NH1 NH2 REMARK 470 MET A 82 CG SD CE REMARK 470 VAL A 108 CG1 CG2 REMARK 470 GLU A 119 CG CD OE1 OE2 REMARK 470 GLU A 130 CG CD OE1 OE2 REMARK 470 ARG A 137 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 179 CG CD1 CD2 REMARK 470 LEU A 189 CG CD1 CD2 REMARK 470 PRO A 190 CG CD REMARK 470 LYS A 191 CG CD CE NZ REMARK 470 ARG A 192 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 194 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 195 CG OD1 ND2 REMARK 470 TYR A 197 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 199 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 200 CG CD NE CZ NH1 NH2 REMARK 470 TRP A 202 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 202 CZ3 CH2 REMARK 470 GLU A 203 CG CD OE1 OE2 REMARK 470 LEU A 204 CG CD1 CD2 REMARK 470 LEU A 205 CG CD1 CD2 REMARK 470 ARG A 206 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 207 CG CD1 CD2 REMARK 470 GLU A 210 CG CD OE1 OE2 REMARK 470 ASP A 211 CG OD1 OD2 REMARK 470 PRO A 212 CG CD REMARK 470 LEU A 224 CG CD1 CD2 REMARK 470 SER A 229 OG REMARK 470 LYS A 230 CG CD CE NZ REMARK 470 ARG A 232 CG CD NE CZ NH1 NH2 REMARK 470 THR A 266 OG1 CG2 REMARK 470 LEU A 267 CG CD1 CD2 REMARK 470 GLU A 268 CG CD OE1 OE2 REMARK 470 ASP A 269 CG OD1 OD2 REMARK 470 LEU A 270 CG CD1 CD2 REMARK 470 HIS A 271 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 272 CG CD OE1 OE2 REMARK 470 LEU A 279 CG CD1 CD2 REMARK 470 LYS A 320 CG CD CE NZ REMARK 470 ARG A 340 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 367 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 389 CG CD1 CD2 REMARK 470 ARG A 396 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 401 CG CD OE1 OE2 REMARK 470 SER A 466 OG REMARK 470 GLU A 483 CG CD OE1 OE2 REMARK 470 PRO A 506 CG CD REMARK 470 GLU A 507 CG CD OE1 OE2 REMARK 470 GLN A 509 CB CG CD OE1 NE2 REMARK 470 ARG A 532 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 548 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 564 CG CD OE1 OE2 REMARK 470 LYS A 575 CG CD CE NZ REMARK 470 GLN A 585 CG CD OE1 NE2 REMARK 470 ARG A 587 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 608 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 609 CG OD1 OD2 REMARK 470 PHE A 610 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 611 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 664 CG CD CE NZ REMARK 470 ARG A 672 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 674 CG CD1 CD2 REMARK 470 DG C 11 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DG C 11 N9 C8 N7 C5 C6 O6 N1 REMARK 470 DG C 11 C2 N2 N3 C4 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 PRO A 143 CG CD 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 DT C 1 P DT C 1 OP3 -0.083 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 PRO A 103 C - N - CD ANGL. DEV. = -17.5 DEGREES REMARK 500 PRO A 103 CA - N - CD ANGL. DEV. = -12.5 DEGREES REMARK 500 DG C 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT C 9 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DA C 10 N9 - C1' - C2' ANGL. DEV. = -12.8 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 ASN A 12 32.03 -73.60 REMARK 500 LEU A 16 -165.35 -128.31 REMARK 500 PRO A 37 -70.59 -45.90 REMARK 500 ARG A 39 -47.40 -13.60 REMARK 500 PRO A 92 86.54 -58.35 REMARK 500 LYS A 93 49.78 -81.29 REMARK 500 ARG A 141 -142.75 -158.43 REMARK 500 SER A 158 169.25 -49.81 REMARK 500 ALA A 184 -96.36 -47.46 REMARK 500 GLN A 185 -53.41 -18.03 REMARK 500 PRO A 188 -158.27 -69.24 REMARK 500 ASN A 195 163.96 -49.94 REMARK 500 ARG A 206 176.14 173.96 REMARK 500 GLU A 209 56.42 -65.65 REMARK 500 GLU A 210 -143.09 -112.12 REMARK 500 THR A 266 -68.82 -146.26 REMARK 500 LEU A 267 50.23 -117.94 REMARK 500 LEU A 279 -34.51 -39.52 REMARK 500 ARG A 300 46.41 -157.76 REMARK 500 PRO A 330 -37.24 -28.37 REMARK 500 TYR A 339 -88.13 -67.50 REMARK 500 ASP A 352 -143.67 -106.39 REMARK 500 ALA A 354 178.06 -49.30 REMARK 500 GLN A 355 -81.72 -112.51 REMARK 500 HIS A 382 51.38 -110.34 REMARK 500 PRO A 385 -25.71 -39.05 REMARK 500 GLN A 387 0.74 -55.38 REMARK 500 VAL A 403 127.21 -32.92 REMARK 500 PRO A 412 134.00 -36.37 REMARK 500 TRP A 415 -52.99 -25.80 REMARK 500 GLU A 428 7.29 -69.01 REMARK 500 PRO A 438 89.65 -45.03 REMARK 500 GLU A 443 34.35 -78.52 REMARK 500 ARG A 444 -64.50 -24.56 REMARK 500 PHE A 487 54.97 -112.21 REMARK 500 ALA A 508 141.96 -23.09 REMARK 500 GLN A 509 -146.56 166.10 REMARK 500 ALA A 510 116.76 155.16 REMARK 500 ARG A 513 127.32 -170.18 REMARK 500 ILE A 514 107.06 -35.25 REMARK 500 ARG A 532 3.55 -64.95 REMARK 500 ALA A 534 -20.54 -140.37 REMARK 500 PRO A 550 -146.90 -39.83 REMARK 500 GLN A 551 -48.90 -140.38 REMARK 500 ASP A 552 -6.90 -54.80 REMARK 500 LEU A 596 -138.52 -103.10 REMARK 500 GLU A 597 -166.16 -61.87 REMARK 500 HIS A 607 89.09 -164.77 REMARK 500 ALA A 623 138.43 -179.04 REMARK 500 SER A 645 -82.43 -89.10 REMARK 500 REMARK 500 THIS ENTRY HAS 54 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DA C 10 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 30 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HGE RELATED DB: PDB REMARK 900 MUTANT PROTEIN D546N COMPLEXED WITH SAME DNA GUIDE AND 20-NT RNA REMARK 900 TAGET CONTAINING ONE NUCLEIC ACID BULGE REMARK 900 RELATED ID: 3HJF RELATED DB: PDB REMARK 900 MUTANT PROTEIN D546E COMPLEXED WITH SAME DNA GUIDE AND 15-NT RNA REMARK 900 GUIDE REMARK 900 RELATED ID: 3HK2 RELATED DB: PDB REMARK 900 MUTANT PROTEIN D478N COMPLEXED WITH SAME DNA GUIDE AND 19-NT RNA REMARK 900 GUIDE REMARK 900 RELATED ID: 3DLH RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH SAME DNA GUIDE STRAND REMARK 900 RELATED ID: 3F73 RELATED DB: PDB REMARK 900 ANOTHER CRYSTAL FORM OF ARGONAUTE COMPLEXED WITH THE SAME DNA GUIDE REMARK 900 STRAND AND RNA TARGET DUPLEX. REMARK 900 RELATED ID: 3DLB RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH 10-NT DNA GUIDE STRAND DBREF 3HXM A 1 685 UNP Q746M7 Q746M7_THET2 1 685 DBREF 3HXM C 1 29 PDB 3HXM 3HXM 1 29 DBREF 3HXM Y 1 20 PDB 3HXM 3HXM 1 20 SEQRES 1 A 685 MET ASN HIS LEU GLY LYS THR GLU VAL PHE LEU ASN ARG SEQRES 2 A 685 PHE ALA LEU ARG PRO LEU ASN PRO GLU GLU LEU ARG PRO SEQRES 3 A 685 TRP ARG LEU GLU VAL VAL LEU ASP PRO PRO PRO GLY ARG SEQRES 4 A 685 GLU GLU VAL TYR PRO LEU LEU ALA GLN VAL ALA ARG ARG SEQRES 5 A 685 ALA GLY GLY VAL THR VAL ARG MET GLY ASP GLY LEU ALA SEQRES 6 A 685 SER TRP SER PRO PRO GLU VAL LEU VAL LEU GLU GLY THR SEQRES 7 A 685 LEU ALA ARG MET GLY GLN THR TYR ALA TYR ARG LEU TYR SEQRES 8 A 685 PRO LYS GLY ARG ARG PRO LEU ASP PRO LYS ASP PRO GLY SEQRES 9 A 685 GLU ARG SER VAL LEU SER ALA LEU ALA ARG ARG LEU LEU SEQRES 10 A 685 GLN GLU ARG LEU ARG ARG LEU GLU GLY VAL TRP VAL GLU SEQRES 11 A 685 GLY LEU ALA VAL TYR ARG ARG GLU HIS ALA ARG GLY PRO SEQRES 12 A 685 GLY TRP ARG VAL LEU GLY GLY ALA VAL LEU ASP LEU TRP SEQRES 13 A 685 VAL SER ASP SER GLY ALA PHE LEU LEU GLU VAL ASP PRO SEQRES 14 A 685 ALA TYR ARG ILE LEU CYS GLU MET SER LEU GLU ALA TRP SEQRES 15 A 685 LEU ALA GLN GLY HIS PRO LEU PRO LYS ARG VAL ARG ASN SEQRES 16 A 685 ALA TYR ASP ARG ARG THR TRP GLU LEU LEU ARG LEU GLY SEQRES 17 A 685 GLU GLU ASP PRO LYS GLU LEU PRO LEU PRO GLY GLY LEU SEQRES 18 A 685 SER LEU LEU ASP TYR HIS ALA SER LYS GLY ARG LEU GLN SEQRES 19 A 685 GLY ARG GLU GLY GLY ARG VAL ALA TRP VAL ALA ASP PRO SEQRES 20 A 685 LYS ASP PRO ARG LYS PRO ILE PRO HIS LEU THR GLY LEU SEQRES 21 A 685 LEU VAL PRO VAL LEU THR LEU GLU ASP LEU HIS GLU GLU SEQRES 22 A 685 GLU GLY SER LEU ALA LEU SER LEU PRO TRP GLU GLU ARG SEQRES 23 A 685 ARG ARG ARG THR ARG GLU ILE ALA SER TRP ILE GLY ARG SEQRES 24 A 685 ARG LEU GLY LEU GLY THR PRO GLU ALA VAL ARG ALA GLN SEQRES 25 A 685 ALA TYR ARG LEU SER ILE PRO LYS LEU MET GLY ARG ARG SEQRES 26 A 685 ALA VAL SER LYS PRO ALA ASP ALA LEU ARG VAL GLY PHE SEQRES 27 A 685 TYR ARG ALA GLN GLU THR ALA LEU ALA LEU LEU ARG LEU SEQRES 28 A 685 ASP GLY ALA GLN GLY TRP PRO GLU PHE LEU ARG ARG ALA SEQRES 29 A 685 LEU LEU ARG ALA PHE GLY ALA SER GLY ALA SER LEU ARG SEQRES 30 A 685 LEU HIS THR LEU HIS ALA HIS PRO SER GLN GLY LEU ALA SEQRES 31 A 685 PHE ARG GLU ALA LEU ARG LYS ALA LYS GLU GLU GLY VAL SEQRES 32 A 685 GLN ALA VAL LEU VAL LEU THR PRO PRO MET ALA TRP GLU SEQRES 33 A 685 ASP ARG ASN ARG LEU LYS ALA LEU LEU LEU ARG GLU GLY SEQRES 34 A 685 LEU PRO SER GLN ILE LEU ASN VAL PRO LEU ARG GLU GLU SEQRES 35 A 685 GLU ARG HIS ARG TRP GLU ASN ALA LEU LEU GLY LEU LEU SEQRES 36 A 685 ALA LYS ALA GLY LEU GLN VAL VAL ALA LEU SER GLY ALA SEQRES 37 A 685 TYR PRO ALA GLU LEU ALA VAL GLY PHE ASP ALA GLY GLY SEQRES 38 A 685 ARG GLU SER PHE ARG PHE GLY GLY ALA ALA CYS ALA VAL SEQRES 39 A 685 GLY GLY ASP GLY GLY HIS LEU LEU TRP THR LEU PRO GLU SEQRES 40 A 685 ALA GLN ALA GLY GLU ARG ILE PRO GLN GLU VAL VAL TRP SEQRES 41 A 685 ASP LEU LEU GLU GLU THR LEU TRP ALA PHE ARG ARG LYS SEQRES 42 A 685 ALA GLY ARG LEU PRO SER ARG VAL LEU LEU LEU ARG ASP SEQRES 43 A 685 GLY ARG VAL PRO GLN ASP GLU PHE ALA LEU ALA LEU GLU SEQRES 44 A 685 ALA LEU ALA ARG GLU GLY ILE ALA TYR ASP LEU VAL SER SEQRES 45 A 685 VAL ARG LYS SER GLY GLY GLY ARG VAL TYR PRO VAL GLN SEQRES 46 A 685 GLY ARG LEU ALA ASP GLY LEU TYR VAL PRO LEU GLU ASP SEQRES 47 A 685 LYS THR PHE LEU LEU LEU THR VAL HIS ARG ASP PHE ARG SEQRES 48 A 685 GLY THR PRO ARG PRO LEU LYS LEU VAL HIS GLU ALA GLY SEQRES 49 A 685 ASP THR PRO LEU GLU ALA LEU ALA HIS GLN ILE PHE HIS SEQRES 50 A 685 LEU THR ARG LEU TYR PRO ALA SER GLY PHE ALA PHE PRO SEQRES 51 A 685 ARG LEU PRO ALA PRO LEU HIS LEU ALA ASP ARG LEU VAL SEQRES 52 A 685 LYS GLU VAL GLY ARG LEU GLY ILE ARG HIS LEU LYS GLU SEQRES 53 A 685 VAL ASP ARG GLU LYS LEU PHE PHE VAL SEQRES 1 C 21 DT DG DA DG DG DT DA DG DT DA DG DG DT SEQRES 2 C 21 DT DG DT DA DT DA DG DT SEQRES 1 Y 20 U A U A C A A C U C A C U SEQRES 2 Y 20 A C C U C G U HET MG C 30 1 HETNAM MG MAGNESIUM ION FORMUL 4 MG MG 2+ HELIX 1 1 ASN A 20 ARG A 25 1 6 HELIX 2 2 GLU A 41 GLY A 54 1 14 HELIX 3 3 ASP A 102 ARG A 123 1 22 HELIX 4 4 SER A 178 GLY A 186 1 9 HELIX 5 5 SER A 222 GLY A 231 1 10 HELIX 6 6 PRO A 282 GLY A 298 1 17 HELIX 7 7 ARG A 299 LEU A 301 5 3 HELIX 8 8 LYS A 329 ALA A 331 5 3 HELIX 9 9 ASP A 332 GLY A 337 1 6 HELIX 10 10 PRO A 358 SER A 372 1 15 HELIX 11 11 HIS A 384 GLN A 387 5 4 HELIX 12 12 GLY A 388 GLU A 401 1 14 HELIX 13 13 ALA A 414 GLU A 428 1 15 HELIX 14 14 GLU A 443 GLY A 459 1 17 HELIX 15 15 ILE A 514 GLY A 535 1 22 HELIX 16 16 GLN A 551 GLU A 553 5 3 HELIX 17 17 PHE A 554 GLU A 564 1 11 HELIX 18 18 PRO A 627 LEU A 638 1 12 HELIX 19 19 PRO A 653 LEU A 669 1 17 SHEET 1 A 6 TRP A 128 GLU A 130 0 SHEET 2 A 6 ALA A 133 GLU A 138 -1 O TYR A 135 N TRP A 128 SHEET 3 A 6 TRP A 145 VAL A 157 -1 O GLY A 149 N ARG A 137 SHEET 4 A 6 ALA A 162 CYS A 175 -1 O GLU A 166 N ASP A 154 SHEET 5 A 6 GLU A 8 PRO A 18 -1 N PHE A 14 O LEU A 165 SHEET 6 A 6 GLU A 307 GLN A 312 -1 O ALA A 311 N VAL A 9 SHEET 1 B 6 TRP A 128 GLU A 130 0 SHEET 2 B 6 ALA A 133 GLU A 138 -1 O TYR A 135 N TRP A 128 SHEET 3 B 6 TRP A 145 VAL A 157 -1 O GLY A 149 N ARG A 137 SHEET 4 B 6 ALA A 162 CYS A 175 -1 O GLU A 166 N ASP A 154 SHEET 5 B 6 GLU A 8 PRO A 18 -1 N PHE A 14 O LEU A 165 SHEET 6 B 6 VAL A 581 PRO A 583 -1 O TYR A 582 N PHE A 10 SHEET 1 C 5 THR A 57 MET A 60 0 SHEET 2 C 5 GLY A 63 SER A 66 -1 O GLY A 63 N MET A 60 SHEET 3 C 5 TRP A 27 ASP A 34 -1 N LEU A 29 O LEU A 64 SHEET 4 C 5 GLN A 84 ARG A 95 -1 O GLY A 94 N ARG A 28 SHEET 5 C 5 GLU A 76 ARG A 81 -1 N LEU A 79 O TYR A 86 SHEET 1 D 3 TRP A 202 GLU A 203 0 SHEET 2 D 3 ARG A 192 VAL A 193 -1 N VAL A 193 O TRP A 202 SHEET 3 D 3 PRO A 263 VAL A 264 -1 O VAL A 264 N ARG A 192 SHEET 1 E 2 LEU A 321 MET A 322 0 SHEET 2 E 2 ALA A 464 LEU A 465 -1 O ALA A 464 N MET A 322 SHEET 1 F 4 LEU A 376 THR A 380 0 SHEET 2 F 4 THR A 344 ARG A 350 1 N LEU A 348 O HIS A 379 SHEET 3 F 4 ALA A 405 THR A 410 1 O LEU A 407 N ALA A 347 SHEET 4 F 4 SER A 432 ASN A 436 1 O GLN A 433 N VAL A 408 SHEET 1 G 8 LEU A 501 LEU A 505 0 SHEET 2 G 8 SER A 484 VAL A 494 -1 N ALA A 491 O THR A 504 SHEET 3 G 8 LEU A 473 GLY A 481 -1 N GLY A 476 O CYS A 492 SHEET 4 G 8 ARG A 540 ARG A 545 1 O LEU A 544 N VAL A 475 SHEET 5 G 8 ALA A 567 ARG A 574 1 O VAL A 573 N ARG A 545 SHEET 6 G 8 LEU A 617 ALA A 623 -1 O ALA A 623 N LEU A 570 SHEET 7 G 8 THR A 600 LEU A 604 -1 N PHE A 601 O LEU A 619 SHEET 8 G 8 LEU A 592 PRO A 595 -1 N VAL A 594 O LEU A 602 CISPEP 1 ASP A 34 PRO A 35 0 1.28 SITE 1 AC1 5 GLN A 433 LYS A 457 VAL A 685 DT C 1 SITE 2 AC1 5 DA C 3 CRYST1 121.839 118.867 59.186 90.00 114.79 90.00 C 1 2 1 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 0.008208 0.000000 0.003791 0.00000 SCALE2 0.000000 0.008413 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018611 0.00000