HEADER NUCLEIC ACID BINDING PROTEIN/DNA/RNA 01-JUN-09 3HO1 TITLE CRYSTAL STRUCTURE OF T. THERMOPHILUS ARGONAUTE N546 MUTANT PROTEIN TITLE 2 COMPLEXED WITH DNA GUIDE STRAND AND 12-NT RNA TARGET STRAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARGONAUTE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*T COMPND 8 *AP*GP*T)-3'; COMPND 9 CHAIN: X; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 5'-R(P*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3'; COMPND 13 CHAIN: Y; COMPND 14 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 5 06-SEP-23 3HO1 1 REMARK REVDAT 4 13-OCT-21 3HO1 1 REMARK SEQADV REVDAT 3 13-JUL-11 3HO1 1 VERSN REVDAT 2 20-OCT-09 3HO1 1 JRNL REVDAT 1 06-OCT-09 3HO1 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. 2.60 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) : 2.60 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) (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 22630 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) : 0.220 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1546 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 : 5145 REMARK 3 NUCLEIC ACID ATOMS : 528 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 93 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.49900 REMARK 3 B22 (A**2) : 5.33700 REMARK 3 B33 (A**2) : -10.83600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 14.32800 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) : 0.009 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 : 36.04 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 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : 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 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3HO1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053370. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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 : 23588 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 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 3DLH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CONTAINING 2.5 MM SPERMINE, 10 MM REMARK 280 MGCL2, 5 MM CACL2, 50 MM NA CACODYLATE PH 6.0, 10% (V/V) REMARK 280 ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 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 61.46400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.26550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 61.46400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 59.26550 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, X, 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 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 ASP A 249 REMARK 465 PRO A 250 REMARK 465 ARG A 251 REMARK 465 GLY A 496 REMARK 465 ASP A 497 REMARK 465 DT X 13 REMARK 465 DT X 14 REMARK 465 DG X 15 REMARK 465 DT X 16 REMARK 465 DA X 17 REMARK 465 DT X 18 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 ASN A 2 CG OD1 ND2 REMARK 470 HIS A 3 CG ND1 CD2 CE1 NE2 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 GLU A 71 CG CD OE1 OE2 REMARK 470 MET A 82 CG SD CE REMARK 470 GLN A 84 CG CD OE1 NE2 REMARK 470 LYS A 93 CG CD CE NZ REMARK 470 GLU A 130 CG CD OE1 OE2 REMARK 470 LEU A 189 CG CD1 CD2 REMARK 470 LYS A 191 CG CD CE NZ REMARK 470 GLU A 203 CG CD OE1 OE2 REMARK 470 GLU A 209 CG CD OE1 OE2 REMARK 470 ASP A 211 CG OD1 OD2 REMARK 470 LYS A 213 CG CD CE NZ REMARK 470 GLU A 214 CG CD OE1 OE2 REMARK 470 LEU A 221 CG CD1 CD2 REMARK 470 SER A 229 OG REMARK 470 GLN A 234 CG CD OE1 NE2 REMARK 470 GLU A 237 CG CD OE1 OE2 REMARK 470 VAL A 241 CG1 CG2 REMARK 470 VAL A 244 CG1 CG2 REMARK 470 ASP A 246 CG OD1 OD2 REMARK 470 PRO A 247 CG CD REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 LYS A 252 CG CD CE NZ REMARK 470 PRO A 253 CG CD 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 GLU A 273 CG CD OE1 OE2 REMARK 470 GLU A 274 CG CD OE1 OE2 REMARK 470 SER A 276 OG REMARK 470 LEU A 277 CG CD1 CD2 REMARK 470 ARG A 315 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 320 CG CD CE NZ REMARK 470 ARG A 367 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 CG CD OE1 NE2 REMARK 470 GLU A 564 CG CD OE1 OE2 REMARK 470 GLN A 585 CG CD OE1 NE2 REMARK 470 ARG A 587 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 599 CG CD CE NZ REMARK 470 ARG A 608 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 675 CG CD CE NZ REMARK 470 DA X 19 P OP1 OP2 O5' C5' C4' O4' REMARK 470 DA X 19 C3' C2' C1' N9 C8 N7 C5 REMARK 470 DA X 19 C6 N6 N1 C2 N3 C4 REMARK 470 G Y 12 C5' C4' O4' C3' O3' C2' O2' REMARK 470 G Y 12 C1' N9 C8 N7 C5 C6 O6 REMARK 470 G Y 12 N1 C2 N2 N3 C4 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 OD1 ASN A 195 NE1 TRP A 202 2.06 REMARK 500 NH1 ARG A 324 O ALA A 371 2.11 REMARK 500 ND2 ASN A 449 O SER A 645 2.12 REMARK 500 O GLU A 268 N HIS A 271 2.12 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 DT X 1 P DT X 1 OP3 -0.123 REMARK 500 DA X 19 O3' DG X 20 P -0.084 REMARK 500 C Y 1 P C Y 1 OP3 -0.076 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 ASP A 246 O - C - N ANGL. DEV. = -12.4 DEGREES REMARK 500 PRO A 253 N - CA - CB ANGL. DEV. = 7.3 DEGREES REMARK 500 PRO A 438 C - N - CA ANGL. DEV. = -13.3 DEGREES REMARK 500 DT X 1 OP1 - P - OP2 ANGL. DEV. = -9.8 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 HIS A 3 146.31 -170.79 REMARK 500 LEU A 4 -165.60 -126.22 REMARK 500 ASN A 12 35.83 -73.09 REMARK 500 PRO A 37 -70.91 -59.92 REMARK 500 ARG A 39 -52.63 -21.29 REMARK 500 HIS A 139 -83.46 -100.80 REMARK 500 HIS A 187 154.71 -42.13 REMARK 500 PRO A 188 -123.79 -104.64 REMARK 500 LEU A 189 108.74 -45.68 REMARK 500 ASP A 198 -143.46 -131.38 REMARK 500 GLU A 203 57.87 -141.07 REMARK 500 LEU A 204 129.16 -33.57 REMARK 500 GLU A 209 30.10 -79.16 REMARK 500 PRO A 212 -76.24 -39.50 REMARK 500 SER A 229 20.15 -70.09 REMARK 500 LYS A 230 -7.75 -148.34 REMARK 500 VAL A 244 -159.73 -87.57 REMARK 500 ASP A 246 -80.22 -127.37 REMARK 500 ILE A 254 71.79 -107.78 REMARK 500 PRO A 255 141.38 -29.07 REMARK 500 GLU A 268 -75.62 -56.61 REMARK 500 ASP A 269 -59.76 -27.79 REMARK 500 GLU A 273 170.68 82.55 REMARK 500 ARG A 325 -163.74 -108.89 REMARK 500 TYR A 339 -88.32 -46.89 REMARK 500 ASP A 352 -147.16 -101.60 REMARK 500 GLN A 355 -67.21 -97.48 REMARK 500 ALA A 374 169.88 -42.11 REMARK 500 PRO A 385 -36.58 -38.33 REMARK 500 GLN A 387 8.66 -67.19 REMARK 500 GLU A 401 11.37 -67.46 REMARK 500 PRO A 438 95.81 -69.77 REMARK 500 GLU A 443 46.49 -71.30 REMARK 500 PHE A 487 51.84 -106.17 REMARK 500 ALA A 508 -31.96 -26.28 REMARK 500 PRO A 538 142.89 -26.96 REMARK 500 PRO A 550 -117.77 -39.94 REMARK 500 GLN A 551 -37.33 -174.23 REMARK 500 LEU A 596 -141.25 -127.91 REMARK 500 LYS A 599 -6.50 84.97 REMARK 500 HIS A 607 94.88 -160.36 REMARK 500 ALA A 623 140.28 -177.07 REMARK 500 SER A 645 -71.19 -90.54 REMARK 500 ARG A 672 -62.32 -126.02 REMARK 500 HIS A 673 70.73 -119.56 REMARK 500 LEU A 674 88.60 -68.73 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 DG X 4 0.09 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 X 22 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HGE RELATED DB: PDB REMARK 900 SAME MUTANT PROTEIN 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 DIFFERENT MUTANT PROTEIN COMPLEXED WITH SAME DNA GUIDE AND 15-NT REMARK 900 RNA GUIDE REMARK 900 RELATED ID: 3DLB RELATED DB: PDB REMARK 900 WILD TYPE PROTEIN COMPLEXED WITH 10-NT DNA GUIDE STRAND REMARK 900 RELATED ID: 3DLH RELATED DB: PDB REMARK 900 WILD TYPE PROTEIN COMPLEXED WITH SAME DNA GUIDE STRAND REMARK 900 RELATED ID: 3F73 RELATED DB: PDB REMARK 900 WILD TYPE PROTEIN COMPLEXED WITH SAME DNA GUIDE STRAND AND 20-NT REMARK 900 RNA TARGET WITH TWO MISMATCHES. REMARK 900 RELATED ID: 3HK2 RELATED DB: PDB REMARK 900 DIFFERENT MUTANT PROTEIN COMPLEXED WITH SAME DNA GUIDE AND 19-NT REMARK 900 RNA GUIDE DBREF 3HO1 A 1 685 UNP Q746M7 Q746M7_THET2 1 685 DBREF 3HO1 X 1 21 PDB 3HO1 3HO1 1 21 DBREF 3HO1 Y 1 12 PDB 3HO1 3HO1 1 12 SEQADV 3HO1 ASN A 546 UNP Q746M7 ASP 546 ENGINEERED MUTATION 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 ASN 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 X 21 DT DG DA DG DG DT DA DG DT DA DG DG DT SEQRES 2 X 21 DT DG DT DA DT DA DG DT SEQRES 1 Y 12 C C U A C U A C C U C G HET MG X 22 1 HETNAM MG MAGNESIUM ION FORMUL 4 MG MG 2+ FORMUL 5 HOH *93(H2 O) HELIX 1 1 GLU A 41 ALA A 53 1 13 HELIX 2 2 ASP A 102 ARG A 123 1 22 HELIX 3 3 SER A 178 GLY A 186 1 9 HELIX 4 4 PRO A 282 ARG A 300 1 19 HELIX 5 5 LYS A 329 ALA A 331 5 3 HELIX 6 6 ASP A 332 GLY A 337 1 6 HELIX 7 7 PRO A 358 ALA A 371 1 14 HELIX 8 8 HIS A 384 GLN A 387 5 4 HELIX 9 9 GLY A 388 GLU A 401 1 14 HELIX 10 10 ALA A 414 GLU A 428 1 15 HELIX 11 11 GLU A 443 GLY A 459 1 17 HELIX 12 12 ILE A 514 GLY A 535 1 22 HELIX 13 13 GLN A 551 GLU A 553 5 3 HELIX 14 14 PHE A 554 GLU A 564 1 11 HELIX 15 15 PRO A 627 LEU A 638 1 12 HELIX 16 16 THR A 639 LEU A 641 5 3 HELIX 17 17 PRO A 653 LEU A 669 1 17 SHEET 1 A14 TRP A 128 GLU A 130 0 SHEET 2 A14 ALA A 133 GLY A 142 -1 O TYR A 135 N TRP A 128 SHEET 3 A14 TRP A 145 VAL A 157 -1 O VAL A 147 N HIS A 139 SHEET 4 A14 ALA A 162 CYS A 175 -1 O ALA A 170 N GLY A 150 SHEET 5 A14 THR A 7 PRO A 18 -1 N PHE A 14 O LEU A 165 SHEET 6 A14 GLU A 307 ARG A 315 -1 O ALA A 313 N THR A 7 SHEET 7 A14 LEU A 592 PRO A 595 -1 O TYR A 593 N TYR A 314 SHEET 8 A14 THR A 600 LEU A 604 -1 O LEU A 602 N VAL A 594 SHEET 9 A14 LEU A 617 GLY A 624 -1 O LEU A 619 N PHE A 601 SHEET 10 A14 ALA A 567 ARG A 574 -1 N LEU A 570 O ALA A 623 SHEET 11 A14 ARG A 540 ARG A 545 1 N LEU A 543 O ASP A 569 SHEET 12 A14 LEU A 473 GLY A 481 1 N VAL A 475 O LEU A 544 SHEET 13 A14 SER A 484 VAL A 494 -1 O GLY A 488 N GLY A 480 SHEET 14 A14 LEU A 502 LEU A 505 -1 O THR A 504 N ALA A 491 SHEET 1 B 6 TRP A 128 GLU A 130 0 SHEET 2 B 6 ALA A 133 GLY A 142 -1 O TYR A 135 N TRP A 128 SHEET 3 B 6 TRP A 145 VAL A 157 -1 O VAL A 147 N HIS A 139 SHEET 4 B 6 ALA A 162 CYS A 175 -1 O ALA A 170 N GLY A 150 SHEET 5 B 6 THR A 7 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 TRP A 27 O SER A 66 SHEET 4 C 5 THR A 85 ARG A 95 -1 O LYS A 93 N ARG A 28 SHEET 5 C 5 GLU A 76 ALA A 80 -1 N LEU A 79 O TYR A 86 SHEET 1 D 3 THR A 201 TRP A 202 0 SHEET 2 D 3 ARG A 192 ASN A 195 -1 N VAL A 193 O TRP A 202 SHEET 3 D 3 LEU A 261 VAL A 264 -1 O VAL A 262 N ARG A 194 SHEET 1 E 3 ARG A 206 GLY A 208 0 SHEET 2 E 3 VAL A 241 VAL A 244 -1 O VAL A 241 N GLY A 208 SHEET 3 E 3 ILE A 254 LEU A 257 -1 O HIS A 256 N ALA A 242 SHEET 1 F 2 LEU A 321 MET A 322 0 SHEET 2 F 2 ALA A 464 LEU A 465 -1 O ALA A 464 N MET A 322 SHEET 1 G 4 LEU A 376 THR A 380 0 SHEET 2 G 4 THR A 344 ARG A 350 1 N LEU A 346 O HIS A 379 SHEET 3 G 4 ALA A 405 THR A 410 1 O LEU A 407 N ALA A 347 SHEET 4 G 4 SER A 432 ASN A 436 1 O GLN A 433 N VAL A 408 CISPEP 1 ASP A 34 PRO A 35 0 0.05 SITE 1 AC1 3 VAL A 685 DT X 1 DA X 3 CRYST1 122.928 118.531 59.533 90.00 114.91 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 0.008135 0.000000 0.003778 0.00000 SCALE2 0.000000 0.008437 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018520 0.00000