HEADER DNA BINDING PROTEIN 01-JUN-17 5XPA TITLE CRYSTAL STRUCTURE OF T. THERMOPHILUS ARGONAUTE PROTEIN COMPLEXED WITH TITLE 2 A BULGE 9'U10' ON THE TARGET STRAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN AGO; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'- COMPND 8 D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)- COMPND 9 3'); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: RNA (5'- COMPND 14 R(P*AP*UP*AP*CP*AP*AP*CP*CP*GP*UP*UP*CP*UP*AP*CP*UP*CP*CP*G)-3'); COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS (STRAIN HB27 / ATCC BAA- SOURCE 3 163 / DSM 7039); SOURCE 4 ORGANISM_TAXID: 262724; SOURCE 5 STRAIN: HB27 / ATCC BAA-163 / DSM 7039; SOURCE 6 GENE: TT_P0026; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 13 ORGANISM_TAXID: 274; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 17 ORGANISM_TAXID: 274 KEYWDS ARGONAUTE, MIRNA, BULGE, MISMATCH, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.SHENG,T.GOGAKOS,J.WANG,H.ZHAO,A.SERGANOV,S.JURANEK,T.TUSCHL, AUTHOR 2 J.D.PATEL,Y.WANG REVDAT 3 22-NOV-23 5XPA 1 LINK REVDAT 2 01-MAY-19 5XPA 1 JRNL REVDAT 1 18-APR-18 5XPA 0 JRNL AUTH G.SHENG,T.GOGAKOS,J.WANG,H.ZHAO,A.SERGANOV,S.JURANEK, JRNL AUTH 2 T.TUSCHL,D.J.PATEL,Y.WANG JRNL TITL STRUCTURE/CLEAVAGE-BASED INSIGHTS INTO HELICAL PERTURBATIONS JRNL TITL 2 AT BULGE SITES WITHIN T. THERMOPHILUS ARGONAUTE SILENCING JRNL TITL 3 COMPLEXES. JRNL REF NUCLEIC ACIDS RES. V. 45 9149 2017 JRNL REFN ESSN 1362-4962 JRNL PMID 28911094 JRNL DOI 10.1093/NAR/GKX547 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 25323 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1292 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 43.1547 - 6.0356 0.99 2872 141 0.2069 0.2756 REMARK 3 2 6.0356 - 4.7927 1.00 2717 145 0.2176 0.2770 REMARK 3 3 4.7927 - 4.1874 1.00 2705 115 0.1868 0.2274 REMARK 3 4 4.1874 - 3.8048 1.00 2649 165 0.1991 0.2787 REMARK 3 5 3.8048 - 3.5322 1.00 2621 153 0.2177 0.3136 REMARK 3 6 3.5322 - 3.3241 1.00 2627 150 0.2295 0.2740 REMARK 3 7 3.3241 - 3.1576 1.00 2600 163 0.2515 0.3288 REMARK 3 8 3.1576 - 3.0202 1.00 2619 138 0.2799 0.3349 REMARK 3 9 3.0202 - 2.9040 1.00 2621 122 0.2939 0.3815 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 6176 REMARK 3 ANGLE : 0.979 8573 REMARK 3 CHIRALITY : 0.038 975 REMARK 3 PLANARITY : 0.004 972 REMARK 3 DIHEDRAL : 16.448 2335 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5XPA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1300003939. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97892 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25323 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 46.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 4KPY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.1 M NH4-ACETATE, 0. 1 M BIS-TRIS REMARK 280 PROPANE, PH 7.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 308K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 92.34250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 54.56700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 54.56700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 138.51375 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 54.56700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 54.56700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 46.17125 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 54.56700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.56700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 138.51375 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 54.56700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.56700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 46.17125 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 92.34250 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: 6220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 GLU A 274 REMARK 465 GLY A 275 REMARK 465 SER A 276 REMARK 465 GLY A 496 REMARK 465 U D 1 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 HIS A 3 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 4 CG CD1 CD2 REMARK 470 LYS A 6 CG CD CE NZ REMARK 470 ARG A 28 CG CD NE CZ NH1 NH2 REMARK 470 PRO A 37 CG CD 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 VAL A 42 CG1 CG2 REMARK 470 MET A 82 CG SD CE REMARK 470 GLN A 84 CG CD OE1 NE2 REMARK 470 SER A 107 OG REMARK 470 GLU A 125 CG CD OE1 OE2 REMARK 470 ARG A 141 CG CD NE CZ NH1 NH2 REMARK 470 PRO A 143 CG CD REMARK 470 GLU A 176 CG CD OE1 OE2 REMARK 470 HIS A 187 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 189 CG CD1 CD2 REMARK 470 LYS A 191 CG CD CE NZ REMARK 470 ARG A 200 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 203 CG CD OE1 OE2 REMARK 470 LYS A 213 CG CD CE NZ REMARK 470 PRO A 218 CG CD REMARK 470 GLU A 237 CG CD OE1 OE2 REMARK 470 ASP A 246 CG OD1 OD2 REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 ASP A 249 CG OD1 OD2 REMARK 470 ARG A 251 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 252 CG CD CE NZ REMARK 470 LEU A 265 CG CD1 CD2 REMARK 470 THR A 266 OG1 CG2 REMARK 470 GLU A 272 CG CD OE1 OE2 REMARK 470 GLU A 273 CG CD OE1 OE2 REMARK 470 LEU A 277 CG CD1 CD2 REMARK 470 PRO A 282 CG CD REMARK 470 GLU A 284 CG CD OE1 OE2 REMARK 470 LYS A 320 CG CD CE NZ REMARK 470 GLN A 342 CG CD OE1 NE2 REMARK 470 SER A 386 OG REMARK 470 ARG A 444 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 483 CG CD OE1 OE2 REMARK 470 ASP A 497 CG OD1 OD2 REMARK 470 HIS A 500 CG ND1 CD2 CE1 NE2 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 512 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 LEU A 588 CG CD1 CD2 REMARK 470 GLU A 597 CG CD OE1 OE2 REMARK 470 ASP A 598 CG OD1 OD2 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 ILE A 671 CG1 CG2 CD1 REMARK 470 ARG A 672 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 673 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 675 CG CD CE NZ REMARK 470 GLU A 676 CG CD OE1 OE2 REMARK 470 DT C 14 C7 REMARK 470 DT C 18 C7 REMARK 470 A D 2 O2' REMARK 470 G D 20 C5' C4' O4' C3' O3' C2' O2' REMARK 470 G D 20 C1' N9 C8 N7 C5 C6 O6 REMARK 470 G D 20 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 OE1 GLU A 130 NH1 ARG A 172 1.60 REMARK 500 CB TRP A 202 CG2 VAL A 244 1.66 REMARK 500 O ALA A 184 N GLY A 186 1.88 REMARK 500 OE1 GLU A 180 OG1 THR A 258 2.06 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 C 1 P DT C 1 OP3 -0.128 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 247 C - N - CD ANGL. DEV. = -19.2 DEGREES REMARK 500 PRO A 250 C - N - CD ANGL. DEV. = -48.6 DEGREES REMARK 500 PRO A 438 C - N - CA ANGL. DEV. = -10.6 DEGREES REMARK 500 DA C 3 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA C 7 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA C 10 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 DA C 10 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG C 11 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DT C 16 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG C 20 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 U D 12 C5 - C6 - N1 ANGL. DEV. = 3.7 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 LEU A 4 -127.40 -154.13 REMARK 500 LYS A 6 144.65 -172.77 REMARK 500 ASN A 12 29.56 -77.74 REMARK 500 LEU A 16 -166.77 -117.89 REMARK 500 PRO A 36 -70.18 -53.16 REMARK 500 PRO A 37 -163.22 59.12 REMARK 500 ARG A 39 -39.12 64.84 REMARK 500 VAL A 42 47.15 -89.29 REMARK 500 TYR A 43 -45.51 -137.24 REMARK 500 ARG A 136 -82.71 -96.34 REMARK 500 ARG A 137 175.20 -59.35 REMARK 500 PRO A 143 69.46 37.95 REMARK 500 MET A 177 -161.13 -163.77 REMARK 500 GLN A 185 -13.38 -34.87 REMARK 500 LYS A 191 -75.89 -68.72 REMARK 500 ASP A 198 -162.71 -160.24 REMARK 500 LEU A 205 -64.59 -94.07 REMARK 500 LEU A 215 109.01 -53.02 REMARK 500 PRO A 218 80.70 -60.22 REMARK 500 ARG A 232 -26.03 -140.32 REMARK 500 GLN A 234 94.49 -69.16 REMARK 500 LYS A 248 -120.62 -83.23 REMARK 500 ALA A 278 78.56 57.84 REMARK 500 GLN A 355 -84.61 -93.74 REMARK 500 ALA A 371 8.14 -69.84 REMARK 500 SER A 375 116.68 72.32 REMARK 500 PRO A 412 112.51 -35.81 REMARK 500 PRO A 438 84.85 -67.69 REMARK 500 VAL A 462 -39.36 57.10 REMARK 500 HIS A 500 138.41 62.10 REMARK 500 ALA A 508 60.61 -163.32 REMARK 500 GLN A 509 175.61 61.01 REMARK 500 LEU A 596 -134.05 -130.10 REMARK 500 GLU A 597 -160.69 -65.04 REMARK 500 ASP A 598 99.52 -53.02 REMARK 500 HIS A 607 91.59 -167.15 REMARK 500 ARG A 608 -162.67 -118.38 REMARK 500 ASP A 609 65.12 -67.74 REMARK 500 LEU A 641 53.38 -103.53 REMARK 500 LEU A 669 -152.81 -106.78 REMARK 500 ILE A 671 54.84 -156.26 REMARK 500 ARG A 672 -84.43 -26.84 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 MG A 701 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 685 O REMARK 620 2 VAL A 685 OXT 57.6 REMARK 620 3 DT C 1 OP2 126.2 140.1 REMARK 620 4 DA C 3 OP1 138.6 81.0 85.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 701 DBREF 5XPA A 1 685 UNP Q746M7 Q746M7_THET2 1 685 DBREF 5XPA C 1 21 PDB 5XPA 5XPA 1 21 DBREF 5XPA D 1 20 PDB 5XPA 5XPA 1 20 SEQADV 5XPA 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 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 D 20 U A U A C A A C C G U U C SEQRES 2 D 20 U A C C U C G HET MG A 701 1 HETNAM MG MAGNESIUM ION FORMUL 4 MG MG 2+ HELIX 1 AA1 TYR A 43 ALA A 53 1 11 HELIX 2 AA2 PRO A 69 LEU A 73 5 5 HELIX 3 AA3 ASP A 102 ARG A 123 1 22 HELIX 4 AA4 SER A 178 GLN A 185 1 8 HELIX 5 AA5 SER A 222 LYS A 230 1 9 HELIX 6 AA6 THR A 266 GLU A 272 1 7 HELIX 7 AA7 PRO A 282 GLY A 302 1 21 HELIX 8 AA8 LYS A 329 ALA A 331 5 3 HELIX 9 AA9 ASP A 332 GLY A 337 1 6 HELIX 10 AB1 PRO A 358 ALA A 371 1 14 HELIX 11 AB2 HIS A 384 GLN A 387 5 4 HELIX 12 AB3 GLY A 388 GLU A 401 1 14 HELIX 13 AB4 ALA A 414 GLU A 428 1 15 HELIX 14 AB5 GLU A 443 GLY A 459 1 17 HELIX 15 AB6 SER A 484 GLY A 488 5 5 HELIX 16 AB7 ILE A 514 GLY A 535 1 22 HELIX 17 AB8 PRO A 550 GLU A 553 5 4 HELIX 18 AB9 PHE A 554 GLU A 564 1 11 HELIX 19 AC1 PRO A 627 THR A 639 1 13 HELIX 20 AC2 PRO A 653 LEU A 669 1 17 SHEET 1 AA114 TRP A 128 VAL A 129 0 SHEET 2 AA114 ALA A 133 GLY A 142 -1 O TYR A 135 N TRP A 128 SHEET 3 AA114 TRP A 145 VAL A 157 -1 O VAL A 147 N ALA A 140 SHEET 4 AA114 ALA A 162 LEU A 174 -1 O ASP A 168 N VAL A 152 SHEET 5 AA114 THR A 7 PRO A 18 -1 N LEU A 16 O PHE A 163 SHEET 6 AA114 GLU A 307 ARG A 315 -1 O GLU A 307 N ALA A 15 SHEET 7 AA114 LEU A 592 PRO A 595 -1 O TYR A 593 N TYR A 314 SHEET 8 AA114 THR A 600 LEU A 604 -1 O LEU A 602 N VAL A 594 SHEET 9 AA114 LEU A 617 ALA A 623 -1 O LEU A 619 N PHE A 601 SHEET 10 AA114 ALA A 567 ARG A 574 -1 N ARG A 574 O LYS A 618 SHEET 11 AA114 ARG A 540 ARG A 545 1 N LEU A 543 O VAL A 571 SHEET 12 AA114 LEU A 473 ASP A 478 1 N PHE A 477 O LEU A 544 SHEET 13 AA114 ALA A 490 GLY A 495 -1 O VAL A 494 N ALA A 474 SHEET 14 AA114 GLY A 499 THR A 504 -1 O LEU A 502 N ALA A 493 SHEET 1 AA2 6 TRP A 128 VAL A 129 0 SHEET 2 AA2 6 ALA A 133 GLY A 142 -1 O TYR A 135 N TRP A 128 SHEET 3 AA2 6 TRP A 145 VAL A 157 -1 O VAL A 147 N ALA A 140 SHEET 4 AA2 6 ALA A 162 LEU A 174 -1 O ASP A 168 N VAL A 152 SHEET 5 AA2 6 THR A 7 PRO A 18 -1 N LEU A 16 O PHE A 163 SHEET 6 AA2 6 VAL A 581 PRO A 583 -1 O TYR A 582 N PHE A 10 SHEET 1 AA3 5 THR A 57 MET A 60 0 SHEET 2 AA3 5 GLY A 63 SER A 66 -1 O GLY A 63 N MET A 60 SHEET 3 AA3 5 TRP A 27 ASP A 34 -1 N TRP A 27 O SER A 66 SHEET 4 AA3 5 GLN A 84 ARG A 95 -1 O GLY A 94 N ARG A 28 SHEET 5 AA3 5 GLU A 76 ARG A 81 -1 N ARG A 81 O GLN A 84 SHEET 1 AA4 5 ILE A 254 LEU A 257 0 SHEET 2 AA4 5 VAL A 241 ALA A 245 -1 N VAL A 244 O ILE A 254 SHEET 3 AA4 5 THR A 201 LEU A 207 -1 N ARG A 206 O TRP A 243 SHEET 4 AA4 5 ARG A 192 ASN A 195 -1 N VAL A 193 O TRP A 202 SHEET 5 AA4 5 LEU A 261 PRO A 263 -1 O VAL A 262 N ARG A 194 SHEET 1 AA5 3 ALA A 326 VAL A 327 0 SHEET 2 AA5 3 LEU A 321 MET A 322 -1 N LEU A 321 O VAL A 327 SHEET 3 AA5 3 ALA A 464 LEU A 465 -1 O ALA A 464 N MET A 322 SHEET 1 AA6 4 LEU A 376 LEU A 381 0 SHEET 2 AA6 4 THR A 344 ARG A 350 1 N LEU A 348 O LEU A 381 SHEET 3 AA6 4 VAL A 403 THR A 410 1 O LEU A 407 N ALA A 347 SHEET 4 AA6 4 SER A 432 ASN A 436 1 O LEU A 435 N VAL A 408 LINK O VAL A 685 MG MG A 701 1555 1555 2.12 LINK OXT VAL A 685 MG MG A 701 1555 1555 2.24 LINK MG MG A 701 OP2 DT C 1 1555 1555 1.98 LINK MG MG A 701 OP1 DA C 3 1555 1555 2.22 CISPEP 1 ASP A 34 PRO A 35 0 -0.86 CISPEP 2 GLY A 670 ILE A 671 0 -0.77 SITE 1 AC1 5 GLN A 433 LYS A 457 VAL A 685 DT C 1 SITE 2 AC1 5 DA C 3 CRYST1 109.134 109.134 184.685 90.00 90.00 90.00 P 43 21 2 8 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 0.009163 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009163 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005415 0.00000