HEADER PROTEIN/DNA COMPLEX 19-NOV-08 2W42 TITLE THE STRUCTURE OF A PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED TITLE 2 WITH A 16NT DNA DUPLEX. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PIWI; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*TP*TP*CP*GP*AP*CP*GP*CP)-3'; COMPND 8 CHAIN: P, R; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5'-D(*GP*TP*CP*GP*AP*AP*TP*TP)-3'; COMPND 12 CHAIN: Q, S; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARCHAEOGLOBUS FULGIDUS; SOURCE 3 ORGANISM_TAXID: 2234; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET-17B; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS RNAI, RISC, ARGONAUTE, PIWI DOMAIN, PROTEIN-DNA COMPLEX, PROTEIN-DNA KEYWDS 2 COMPLEX COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.S.PARKER,S.M.ROE,D.BARFORD REVDAT 3 13-DEC-23 2W42 1 LINK REVDAT 2 17-FEB-09 2W42 1 JRNL REMARK REVDAT 1 09-DEC-08 2W42 0 JRNL AUTH J.S.PARKER,E.A.PARIZOTTO,M.WANG,S.M.ROE,D.BARFORD JRNL TITL ENHANCEMENT OF THE SEED-TARGET RECOGNITION STEP IN RNA JRNL TITL 2 SILENCING BY A PIWI-MID DOMAIN PROTEIN JRNL REF MOL.CELL V. 33 204 2009 JRNL REFN ISSN 1097-2765 JRNL PMID 19187762 JRNL DOI 10.1016/J.MOLCEL.2008.12.012 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 24/04/2001 REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 98.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 89899 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 + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 4463 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6249 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2820 REMARK 3 BIN FREE R VALUE SET COUNT : 313 REMARK 3 BIN FREE R VALUE : 0.3250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6370 REMARK 3 NUCLEIC ACID ATOMS : 452 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 411 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.99800 REMARK 3 B22 (A**2) : 1.43300 REMARK 3 B33 (A**2) : -0.47800 REMARK 3 B12 (A**2) : 0.00400 REMARK 3 B13 (A**2) : 0.60400 REMARK 3 B23 (A**2) : -0.51600 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.144 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.139 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.105 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.578 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7026 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9617 ; 1.766 ; 2.044 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 775 ; 6.233 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 286 ;43.156 ;24.615 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1168 ;16.316 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;20.451 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1079 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5054 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3313 ; 0.231 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4746 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 461 ; 0.191 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 84 ; 0.190 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 23 ; 0.134 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4030 ; 1.241 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6386 ; 1.987 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3625 ; 2.624 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3231 ; 3.828 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2W42 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1290038149. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 89928 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 32.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 2.090 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.09 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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 1W9H REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 2770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P, Q 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 350 REMARK 350 BIOMOLECULE: 2 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: 2520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, R, S 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 MET A 2 REMARK 465 GLU A 3 REMARK 465 TYR A 4 REMARK 465 LYS A 5 REMARK 465 ILE A 6 REMARK 465 VAL A 7 REMARK 465 GLU A 8 REMARK 465 ASN A 9 REMARK 465 GLY A 10 REMARK 465 ASP A 303 REMARK 465 PRO A 304 REMARK 465 ASN A 305 REMARK 465 ASN A 306 REMARK 465 ARG A 307 REMARK 465 PHE A 308 REMARK 465 HIS A 309 REMARK 465 PRO A 310 REMARK 465 PRO A 330 REMARK 465 TYR A 331 REMARK 465 LEU A 332 REMARK 465 LYS A 333 REMARK 465 ARG A 334 REMARK 465 ASN A 335 REMARK 465 GLY A 336 REMARK 465 LEU A 337 REMARK 465 GLU A 338 REMARK 465 ASN A 413 REMARK 465 PRO A 414 REMARK 465 GLU A 415 REMARK 465 GLY A 416 REMARK 465 ASN A 417 REMARK 465 MET B 1 REMARK 465 MET B 2 REMARK 465 GLU B 3 REMARK 465 TYR B 4 REMARK 465 LYS B 5 REMARK 465 ILE B 6 REMARK 465 VAL B 7 REMARK 465 GLU B 8 REMARK 465 ASN B 9 REMARK 465 GLY B 10 REMARK 465 LEU B 144 REMARK 465 SER B 145 REMARK 465 ASN B 146 REMARK 465 ARG B 147 REMARK 465 ASP B 303 REMARK 465 PRO B 304 REMARK 465 ASN B 305 REMARK 465 ASN B 306 REMARK 465 ARG B 307 REMARK 465 PHE B 308 REMARK 465 HIS B 309 REMARK 465 PRO B 310 REMARK 465 PRO B 330 REMARK 465 TYR B 331 REMARK 465 LEU B 332 REMARK 465 LYS B 333 REMARK 465 ARG B 334 REMARK 465 ASN B 335 REMARK 465 GLY B 336 REMARK 465 LEU B 337 REMARK 465 GLU B 338 REMARK 465 MET B 339 REMARK 465 ASN B 413 REMARK 465 PRO B 414 REMARK 465 GLU B 415 REMARK 465 GLY B 416 REMARK 465 ASN B 417 REMARK 465 ARG B 418 REMARK 465 DG P 7 REMARK 465 DC P 8 REMARK 465 DT Q 15 REMARK 465 DT Q 16 REMARK 465 DG R 7 REMARK 465 DC R 8 REMARK 465 DG S 9 REMARK 465 DT S 10 REMARK 465 DT S 15 REMARK 465 DT S 16 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 ARG A 418 CG CD NE CZ NH1 NH2 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 NE ARG A 257 O HOH A 2163 1.66 REMARK 500 NH1 ARG A 257 OE2 GLU A 264 1.78 REMARK 500 SD MET A 200 O HOH A 2127 1.81 REMARK 500 NZ LYS A 231 OE1 GLU A 274 2.06 REMARK 500 CB THR A 314 O HOH A 2193 2.13 REMARK 500 ND2 ASN A 211 O HOH A 2126 2.16 REMARK 500 CZ ARG A 257 O HOH A 2163 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 DT R 1 P DT R 1 OP3 -0.152 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 ARG A 257 NE - CZ - NH1 ANGL. DEV. = -4.6 DEGREES REMARK 500 LEU A 325 CB - CG - CD2 ANGL. DEV. = -10.5 DEGREES REMARK 500 DT P 2 O4' - C1' - C2' ANGL. DEV. = 4.2 DEGREES REMARK 500 DT P 2 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 DT P 2 C4 - C5 - C7 ANGL. DEV. = 4.7 DEGREES REMARK 500 DT P 2 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DC P 3 O3' - P - O5' ANGL. DEV. = 11.5 DEGREES REMARK 500 DC P 3 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 DC P 3 O4' - C1' - N1 ANGL. DEV. = -6.1 DEGREES REMARK 500 DC P 6 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DT Q 10 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT R 1 C4 - C5 - C7 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT R 2 O5' - C5' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG R 4 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA R 5 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DC R 6 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC S 11 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 DC S 11 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA S 13 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA S 14 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 ILE A 15 -153.36 -113.44 REMARK 500 ASN A 25 89.33 -151.56 REMARK 500 ASP A 191 -166.34 -167.29 REMARK 500 TRP A 244 94.55 -69.76 REMARK 500 MET A 260 42.51 -163.14 REMARK 500 ILE B 15 -150.62 -111.26 REMARK 500 ASN B 25 86.29 -156.28 REMARK 500 TYR B 118 104.57 -43.42 REMARK 500 ASP B 142 24.91 -78.02 REMARK 500 ASP B 191 -168.04 -169.03 REMARK 500 GLU B 279 23.11 45.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN B 148 LEU B 149 -32.60 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 MN A1428 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 159 OE1 REMARK 620 2 LEU A 427 O 84.8 REMARK 620 3 LEU A 427 OXT 89.6 54.3 REMARK 620 4 HOH A2244 O 172.1 88.8 90.5 REMARK 620 5 DT P 1 OP3 86.1 99.2 153.4 90.2 REMARK 620 6 DC P 3 OP1 96.5 154.1 99.9 91.3 106.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B1428 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN B 159 OE1 REMARK 620 2 LEU B 427 O 82.7 REMARK 620 3 LEU B 427 OXT 90.9 54.4 REMARK 620 4 HOH B2143 O 165.6 82.9 80.0 REMARK 620 5 DT R 1 OP3 89.4 97.1 151.2 93.3 REMARK 620 6 DC R 3 OP1 96.0 152.3 98.0 96.3 110.6 REMARK 620 N 1 2 3 4 5 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1428 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B1428 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BGG RELATED DB: PDB REMARK 900 THE STRUCTURE OF A PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS REMARK 900 COMPLEXED WITH A 16NT SIRNA DUPLEX. REMARK 900 RELATED ID: 1W9H RELATED DB: PDB REMARK 900 THE STRUCTURE OF A PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS. DBREF 2W42 A 1 427 UNP O28951 O28951_ARCFU 1 427 DBREF 2W42 B 1 427 UNP O28951 O28951_ARCFU 1 427 DBREF 2W42 P 1 8 PDB 2W42 2W42 1 8 DBREF 2W42 Q 9 16 PDB 2W42 2W42 9 16 DBREF 2W42 R 1 8 PDB 2W42 2W42 1 8 DBREF 2W42 S 9 16 PDB 2W42 2W42 9 16 SEQRES 1 A 427 MET MET GLU TYR LYS ILE VAL GLU ASN GLY LEU THR TYR SEQRES 2 A 427 ARG ILE GLY ASN GLY ALA SER VAL PRO ILE SER ASN THR SEQRES 3 A 427 GLY GLU LEU ILE LYS GLY LEU ARG ASN TYR GLY PRO TYR SEQRES 4 A 427 GLU VAL PRO SER LEU LYS TYR ASN GLN ILE ALA LEU ILE SEQRES 5 A 427 HIS ASN ASN GLN PHE SER SER LEU ILE ASN GLN LEU LYS SEQRES 6 A 427 SER GLN ILE SER SER LYS ILE ASP GLU VAL TRP HIS ILE SEQRES 7 A 427 HIS ASN ILE ASN ILE SER GLU PHE ILE TYR ASP SER PRO SEQRES 8 A 427 HIS PHE ASP SER ILE LYS SER GLN VAL ASP ASN ALA ILE SEQRES 9 A 427 ASP THR GLY VAL ASP GLY ILE MET LEU VAL LEU PRO GLU SEQRES 10 A 427 TYR ASN THR PRO LEU TYR TYR LYS LEU LYS SER TYR LEU SEQRES 11 A 427 ILE ASN SER ILE PRO SER GLN PHE MET ARG TYR ASP ILE SEQRES 12 A 427 LEU SER ASN ARG ASN LEU THR PHE TYR VAL ASP ASN LEU SEQRES 13 A 427 LEU VAL GLN PHE VAL SER LYS LEU GLY GLY LYS PRO TRP SEQRES 14 A 427 ILE LEU ASN VAL ASP PRO GLU LYS GLY SER ASP ILE ILE SEQRES 15 A 427 ILE GLY THR GLY ALA THR ARG ILE ASP ASN VAL ASN LEU SEQRES 16 A 427 PHE CYS PHE ALA MET VAL PHE LYS LYS ASP GLY THR MET SEQRES 17 A 427 LEU TRP ASN GLU ILE SER PRO ILE VAL THR SER SER GLU SEQRES 18 A 427 TYR LEU THR TYR LEU LYS SER THR ILE LYS LYS VAL VAL SEQRES 19 A 427 TYR GLY PHE LYS LYS SER ASN PRO ASP TRP ASP VAL GLU SEQRES 20 A 427 LYS LEU THR LEU HIS VAL SER GLY LYS ARG PRO LYS MET SEQRES 21 A 427 LYS ASP GLY GLU THR LYS ILE LEU LYS GLU THR VAL GLU SEQRES 22 A 427 GLU LEU LYS LYS GLN GLU MET VAL SER ARG ASP VAL LYS SEQRES 23 A 427 TYR ALA ILE LEU HIS LEU ASN GLU THR HIS PRO PHE TRP SEQRES 24 A 427 VAL MET GLY ASP PRO ASN ASN ARG PHE HIS PRO TYR GLU SEQRES 25 A 427 GLY THR LYS VAL LYS LEU SER SER LYS ARG TYR LEU LEU SEQRES 26 A 427 THR LEU LEU GLN PRO TYR LEU LYS ARG ASN GLY LEU GLU SEQRES 27 A 427 MET VAL THR PRO ILE LYS PRO LEU SER VAL GLU ILE VAL SEQRES 28 A 427 SER ASP ASN TRP THR SER GLU GLU TYR TYR HIS ASN VAL SEQRES 29 A 427 HIS GLU ILE LEU ASP GLU ILE TYR TYR LEU SER LYS MET SEQRES 30 A 427 ASN TRP ARG GLY PHE ARG SER ARG ASN LEU PRO VAL THR SEQRES 31 A 427 VAL ASN TYR PRO LYS LEU VAL ALA GLY ILE ILE ALA ASN SEQRES 32 A 427 VAL ASN ARG TYR GLY GLY TYR PRO ILE ASN PRO GLU GLY SEQRES 33 A 427 ASN ARG SER LEU GLN THR ASN PRO TRP PHE LEU SEQRES 1 B 427 MET MET GLU TYR LYS ILE VAL GLU ASN GLY LEU THR TYR SEQRES 2 B 427 ARG ILE GLY ASN GLY ALA SER VAL PRO ILE SER ASN THR SEQRES 3 B 427 GLY GLU LEU ILE LYS GLY LEU ARG ASN TYR GLY PRO TYR SEQRES 4 B 427 GLU VAL PRO SER LEU LYS TYR ASN GLN ILE ALA LEU ILE SEQRES 5 B 427 HIS ASN ASN GLN PHE SER SER LEU ILE ASN GLN LEU LYS SEQRES 6 B 427 SER GLN ILE SER SER LYS ILE ASP GLU VAL TRP HIS ILE SEQRES 7 B 427 HIS ASN ILE ASN ILE SER GLU PHE ILE TYR ASP SER PRO SEQRES 8 B 427 HIS PHE ASP SER ILE LYS SER GLN VAL ASP ASN ALA ILE SEQRES 9 B 427 ASP THR GLY VAL ASP GLY ILE MET LEU VAL LEU PRO GLU SEQRES 10 B 427 TYR ASN THR PRO LEU TYR TYR LYS LEU LYS SER TYR LEU SEQRES 11 B 427 ILE ASN SER ILE PRO SER GLN PHE MET ARG TYR ASP ILE SEQRES 12 B 427 LEU SER ASN ARG ASN LEU THR PHE TYR VAL ASP ASN LEU SEQRES 13 B 427 LEU VAL GLN PHE VAL SER LYS LEU GLY GLY LYS PRO TRP SEQRES 14 B 427 ILE LEU ASN VAL ASP PRO GLU LYS GLY SER ASP ILE ILE SEQRES 15 B 427 ILE GLY THR GLY ALA THR ARG ILE ASP ASN VAL ASN LEU SEQRES 16 B 427 PHE CYS PHE ALA MET VAL PHE LYS LYS ASP GLY THR MET SEQRES 17 B 427 LEU TRP ASN GLU ILE SER PRO ILE VAL THR SER SER GLU SEQRES 18 B 427 TYR LEU THR TYR LEU LYS SER THR ILE LYS LYS VAL VAL SEQRES 19 B 427 TYR GLY PHE LYS LYS SER ASN PRO ASP TRP ASP VAL GLU SEQRES 20 B 427 LYS LEU THR LEU HIS VAL SER GLY LYS ARG PRO LYS MET SEQRES 21 B 427 LYS ASP GLY GLU THR LYS ILE LEU LYS GLU THR VAL GLU SEQRES 22 B 427 GLU LEU LYS LYS GLN GLU MET VAL SER ARG ASP VAL LYS SEQRES 23 B 427 TYR ALA ILE LEU HIS LEU ASN GLU THR HIS PRO PHE TRP SEQRES 24 B 427 VAL MET GLY ASP PRO ASN ASN ARG PHE HIS PRO TYR GLU SEQRES 25 B 427 GLY THR LYS VAL LYS LEU SER SER LYS ARG TYR LEU LEU SEQRES 26 B 427 THR LEU LEU GLN PRO TYR LEU LYS ARG ASN GLY LEU GLU SEQRES 27 B 427 MET VAL THR PRO ILE LYS PRO LEU SER VAL GLU ILE VAL SEQRES 28 B 427 SER ASP ASN TRP THR SER GLU GLU TYR TYR HIS ASN VAL SEQRES 29 B 427 HIS GLU ILE LEU ASP GLU ILE TYR TYR LEU SER LYS MET SEQRES 30 B 427 ASN TRP ARG GLY PHE ARG SER ARG ASN LEU PRO VAL THR SEQRES 31 B 427 VAL ASN TYR PRO LYS LEU VAL ALA GLY ILE ILE ALA ASN SEQRES 32 B 427 VAL ASN ARG TYR GLY GLY TYR PRO ILE ASN PRO GLU GLY SEQRES 33 B 427 ASN ARG SER LEU GLN THR ASN PRO TRP PHE LEU SEQRES 1 P 8 DT DT DC DG DA DC DG DC SEQRES 1 Q 8 DG DT DC DG DA DA DT DT SEQRES 1 R 8 DT DT DC DG DA DC DG DC SEQRES 1 S 8 DG DT DC DG DA DA DT DT HET MN A1428 1 HET MN B1428 1 HETNAM MN MANGANESE (II) ION FORMUL 7 MN 2(MN 2+) FORMUL 9 HOH *411(H2 O) HELIX 1 1 GLY A 16 GLY A 18 5 3 HELIX 2 2 ASN A 25 GLY A 37 1 13 HELIX 3 3 SER A 58 VAL A 75 1 18 HELIX 4 4 HIS A 92 GLY A 107 1 16 HELIX 5 5 ASN A 119 ASN A 132 1 14 HELIX 6 6 ASP A 142 LEU A 144 5 3 HELIX 7 7 ASN A 148 LEU A 164 1 17 HELIX 8 8 GLU A 221 ASN A 241 1 21 HELIX 9 9 MET A 260 GLN A 278 1 19 HELIX 10 10 GLU A 359 LYS A 376 1 18 HELIX 11 11 PRO A 388 TYR A 407 1 20 HELIX 12 12 ARG A 418 ASN A 423 1 6 HELIX 13 13 GLY B 16 GLY B 18 5 3 HELIX 14 14 ASN B 25 GLY B 37 1 13 HELIX 15 15 SER B 58 VAL B 75 1 18 HELIX 16 16 HIS B 92 GLY B 107 1 16 HELIX 17 17 ASN B 119 ASN B 132 1 14 HELIX 18 18 LEU B 149 LEU B 164 1 16 HELIX 19 19 GLU B 221 ASN B 241 1 21 HELIX 20 20 MET B 260 GLN B 278 1 19 HELIX 21 21 GLU B 359 SER B 375 1 17 HELIX 22 22 PRO B 388 TYR B 407 1 20 SHEET 1 AA 3 SER A 20 PRO A 22 0 SHEET 2 AA 3 THR A 12 ARG A 14 -1 O TYR A 13 N VAL A 21 SHEET 3 AA 3 ILE A 170 LEU A 171 -1 O ILE A 170 N ARG A 14 SHEET 1 AB 4 ASN A 82 ILE A 87 0 SHEET 2 AB 4 GLN A 48 HIS A 53 1 O ILE A 49 N SER A 84 SHEET 3 AB 4 GLY A 110 LEU A 115 1 O GLY A 110 N ALA A 50 SHEET 4 AB 4 SER A 136 ARG A 140 1 O GLN A 137 N LEU A 113 SHEET 1 AC 6 MET A 208 ILE A 213 0 SHEET 2 AC 6 ASN A 194 PHE A 202 -1 O ALA A 199 N GLU A 212 SHEET 3 AC 6 ILE A 181 ARG A 189 -1 O ILE A 182 N PHE A 202 SHEET 4 AC 6 LYS A 248 SER A 254 1 O THR A 250 N ILE A 183 SHEET 5 AC 6 LYS A 286 GLU A 294 1 O LYS A 286 N LEU A 249 SHEET 6 AC 6 VAL A 340 ASP A 353 -1 O SER A 347 N ASN A 293 SHEET 1 AD 3 MET A 208 ILE A 213 0 SHEET 2 AD 3 ASN A 194 PHE A 202 -1 O ALA A 199 N GLU A 212 SHEET 3 AD 3 VAL A 217 THR A 218 -1 O VAL A 217 N LEU A 195 SHEET 1 BA 3 SER B 20 PRO B 22 0 SHEET 2 BA 3 THR B 12 ARG B 14 -1 O TYR B 13 N VAL B 21 SHEET 3 BA 3 ILE B 170 LEU B 171 -1 O ILE B 170 N ARG B 14 SHEET 1 BB 4 ASN B 82 ILE B 87 0 SHEET 2 BB 4 GLN B 48 HIS B 53 1 O ILE B 49 N SER B 84 SHEET 3 BB 4 GLY B 110 LEU B 115 1 O GLY B 110 N ALA B 50 SHEET 4 BB 4 SER B 136 ARG B 140 1 O GLN B 137 N LEU B 113 SHEET 1 BC 6 MET B 208 ILE B 213 0 SHEET 2 BC 6 ASN B 194 PHE B 202 -1 O ALA B 199 N GLU B 212 SHEET 3 BC 6 ILE B 181 ARG B 189 -1 O ILE B 182 N PHE B 202 SHEET 4 BC 6 LYS B 248 SER B 254 1 O THR B 250 N ILE B 183 SHEET 5 BC 6 LYS B 286 GLU B 294 1 O LYS B 286 N LEU B 249 SHEET 6 BC 6 THR B 341 ASP B 353 -1 O SER B 347 N ASN B 293 SHEET 1 BD 3 MET B 208 ILE B 213 0 SHEET 2 BD 3 ASN B 194 PHE B 202 -1 O ALA B 199 N GLU B 212 SHEET 3 BD 3 VAL B 217 THR B 218 -1 O VAL B 217 N LEU B 195 LINK OE1 GLN A 159 MN MN A1428 1555 1555 2.04 LINK O LEU A 427 MN MN A1428 1555 1555 2.46 LINK OXT LEU A 427 MN MN A1428 1555 1555 2.24 LINK MN MN A1428 O HOH A2244 1555 1555 2.20 LINK MN MN A1428 OP3 DT P 1 1555 1555 1.98 LINK MN MN A1428 OP1 DC P 3 1555 1555 2.10 LINK OE1 GLN B 159 MN MN B1428 1555 1555 2.22 LINK O LEU B 427 MN MN B1428 1555 1555 2.45 LINK OXT LEU B 427 MN MN B1428 1555 1555 1.93 LINK MN MN B1428 O HOH B2143 1555 1555 2.21 LINK MN MN B1428 OP3 DT R 1 1555 1555 2.13 LINK MN MN B1428 OP1 DC R 3 1555 1555 2.13 SITE 1 AC1 5 GLN A 159 LEU A 427 HOH A2244 DT P 1 SITE 2 AC1 5 DC P 3 SITE 1 AC2 5 GLN B 159 LEU B 427 HOH B2143 DT R 1 SITE 2 AC2 5 DC R 3 CRYST1 51.838 61.384 103.540 75.80 75.86 79.47 P 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 0.019291 -0.003586 -0.004199 0.00000 SCALE2 0.000000 0.016570 -0.003568 0.00000 SCALE3 0.000000 0.000000 0.010188 0.00000