HEADER RNA BINDING PROTEIN 10-MAY-10 2XDY TITLE CRYSTAL STRUCTURE OF THE N. CRASSA QDE-2 AGO MID DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: POST-TRANSCRIPTIONAL GENE SILENCING PROTEIN QDE-2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MID DOMAIN, RESIDUES 506-646; COMPND 5 SYNONYM: QDE-2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEUROSPORA CRASSA; SOURCE 3 ORGANISM_TAXID: 5141; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: K-12; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PETM60 KEYWDS ARGONAUTE, GENE SILENCING, RNA-INDUCED SILENCING COMPLEX, 5' END KEYWDS 2 BINDING, ROSSMANN-LIKE FOLD, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.BOLAND,F.TRITSCHLER,O.WEICHENRIEDER REVDAT 4 25-MAY-11 2XDY 1 HETSYN REVDAT 3 18-MAY-11 2XDY 1 JRNL REMARK REVDAT 2 23-JUN-10 2XDY 1 JRNL REVDAT 1 16-JUN-10 2XDY 0 JRNL AUTH A.BOLAND,F.TRITSCHLER,S.HEIMSTAEDT,E.IZAURRALDE, JRNL AUTH 2 O.WEICHENRIEDER JRNL TITL CRYSTAL STRUCTURE AND LIGAND BINDING OF THE MID JRNL TITL 2 DOMAIN OF A EUKARYOTIC ARGONAUTE PROTEIN. JRNL REF EMBO REP. V. 11 522 2010 JRNL REFN ISSN 1469-221X JRNL PMID 20539312 JRNL DOI 10.1038/EMBOR.2010.81 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.200 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.288 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 99.28 REMARK 3 NUMBER OF REFLECTIONS : 8274 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1943 REMARK 3 R VALUE (WORKING SET) : 0.1929 REMARK 3 FREE R VALUE : 0.2229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.9 REMARK 3 FREE R VALUE TEST SET COUNT : 405 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 31.2911 - 3.1725 0.99 2697 136 0.1756 0.1897 REMARK 3 2 3.1725 - 2.5185 0.99 2590 130 0.2060 0.2679 REMARK 3 3 2.5185 - 2.2002 1.00 2582 139 0.2372 0.2885 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.369 REMARK 3 B_SOL : 41.801 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.29 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 12.9573 REMARK 3 B22 (A**2) : -5.7809 REMARK 3 B33 (A**2) : -7.1765 REMARK 3 B12 (A**2) : 0.0000 REMARK 3 B13 (A**2) : 0.0000 REMARK 3 B23 (A**2) : 0.0000 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 : 0.004 1024 REMARK 3 ANGLE : 0.776 1377 REMARK 3 CHIRALITY : 0.052 151 REMARK 3 PLANARITY : 0.003 171 REMARK 3 DIHEDRAL : 14.447 373 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: THE RESIDUES ARISEING FROM THE REMARK 3 CLONING SITE AS WELL AS RESIDUES 506 - 513 AND RESIDUES REMARK 3 641 - 646 ARE DISORDERED REMARK 4 REMARK 4 2XDY COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-MAY-10. REMARK 100 THE PDBE ID CODE IS EBI-43874. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8285 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.20 REMARK 200 RESOLUTION RANGE LOW (A) : 60.20 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.00 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.6 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05 REMARK 200 FOR THE DATA SET : 18.40 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.6 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.50 REMARK 200 FOR SHELL : 2.94 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX C/D, AUTOSHARP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM AMMONIUM SULFATE 16% REMARK 280 PEG4000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 21.46500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.46500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 40.05000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.69500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.05000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.69500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 21.46500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.05000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.69500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 21.46500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.05000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.69500 REMARK 290 SMTRY3 8 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2003 LIES ON A SPECIAL POSITION. 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 GLY A 502 REMARK 465 ALA A 503 REMARK 465 MET A 504 REMARK 465 ALA A 505 REMARK 465 VAL A 506 REMARK 465 LYS A 507 REMARK 465 VAL A 508 REMARK 465 ALA A 509 REMARK 465 ARG A 510 REMARK 465 PRO A 511 REMARK 465 CYS A 512 REMARK 465 ARG A 513 REMARK 465 GLY A 641 REMARK 465 THR A 642 REMARK 465 ASN A 643 REMARK 465 HIS A 644 REMARK 465 ASN A 645 REMARK 465 ILE A 646 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: PROVIDED BY DEPOSITOR. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1641 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1642 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1643 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE FIRST 4 AMINO ACIDS (GAMA) ARISE FROM THE CLONING SITE. DBREF 2XDY A 506 646 UNP Q9P8T1 Q9P8T1_NEUCR 506 646 SEQADV 2XDY GLY A 502 UNP Q9P8T1 EXPRESSION TAG SEQADV 2XDY ALA A 503 UNP Q9P8T1 EXPRESSION TAG SEQADV 2XDY MET A 504 UNP Q9P8T1 EXPRESSION TAG SEQADV 2XDY ALA A 505 UNP Q9P8T1 EXPRESSION TAG SEQRES 1 A 145 GLY ALA MET ALA VAL LYS VAL ALA ARG PRO CYS ARG LYS SEQRES 2 A 145 ILE GLU LYS TRP THR TYR LEU GLU LEU LYS GLY SER LYS SEQRES 3 A 145 ALA ASN GLU GLY VAL PRO GLN ALA MET THR ALA PHE ALA SEQRES 4 A 145 GLU PHE LEU ASN ARG THR GLY ILE PRO ILE ASN PRO ARG SEQRES 5 A 145 PHE SER PRO GLY MET SER MET SER VAL PRO GLY SER GLU SEQRES 6 A 145 LYS GLU PHE PHE ALA LYS VAL LYS GLU LEU MET SER SER SEQRES 7 A 145 HIS GLN PHE VAL VAL VAL LEU LEU PRO ARG LYS ASP VAL SEQRES 8 A 145 ALA ILE TYR ASN MET VAL LYS ARG ALA ALA ASP ILE THR SEQRES 9 A 145 PHE GLY VAL HIS THR VAL CYS CYS VAL ALA GLU LYS PHE SEQRES 10 A 145 LEU SER THR LYS GLY GLN LEU GLY TYR PHE ALA ASN VAL SEQRES 11 A 145 GLY LEU LYS VAL ASN LEU LYS PHE GLY GLY THR ASN HIS SEQRES 12 A 145 ASN ILE HET SO4 A1641 5 HET SO4 A1642 5 HET GOL A1643 6 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN FORMUL 2 SO4 2(O4 S 2-) FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *52(H2 O) HELIX 1 1 VAL A 532 THR A 546 1 15 HELIX 2 2 GLU A 566 SER A 579 1 14 HELIX 3 3 VAL A 592 ILE A 604 1 13 HELIX 4 4 ALA A 615 LEU A 619 1 5 HELIX 5 5 GLN A 624 PHE A 639 1 16 SHEET 1 AA 4 MET A 558 MET A 560 0 SHEET 2 AA 4 TRP A 518 LEU A 523 1 O TYR A 520 N MET A 558 SHEET 3 AA 4 PHE A 582 LEU A 587 1 O PHE A 582 N THR A 519 SHEET 4 AA 4 HIS A 609 VAL A 614 1 O HIS A 609 N VAL A 583 SITE 1 AC1 8 TYR A 595 LYS A 599 VAL A 611 CYS A 612 SITE 2 AC1 8 LYS A 634 LYS A 638 HOH A2049 HOH A2050 SITE 1 AC2 6 LYS A 599 ALA A 602 HIS A 609 THR A 610 SITE 2 AC2 6 LYS A 638 HOH A2052 SITE 1 AC3 3 GLU A 566 LYS A 567 ARG A 600 CRYST1 80.100 91.390 42.930 90.00 90.00 90.00 C 2 2 21 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 0.012484 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010942 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023294 0.00000