HEADER GENE REGULATION 09-JUL-12 4G0O TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA AGO5 MID DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN ARGONAUTE 5; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: MID DOMAIN, UNP RESIDUES 562-699; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS,THALE-CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: AGO5, AT2G27880, T1E2.20; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 KEYWDS MID DOMAIN, SMALL RNA 5' NUCLEOTIDE RECOGNITION, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR F.FRANK,J.HAUVER,N.SONENBERG,B.NAGAR REVDAT 4 28-FEB-24 4G0O 1 REMARK SEQADV REVDAT 3 12-SEP-12 4G0O 1 JRNL REVDAT 2 29-AUG-12 4G0O 1 JRNL REVDAT 1 25-JUL-12 4G0O 0 JRNL AUTH F.FRANK,J.HAUVER,N.SONENBERG,B.NAGAR JRNL TITL ARABIDOPSIS ARGONAUTE MID DOMAINS USE THEIR NUCLEOTIDE JRNL TITL 2 SPECIFICITY LOOP TO SORT SMALL RNAS. JRNL REF EMBO J. V. 31 3588 2012 JRNL REFN ISSN 0261-4189 JRNL PMID 22850669 JRNL DOI 10.1038/EMBOJ.2012.204 REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 14216 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.950 REMARK 3 FREE R VALUE TEST SET COUNT : 846 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 30.0000 - 3.9709 0.98 2332 160 0.1900 0.2077 REMARK 3 2 3.9709 - 3.1526 0.97 2296 148 0.2139 0.2838 REMARK 3 3 3.1526 - 2.7543 0.95 2288 142 0.2474 0.2913 REMARK 3 4 2.7543 - 2.5026 0.94 2267 114 0.2431 0.2925 REMARK 3 5 2.5026 - 2.3233 0.94 2217 128 0.2392 0.3183 REMARK 3 6 2.3233 - 2.1860 0.83 1970 154 0.2201 0.3089 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 40.31 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.520 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) : -5.11510 REMARK 3 B22 (A**2) : 1.85690 REMARK 3 B33 (A**2) : 3.25830 REMARK 3 B12 (A**2) : 2.26290 REMARK 3 B13 (A**2) : -4.56370 REMARK 3 B23 (A**2) : 2.72180 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 : 0.009 2190 REMARK 3 ANGLE : 1.137 2954 REMARK 3 CHIRALITY : 0.078 341 REMARK 3 PLANARITY : 0.006 377 REMARK 3 DIHEDRAL : 17.011 856 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 4G0O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073589. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : VARIMAX HF REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16181 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.0 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: PHENIX 1.7.3_928 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 CITRATE, 30% PEG4000, PH 5.4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K 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: 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 SER B 561 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 O HOH B 767 O HOH B 777 2.17 REMARK 500 O HOH B 704 O HOH B 743 2.18 REMARK 500 O HOH A 860 O HOH A 876 2.19 REMARK 500 O1 SO4 A 701 O HOH A 875 2.19 REMARK 500 O HOH B 739 O HOH B 757 2.19 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 SO4 A 701 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4G0M RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA AGO2 MID DOMAIN REMARK 900 RELATED ID: 4G0P RELATED DB: PDB REMARK 900 STRUCTURE OF ARABIDOPSIS THALIANA AGO1 MID DOMAIN IN COMPLEX WITH REMARK 900 UMP REMARK 900 RELATED ID: 4G0Q RELATED DB: PDB REMARK 900 STRUCTURE OF ARABIDOPSIS THALIANA AGO1 MID DOMAIN IN COMPLEX WITH REMARK 900 CMP REMARK 900 RELATED ID: 4G0X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA AGO1 MID DOMAIN REMARK 900 RELATED ID: 4G0Y RELATED DB: PDB REMARK 900 STRUCTURE OF ARABIDOPSIS AGO1 IN COMPLEX WITH AMP REMARK 900 RELATED ID: 4G0Z RELATED DB: PDB REMARK 900 STRUCTURE OF ARABIDOPSIS THALIANA AGO1 MID DOMAIN IN COMPLEX WITH REMARK 900 GMP DBREF 4G0O A 562 699 UNP Q9SJK3 AGO5_ARATH 562 699 DBREF 4G0O B 562 699 UNP Q9SJK3 AGO5_ARATH 562 699 SEQADV 4G0O SER A 561 UNP Q9SJK3 EXPRESSION TAG SEQADV 4G0O SER B 561 UNP Q9SJK3 EXPRESSION TAG SEQRES 1 A 139 SER ASP LYS LYS MET VAL ASN GLY ALA LYS VAL THR SER SEQRES 2 A 139 TRP THR CYS VAL SER PHE SER THR ARG ILE ASP ARG GLY SEQRES 3 A 139 LEU PRO GLN GLU PHE CYS LYS GLN LEU ILE GLY MET CYS SEQRES 4 A 139 VAL SER LYS GLY MET GLU PHE LYS PRO GLN PRO ALA ILE SEQRES 5 A 139 PRO PHE ILE SER CYS PRO PRO GLU HIS ILE GLU GLU ALA SEQRES 6 A 139 LEU LEU ASP ILE HIS LYS ARG ALA PRO GLY LEU GLN LEU SEQRES 7 A 139 LEU ILE VAL ILE LEU PRO ASP VAL THR GLY SER TYR GLY SEQRES 8 A 139 LYS ILE LYS ARG ILE CYS GLU THR GLU LEU GLY ILE VAL SEQRES 9 A 139 SER GLN CYS CYS GLN PRO ARG GLN VAL ASN LYS LEU ASN SEQRES 10 A 139 LYS GLN TYR MET GLU ASN VAL ALA LEU LYS ILE ASN VAL SEQRES 11 A 139 LYS THR GLY GLY ARG ASN THR VAL LEU SEQRES 1 B 139 SER ASP LYS LYS MET VAL ASN GLY ALA LYS VAL THR SER SEQRES 2 B 139 TRP THR CYS VAL SER PHE SER THR ARG ILE ASP ARG GLY SEQRES 3 B 139 LEU PRO GLN GLU PHE CYS LYS GLN LEU ILE GLY MET CYS SEQRES 4 B 139 VAL SER LYS GLY MET GLU PHE LYS PRO GLN PRO ALA ILE SEQRES 5 B 139 PRO PHE ILE SER CYS PRO PRO GLU HIS ILE GLU GLU ALA SEQRES 6 B 139 LEU LEU ASP ILE HIS LYS ARG ALA PRO GLY LEU GLN LEU SEQRES 7 B 139 LEU ILE VAL ILE LEU PRO ASP VAL THR GLY SER TYR GLY SEQRES 8 B 139 LYS ILE LYS ARG ILE CYS GLU THR GLU LEU GLY ILE VAL SEQRES 9 B 139 SER GLN CYS CYS GLN PRO ARG GLN VAL ASN LYS LEU ASN SEQRES 10 B 139 LYS GLN TYR MET GLU ASN VAL ALA LEU LYS ILE ASN VAL SEQRES 11 B 139 LYS THR GLY GLY ARG ASN THR VAL LEU HET SO4 A 701 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *171(H2 O) HELIX 1 1 GLY A 586 GLY A 603 1 18 HELIX 2 2 PRO A 618 GLU A 620 5 3 HELIX 3 3 HIS A 621 ALA A 633 1 13 HELIX 4 4 SER A 649 THR A 659 1 11 HELIX 5 5 GLN A 669 LEU A 676 1 8 HELIX 6 6 ASN A 677 THR A 692 1 16 HELIX 7 7 GLY B 586 LYS B 602 1 17 HELIX 8 8 PRO B 618 GLU B 620 5 3 HELIX 9 9 HIS B 621 ALA B 633 1 13 HELIX 10 10 SER B 649 THR B 659 1 11 HELIX 11 11 GLN B 669 ASN B 674 1 6 HELIX 12 12 ASN B 677 THR B 692 1 16 SHEET 1 A 2 LYS A 563 ASN A 567 0 SHEET 2 A 2 ARG A 695 VAL A 698 -1 O THR A 697 N LYS A 564 SHEET 1 B 2 LYS A 570 VAL A 571 0 SHEET 2 B 2 GLU A 605 PHE A 606 1 O GLU A 605 N VAL A 571 SHEET 1 C 4 ILE A 615 SER A 616 0 SHEET 2 C 4 TRP A 574 SER A 578 1 N SER A 578 O ILE A 615 SHEET 3 C 4 LEU A 638 ILE A 642 1 O ILE A 642 N VAL A 577 SHEET 4 C 4 SER A 665 CYS A 668 1 O GLN A 666 N VAL A 641 SHEET 1 D 2 LYS B 563 ASN B 567 0 SHEET 2 D 2 ARG B 695 VAL B 698 -1 O THR B 697 N LYS B 564 SHEET 1 E 2 LYS B 570 VAL B 571 0 SHEET 2 E 2 GLU B 605 PHE B 606 1 O GLU B 605 N VAL B 571 SHEET 1 F 4 ILE B 615 SER B 616 0 SHEET 2 F 4 TRP B 574 SER B 578 1 N CYS B 576 O ILE B 615 SHEET 3 F 4 LEU B 638 ILE B 642 1 O ILE B 640 N THR B 575 SHEET 4 F 4 SER B 665 CYS B 668 1 O CYS B 668 N VAL B 641 SITE 1 AC1 8 TYR A 650 LYS A 654 GLN A 666 LYS A 691 SITE 2 AC1 8 HOH A 806 HOH A 827 HOH A 875 LEU B 699 CRYST1 34.823 37.078 62.733 75.40 76.06 90.12 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 0.028717 0.000060 -0.007397 0.00000 SCALE2 0.000000 0.026970 -0.007270 0.00000 SCALE3 0.000000 0.000000 0.017010 0.00000