HEADER GENE REGULATION 09-JUL-12 4G0P TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA AGO1 MID DOMAIN IN COMPLEX TITLE 2 WITH UMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN ARGONAUTE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MID DOMAIN, UNP RESIDUES 593-738; 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: AGO1, AT1G48410, F11A17.3, T1N15.2; 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 4G0P 1 REMARK SEQADV REVDAT 3 12-SEP-12 4G0P 1 JRNL REVDAT 2 29-AUG-12 4G0P 1 JRNL REVDAT 1 25-JUL-12 4G0P 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. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.080 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.8 REMARK 3 NUMBER OF REFLECTIONS : 13152 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.360 REMARK 3 FREE R VALUE TEST SET COUNT : 574 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 31.7940 - 2.8569 0.90 3368 159 0.1631 0.1896 REMARK 3 2 2.8569 - 2.2678 0.90 3257 150 0.1752 0.2322 REMARK 3 3 2.2678 - 1.9811 0.88 3139 136 0.1800 0.2241 REMARK 3 4 1.9811 - 1.8000 0.79 2814 129 0.2104 0.2825 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 : 0.35 REMARK 3 B_SOL : 27.23 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.400 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) : 1.40760 REMARK 3 B22 (A**2) : -5.00360 REMARK 3 B33 (A**2) : 3.59600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.016 1197 REMARK 3 ANGLE : 1.362 1623 REMARK 3 CHIRALITY : 0.085 189 REMARK 3 PLANARITY : 0.007 207 REMARK 3 DIHEDRAL : 19.971 488 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 4G0P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073590. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 4.5 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) : NULL 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 : 13152 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 31.794 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.5 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) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.1 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX 1.5_2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRIC ACID, 2 M AMMONIUM REMARK 280 SULFATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 18.64550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.53800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.42100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.53800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.64550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.42100 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 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U5P A 801 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: 4G0O RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA AGO5 MID DOMAIN 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 4G0P A 595 740 UNP O04379 AGO1_ARATH 593 738 SEQADV 4G0P SER A 594 UNP O04379 EXPRESSION TAG SEQRES 1 A 147 SER ASN LYS LYS MET ILE ASN GLY GLY THR VAL ASN ASN SEQRES 2 A 147 TRP ILE CYS ILE ASN PHE SER ARG GLN VAL GLN ASP ASN SEQRES 3 A 147 LEU ALA ARG THR PHE CYS GLN GLU LEU ALA GLN MET CYS SEQRES 4 A 147 TYR VAL SER GLY MET ALA PHE ASN PRO GLU PRO VAL LEU SEQRES 5 A 147 PRO PRO VAL SER ALA ARG PRO GLU GLN VAL GLU LYS VAL SEQRES 6 A 147 LEU LYS THR ARG TYR HIS ASP ALA THR SER LYS LEU SER SEQRES 7 A 147 GLN GLY LYS GLU ILE ASP LEU LEU ILE VAL ILE LEU PRO SEQRES 8 A 147 ASP ASN ASN GLY SER LEU TYR GLY ASP LEU LYS ARG ILE SEQRES 9 A 147 CYS GLU THR GLU LEU GLY ILE VAL SER GLN CYS CYS LEU SEQRES 10 A 147 THR LYS HIS VAL PHE LYS MET SER LYS GLN TYR MET ALA SEQRES 11 A 147 ASN VAL ALA LEU LYS ILE ASN VAL LYS VAL GLY GLY ARG SEQRES 12 A 147 ASN THR VAL LEU HET U5P A 801 21 HETNAM U5P URIDINE-5'-MONOPHOSPHATE FORMUL 2 U5P C9 H13 N2 O9 P FORMUL 3 HOH *161(H2 O) HELIX 1 1 GLN A 617 SER A 635 1 19 HELIX 2 2 ARG A 651 GLU A 653 5 3 HELIX 3 3 GLN A 654 LYS A 669 1 16 HELIX 4 4 SER A 689 GLU A 701 1 13 HELIX 5 5 THR A 711 MET A 717 1 7 HELIX 6 6 SER A 718 VAL A 733 1 16 SHEET 1 A 2 MET A 598 ASN A 600 0 SHEET 2 A 2 ARG A 736 ASN A 737 -1 O ARG A 736 N ILE A 599 SHEET 1 B 2 THR A 603 VAL A 604 0 SHEET 2 B 2 ALA A 638 PHE A 639 1 O ALA A 638 N VAL A 604 SHEET 1 C 4 VAL A 648 SER A 649 0 SHEET 2 C 4 TRP A 607 ASN A 611 1 N ASN A 611 O VAL A 648 SHEET 3 C 4 LEU A 678 LEU A 683 1 O ILE A 680 N ILE A 608 SHEET 4 C 4 SER A 706 LEU A 710 1 O CYS A 709 N VAL A 681 SITE 1 AC1 13 ASN A 687 TYR A 691 LYS A 695 SER A 706 SITE 2 AC1 13 GLN A 707 CYS A 708 LEU A 710 LYS A 728 SITE 3 AC1 13 LYS A 732 HOH A 937 HOH A1032 HOH A1033 SITE 4 AC1 13 HOH A1035 CRYST1 37.291 60.842 69.076 90.00 90.00 90.00 P 21 21 21 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 0.026816 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016436 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014477 0.00000