PDB Short entry for 3LLH HEADER RNA BINDING PROTEIN 29-JAN-10 3LLH TITLE CRYSTAL STRUCTURE OF THE FIRST DSRBD OF TAR RNA-BINDING PROTEIN 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RISC-LOADING COMPLEX SUBUNIT TARBP2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 22-105; COMPND 5 SYNONYM: TAR RNA-BINDING PROTEIN 2, TRANS-ACTIVATION-RESPONSIVE RNA- COMPND 6 BINDING PROTEIN; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: 6895; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX6P-2 KEYWDS DSRBD, DSRM, MICRORNA, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.YAMASHITA,M.KAWAZOE,C.TAKEMOTO,S.SEKINE,M.WAKIYAMA,S.YOKOYAMA REVDAT 2 01-NOV-23 3LLH 1 REMARK SEQADV REVDAT 1 08-DEC-10 3LLH 0 JRNL AUTH S.YAMASHITA,T.NAGATA,M.KAWAZOE,C.TAKEMOTO,Y.MUTO,S.SEKINE, JRNL AUTH 2 M.WAKIYAMA,S.YOKOYAMA JRNL TITL THE STRUCTURES OF DSRBDS OF HUMAN TRBP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 749893.720 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 6899 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 SET) : 0.185 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 329 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.013 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.14 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.27 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1076 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE : 0.2990 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 61 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.038 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 983 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 33 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.35000 REMARK 3 B22 (A**2) : 8.35000 REMARK 3 B33 (A**2) : -16.70000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.29 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.32 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.790 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.45 REMARK 3 BSOL : 71.42 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : MLI_MSD.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : &_1_TOPOLOGY_INFILE_1 REMARK 3 TOPOLOGY FILE 2 : &_1_TOPOLOGY_INFILE_2 REMARK 3 TOPOLOGY FILE 3 : &_1_TOPOLOGY_INFILE_3 REMARK 3 TOPOLOGY FILE 4 : &_1_TOPOLOGY_INFILE_4 REMARK 3 TOPOLOGY FILE 5 : &_1_TOPOLOGY_INFILE_5 REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3LLH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000057423. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : ROTATED-INCLINED DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : RHODIUM-COATED MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6917 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.140 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.15200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.1750 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.80700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PDB ENTRY 1RC7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.44M SODIUM MALONATE PH7.0, 0.2M REMARK 280 AMMONIUM SULFATE, 0.5% V/V ISOPROPANOL, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 14.27600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.55200 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 GLY A 1 REMARK 465 PRO A 2 REMARK 465 LEU A 3 REMARK 465 GLY A 4 REMARK 465 SER A 5 REMARK 465 HIS A 6 REMARK 465 MET A 7 REMARK 465 LEU A 8 REMARK 465 ALA A 9 REMARK 465 ALA A 10 REMARK 465 ASN A 11 REMARK 465 PRO A 12 REMARK 465 GLY A 40 REMARK 465 GLN A 41 REMARK 465 ALA A 42 REMARK 465 HIS A 43 REMARK 465 GLN A 44 REMARK 465 GLY A 82 REMARK 465 GLY A 83 REMARK 465 SER A 84 REMARK 465 MET A 85 REMARK 465 LEU A 86 REMARK 465 GLU A 87 REMARK 465 PRO A 88 REMARK 465 ALA A 89 REMARK 465 LEU A 90 REMARK 465 GLY B 1 REMARK 465 PRO B 2 REMARK 465 LEU B 3 REMARK 465 GLY B 4 REMARK 465 SER B 5 REMARK 465 HIS B 6 REMARK 465 MET B 7 REMARK 465 LEU B 8 REMARK 465 ALA B 9 REMARK 465 ALA B 10 REMARK 465 ASN B 11 REMARK 465 PRO B 12 REMARK 465 GLN B 41 REMARK 465 ALA B 42 REMARK 465 HIS B 43 REMARK 465 GLY B 82 REMARK 465 GLY B 83 REMARK 465 SER B 84 REMARK 465 MET B 85 REMARK 465 LEU B 86 REMARK 465 GLU B 87 REMARK 465 PRO B 88 REMARK 465 ALA B 89 REMARK 465 LEU B 90 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLI B 101 DBREF 3LLH A 7 90 UNP Q15633 TRBP2_HUMAN 22 105 DBREF 3LLH B 7 90 UNP Q15633 TRBP2_HUMAN 22 105 SEQADV 3LLH GLY A 1 UNP Q15633 EXPRESSION TAG SEQADV 3LLH PRO A 2 UNP Q15633 EXPRESSION TAG SEQADV 3LLH LEU A 3 UNP Q15633 EXPRESSION TAG SEQADV 3LLH GLY A 4 UNP Q15633 EXPRESSION TAG SEQADV 3LLH SER A 5 UNP Q15633 EXPRESSION TAG SEQADV 3LLH HIS A 6 UNP Q15633 EXPRESSION TAG SEQADV 3LLH GLY B 1 UNP Q15633 EXPRESSION TAG SEQADV 3LLH PRO B 2 UNP Q15633 EXPRESSION TAG SEQADV 3LLH LEU B 3 UNP Q15633 EXPRESSION TAG SEQADV 3LLH GLY B 4 UNP Q15633 EXPRESSION TAG SEQADV 3LLH SER B 5 UNP Q15633 EXPRESSION TAG SEQADV 3LLH HIS B 6 UNP Q15633 EXPRESSION TAG SEQRES 1 A 90 GLY PRO LEU GLY SER HIS MET LEU ALA ALA ASN PRO GLY SEQRES 2 A 90 LYS THR PRO ILE SER LEU LEU GLN GLU TYR GLY THR ARG SEQRES 3 A 90 ILE GLY LYS THR PRO VAL TYR ASP LEU LEU LYS ALA GLU SEQRES 4 A 90 GLY GLN ALA HIS GLN PRO ASN PHE THR PHE ARG VAL THR SEQRES 5 A 90 VAL GLY ASP THR SER CYS THR GLY GLN GLY PRO SER LYS SEQRES 6 A 90 LYS ALA ALA LYS HIS LYS ALA ALA GLU VAL ALA LEU LYS SEQRES 7 A 90 HIS LEU LYS GLY GLY SER MET LEU GLU PRO ALA LEU SEQRES 1 B 90 GLY PRO LEU GLY SER HIS MET LEU ALA ALA ASN PRO GLY SEQRES 2 B 90 LYS THR PRO ILE SER LEU LEU GLN GLU TYR GLY THR ARG SEQRES 3 B 90 ILE GLY LYS THR PRO VAL TYR ASP LEU LEU LYS ALA GLU SEQRES 4 B 90 GLY GLN ALA HIS GLN PRO ASN PHE THR PHE ARG VAL THR SEQRES 5 B 90 VAL GLY ASP THR SER CYS THR GLY GLN GLY PRO SER LYS SEQRES 6 B 90 LYS ALA ALA LYS HIS LYS ALA ALA GLU VAL ALA LEU LYS SEQRES 7 B 90 HIS LEU LYS GLY GLY SER MET LEU GLU PRO ALA LEU HET MLI B 101 7 HETNAM MLI MALONATE ION FORMUL 3 MLI C3 H2 O4 2- FORMUL 4 HOH *33(H2 O) HELIX 1 1 THR A 15 ILE A 27 1 13 HELIX 2 2 SER A 64 LYS A 81 1 18 HELIX 3 3 THR B 15 ILE B 27 1 13 HELIX 4 4 SER B 64 LYS B 81 1 18 SHEET 1 A 3 VAL A 32 ALA A 38 0 SHEET 2 A 3 PHE A 47 VAL A 53 -1 O THR A 48 N LEU A 36 SHEET 3 A 3 THR A 56 GLY A 62 -1 O THR A 56 N VAL A 53 SHEET 1 B 3 VAL B 32 GLU B 39 0 SHEET 2 B 3 ASN B 46 VAL B 53 -1 O THR B 48 N LEU B 36 SHEET 3 B 3 THR B 56 GLY B 62 -1 O THR B 56 N VAL B 53 SITE 1 AC1 9 ILE A 17 TYR A 33 ARG A 50 SER A 57 SITE 2 AC1 9 CYS A 58 THR A 59 LYS A 69 ARG B 26 SITE 3 AC1 9 HOH B 110 CRYST1 51.184 51.184 42.828 90.00 90.00 120.00 P 31 6 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 0.019537 0.011280 0.000000 0.00000 SCALE2 0.000000 0.022560 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023349 0.00000