HEADER RNA BINDING PROTEIN 19-JUN-12 2LUQ TITLE SOLUTION STRUCTURE OF DOUBLE-STRANDED RNA BINDING DOMAIN OF TITLE 2 S.CEREVISIAE RNASE III (RNT1P) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RIBONUCLEASE III, RNASE III; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 VARIANT: YMR239C; SOURCE 7 GENE: RNT1, YM9408.01C, YM9959.21, YMR239C; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS DSRBD, RNT1P, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Z.WANG,J.FEIGON REVDAT 4 14-JUN-23 2LUQ 1 REMARK SEQADV REVDAT 3 13-FEB-13 2LUQ 1 JRNL REVDAT 2 19-DEC-12 2LUQ 1 JRNL REVDAT 1 05-DEC-12 2LUQ 0 JRNL AUTH E.HARTMAN,Z.WANG,Q.ZHANG,K.ROY,G.CHANFREAU,J.FEIGON JRNL TITL INTRINSIC DYNAMICS OF AN EXTENDED HYDROPHOBIC CORE IN THE S. JRNL TITL 2 CEREVISIAE RNASE III DSRBD CONTRIBUTES TO RECOGNITION OF JRNL TITL 3 SPECIFIC RNA BINDING SITES. JRNL REF J.MOL.BIOL. V. 425 546 2013 JRNL REFN ISSN 0022-2836 JRNL PMID 23201338 JRNL DOI 10.1016/J.JMB.2012.11.025 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.WANG,E.HARTMAN,K.ROY,G.CHANFREAU,J.FEIGON REMARK 1 TITL STRUCTURE OF A YEAST RNASE III DSRBD COMPLEX WITH A REMARK 1 TITL 2 NONCANONICAL RNA SUBSTRATE PROVIDES NEW INSIGHTS INTO REMARK 1 TITL 3 BINDING SPECIFICITY OF DSRBDS. REMARK 1 REF STRUCTURE V. 19 999 2011 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 21742266 REMARK 1 DOI 10.1016/J.STR.2011.03.022 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.0, X-PLOR NIH REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LUQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000102857. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN, 90 % H2O, 10 % [U-100% REMARK 210 2H] D2O, 150 MM SODIUM CHLORIDE, REMARK 210 20 MM SODIUM PHOSPHATE, 90% H2O/ REMARK 210 10% D2O; 1 MM [U-100% 13C; U-100% REMARK 210 15N] PROTEIN, 100 % [U-100% 2H] REMARK 210 D2O, 150 % SODIUM CHLORIDE, 20 REMARK 210 MM SODIUM PHOSPHATE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HNCO; 3D HCCH- REMARK 210 TOCSY; 3D HCCH-COSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW, TALOS, X-PLOR REMARK 210 NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 LYS A 421 H ILE A 425 1.47 REMARK 500 O VAL A 406 H GLY A 409 1.58 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 1 ARG A 384 46.33 30.74 REMARK 500 1 PRO A 398 42.56 -78.00 REMARK 500 1 THR A 414 115.74 -162.04 REMARK 500 1 ALA A 447 32.92 -87.80 REMARK 500 2 SER A 365 151.47 64.71 REMARK 500 2 TYR A 380 129.81 -174.41 REMARK 500 2 ARG A 384 48.09 30.32 REMARK 500 2 PRO A 398 45.69 -79.48 REMARK 500 2 VAL A 411 99.55 -55.93 REMARK 500 2 ALA A 447 32.78 -89.18 REMARK 500 2 ILE A 448 123.38 -33.72 REMARK 500 2 ARG A 450 -155.24 -91.38 REMARK 500 2 SER A 451 91.88 52.67 REMARK 500 3 ARG A 384 51.93 30.69 REMARK 500 3 PRO A 398 48.68 -81.79 REMARK 500 3 ALA A 447 33.16 -90.67 REMARK 500 3 SER A 451 62.18 -165.37 REMARK 500 3 GLU A 452 -88.04 62.46 REMARK 500 4 SER A 365 -60.36 165.55 REMARK 500 4 ARG A 384 61.93 23.94 REMARK 500 4 PRO A 398 44.38 -79.80 REMARK 500 4 ALA A 447 32.40 -93.84 REMARK 500 4 ILE A 448 102.94 -43.20 REMARK 500 5 ASP A 367 -171.11 -55.66 REMARK 500 5 ARG A 384 62.07 25.04 REMARK 500 5 PRO A 398 49.93 -75.79 REMARK 500 5 ALA A 447 32.29 -95.61 REMARK 500 5 SER A 451 -53.40 177.13 REMARK 500 5 GLU A 452 -58.98 79.37 REMARK 500 6 LEU A 383 40.53 -97.82 REMARK 500 6 ARG A 384 79.01 -56.30 REMARK 500 6 PRO A 398 50.24 -69.48 REMARK 500 6 ALA A 447 33.43 -88.01 REMARK 500 6 PRO A 449 48.91 -75.83 REMARK 500 6 ARG A 450 134.18 66.84 REMARK 500 7 LEU A 383 40.64 -89.74 REMARK 500 7 ARG A 384 83.83 -40.05 REMARK 500 7 PRO A 398 43.94 -80.12 REMARK 500 7 ALA A 447 32.83 -87.20 REMARK 500 7 ILE A 448 128.54 -33.11 REMARK 500 7 ARG A 450 -86.33 170.60 REMARK 500 7 SER A 451 92.66 64.67 REMARK 500 7 GLU A 452 -40.45 -154.80 REMARK 500 8 SER A 365 104.26 65.23 REMARK 500 8 ASP A 367 -175.84 -56.01 REMARK 500 8 ARG A 384 83.32 30.11 REMARK 500 8 PRO A 398 45.66 -80.19 REMARK 500 8 ALA A 447 33.10 -88.29 REMARK 500 8 ILE A 448 95.17 -33.02 REMARK 500 8 SER A 451 111.08 69.78 REMARK 500 REMARK 500 THIS ENTRY HAS 133 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18535 RELATED DB: BMRB REMARK 900 RELATED ID: 2LUP RELATED DB: PDB DBREF 2LUQ A 366 453 UNP Q02555 RNT1_YEAST 366 453 SEQADV 2LUQ GLY A 364 UNP Q02555 EXPRESSION TAG SEQADV 2LUQ SER A 365 UNP Q02555 EXPRESSION TAG SEQRES 1 A 90 GLY SER LEU ASP MET ASN ALA LYS ARG GLN LEU TYR SER SEQRES 2 A 90 LEU ILE GLY TYR ALA SER LEU ARG LEU HIS TYR VAL THR SEQRES 3 A 90 VAL LYS LYS PRO THR ALA VAL ASP PRO ASN SER ILE VAL SEQRES 4 A 90 GLU CYS ARG VAL GLY ASP GLY THR VAL LEU GLY THR GLY SEQRES 5 A 90 VAL GLY ARG ASN ILE LYS ILE ALA GLY ILE ARG ALA ALA SEQRES 6 A 90 GLU ASN ALA LEU ARG ASP LYS LYS MET LEU ASP PHE TYR SEQRES 7 A 90 ALA LYS GLN ARG ALA ALA ILE PRO ARG SER GLU SER HELIX 1 1 ASN A 369 ILE A 378 1 10 HELIX 2 2 ASN A 419 ASP A 434 1 16 HELIX 3 3 ASP A 434 ALA A 447 1 14 SHEET 1 A 3 HIS A 386 PRO A 393 0 SHEET 2 A 3 PRO A 398 ARG A 405 -1 O ARG A 405 N HIS A 386 SHEET 3 A 3 VAL A 411 GLY A 417 -1 O LEU A 412 N CYS A 404 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1