HEADER RNA BINDING PROTEIN/RNA 22-APR-10 3MOJ TITLE STRUCTURE OF THE RNA BINDING DOMAIN OF THE BACILLUS SUBTILIS YXIN TITLE 2 PROTEIN COMPLEXED WITH A FRAGMENT OF 23S RIBOSOMAL RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (69-MER); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: E. COLI 23 S RIBOSOMAL RNA (NUCLEOTIDES 2508-2580 WITH GAAA COMPND 5 TETRALOOP IN NUCLEOTIDES 2530-2533 AND A2581 AT 3' END); COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ATP-DEPENDENT RNA HELICASE DBPA; COMPND 9 CHAIN: B; COMPND 10 EC: 3.6.1.-; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 8 ORGANISM_TAXID: 1423; SOURCE 9 GENE: DBPA, DEAD, YXIN, BSU39110, SS8E; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL23(DE3) KEYWDS RNA, RNA RECOGNITION MOTIF, RNA BINDING PROTEIN, RIBOSOMAL RNA, RNA KEYWDS 2 BINDING PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.W.HARDIN,Y.HU,D.B.MCKAY REVDAT 4 21-FEB-24 3MOJ 1 REMARK REVDAT 3 06-OCT-10 3MOJ 1 JRNL REVDAT 2 11-AUG-10 3MOJ 1 JRNL REVDAT 1 04-AUG-10 3MOJ 0 JRNL AUTH J.W.HARDIN,Y.X.HU,D.B.MCKAY JRNL TITL STRUCTURE OF THE RNA BINDING DOMAIN OF A DEAD-BOX HELICASE JRNL TITL 2 BOUND TO ITS RIBOSOMAL RNA TARGET REVEALS A NOVEL MODE OF JRNL TITL 3 RECOGNITION BY AN RNA RECOGNITION MOTIF. JRNL REF J.MOL.BIOL. V. 402 412 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20673833 JRNL DOI 10.1016/J.JMB.2010.07.040 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.WANG,Y.HU,M.T.OVERGAARD,F.V.KARGINOV,O.C.UHLENBECK, REMARK 1 AUTH 2 D.B.MCKAY REMARK 1 TITL THE DOMAIN OF THE BACILLUS SUBTILIS DEAD-BOX HELICASE YXIN REMARK 1 TITL 2 THAT IS RESPONSIBLE FOR SPECIFIC BINDING OF 23S RRNA HAS AN REMARK 1 TITL 3 RNA RECOGNITION MOTIF FOLD. REMARK 1 REF RNA V. 12 959 2006 REMARK 1 REFN ISSN 1355-8382 REMARK 1 PMID 16611943 REMARK 1 DOI 10.1261/RNA.5906 REMARK 2 REMARK 2 RESOLUTION. 2.90 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 3 NUMBER OF REFLECTIONS : 9995 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1039 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 19.8967 - 5.5180 0.97 1471 164 0.2061 0.2642 REMARK 3 2 5.5180 - 4.3953 0.98 1400 166 0.1941 0.2670 REMARK 3 3 4.3953 - 3.8443 0.96 1368 142 0.2106 0.2850 REMARK 3 4 3.8443 - 3.4949 0.96 1324 154 0.2012 0.2666 REMARK 3 5 3.4949 - 3.2455 0.94 1309 161 0.2143 0.2646 REMARK 3 6 3.2455 - 3.0549 0.87 1185 160 0.2274 0.3158 REMARK 3 7 3.0549 - 2.9020 0.64 899 92 0.2656 0.3219 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 : 0.23 REMARK 3 B_SOL : 50.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.005 2221 REMARK 3 ANGLE : 1.060 3329 REMARK 3 CHIRALITY : 0.048 436 REMARK 3 PLANARITY : 0.003 164 REMARK 3 DIHEDRAL : 20.935 904 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 3MOJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058803. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 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 : DOUBLE CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10490 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05400 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29600 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MG/ML PROTEIN-RNA COMPLEX WITH RNA REMARK 280 IN 5% MOLAR EXCESS, 5 MM TRIS-HCL, 200 MM POTASSIUM ACETATE, 26- REMARK 280 30% PEG-3350, PH 8.0, VAPOR DIFFUSION, TEMPERATURE 290K 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 22.50500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.64000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.81500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.64000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.50500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.81500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 A A 2572 REMARK 465 C A 2573 REMARK 465 G A 2574 REMARK 465 C A 2575 REMARK 465 G A 2576 REMARK 465 LYS B 479 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 C A2551 C3' - O3' - P ANGL. DEV. = 10.6 DEGREES REMARK 500 A A2566 C1' - O4' - C4' ANGL. DEV. = -4.2 DEGREES 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 ASN B 409 39.98 -72.24 REMARK 500 LYS B 427 47.42 -73.25 REMARK 500 ASP B 429 98.80 -51.48 REMARK 500 LYS B 460 40.52 -81.83 REMARK 500 VAL B 461 -25.99 -154.45 REMARK 500 LYS B 463 -36.97 -35.62 REMARK 500 LYS B 470 97.06 -166.68 REMARK 500 ASN B 475 167.89 171.47 REMARK 500 LYS B 476 125.47 -37.56 REMARK 500 REMARK 500 REMARK: NULL DBREF 3MOJ B 404 479 UNP P42305 DBPA_BACSU 404 479 DBREF 3MOJ A 2508 2581 PDB 3MOJ 3MOJ 2508 2581 SEQRES 1 A 74 G G C U C A U C A C A U C SEQRES 2 A 74 C U G G G G C U G G A A A SEQRES 3 A 74 C G G U C C C A A G G G U SEQRES 4 A 74 A U G G C U G U U C G C C SEQRES 5 A 74 A U U U A A A G U G G U A SEQRES 6 A 74 C G C G A G C U A SEQRES 1 B 76 MET LYS LEU TYR PHE ASN GLY GLY LYS LYS LYS LYS ILE SEQRES 2 B 76 ARG ALA VAL ASP PHE VAL GLY THR ILE ALA LYS ILE ASP SEQRES 3 B 76 GLY VAL SER ALA ASP ASP ILE GLY ILE ILE THR ILE MET SEQRES 4 B 76 ASP ASN ALA SER TYR VAL GLU ILE LEU ASN GLY LYS GLY SEQRES 5 B 76 PRO HIS VAL LEU LYS VAL MET LYS ASN THR THR VAL LYS SEQRES 6 B 76 GLY LYS GLN LEU LYS VAL ASN LYS ALA ASN LYS HELIX 1 1 GLY B 411 LYS B 415 5 5 HELIX 2 2 ARG B 417 LYS B 427 1 11 HELIX 3 3 SER B 432 ASP B 434 5 3 HELIX 4 4 LYS B 454 LYS B 463 1 10 SHEET 1 A 4 ILE B 436 ILE B 441 0 SHEET 2 A 4 SER B 446 ILE B 450 -1 O TYR B 447 N THR B 440 SHEET 3 A 4 LYS B 405 PHE B 408 -1 N LEU B 406 O VAL B 448 SHEET 4 A 4 VAL B 474 LYS B 476 -1 O ASN B 475 N TYR B 407 CRYST1 45.010 91.630 115.280 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 0.022217 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010914 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008675 0.00000