HEADER HYDROLASE/RNA 29-NOV-12 4I67 TITLE CRYSTAL STRUCTURE OF THE RRM DOMAIN OF RNA HELICASE HERA FROM T. TITLE 2 THERMOPHILUS IN COMPLEX WITH GGGC RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAT RESISTANT RNA DEPENDENT ATPASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RRM DOMAIN (UNP RESIDUES 431-517); COMPND 5 SYNONYM: HERA RNA HELICASE; COMPND 6 EC: 3.6.4.13; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-R(P*GP*GP*GP*(RPC))-3'; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: 23S RIBOSOMAL RNA FRAGMENT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 GENE: TT_C1895; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES KEYWDS UNWINDING, ATPASE, HEAT RESISTANT, RNA RECOGNITION MOTIF, RNA KEYWDS 2 BINDING, DEAD BOX PROTEIN, HYDROLASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.G.RUDOLPH,D.KLOSTERMEIER REVDAT 6 20-SEP-23 4I67 1 LINK REVDAT 5 15-NOV-17 4I67 1 REMARK REVDAT 4 26-NOV-14 4I67 1 KEYWDS REVDAT 3 17-JUL-13 4I67 1 JRNL REVDAT 2 15-MAY-13 4I67 1 JRNL REVDAT 1 24-APR-13 4I67 0 JRNL AUTH L.STEIMER,J.P.WURM,M.H.LINDEN,M.G.RUDOLPH,J.WOHNERT, JRNL AUTH 2 D.KLOSTERMEIER JRNL TITL RECOGNITION OF TWO DISTINCT ELEMENTS IN THE RNA SUBSTRATE BY JRNL TITL 2 THE RNA-BINDING DOMAIN OF THE T. THERMOPHILUS DEAD BOX JRNL TITL 3 HELICASE HERA. JRNL REF NUCLEIC ACIDS RES. V. 41 6259 2013 JRNL REFN ISSN 0305-1048 JRNL PMID 23625962 JRNL DOI 10.1093/NAR/GKT323 REMARK 2 REMARK 2 RESOLUTION. 2.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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) : 2.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 5726 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.540 REMARK 3 FREE R VALUE TEST SET COUNT : 260 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 38.2986 - 2.9358 1.00 2764 143 0.1620 0.2136 REMARK 3 2 2.9358 - 2.3300 1.00 2702 117 0.2720 0.3757 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.490 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 : 0.007 698 REMARK 3 ANGLE : 1.064 964 REMARK 3 CHIRALITY : 0.062 109 REMARK 3 PLANARITY : 0.005 110 REMARK 3 DIHEDRAL : 16.066 280 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' REMARK 3 ORIGIN FOR THE GROUP (A): 39.3680 -9.2319 -5.4987 REMARK 3 T TENSOR REMARK 3 T11: 0.6042 T22: 0.5124 REMARK 3 T33: 0.4608 T12: 0.0346 REMARK 3 T13: 0.0633 T23: -0.0763 REMARK 3 L TENSOR REMARK 3 L11: 9.1949 L22: 9.4716 REMARK 3 L33: 9.2553 L12: 0.8720 REMARK 3 L13: 2.3457 L23: -3.4924 REMARK 3 S TENSOR REMARK 3 S11: 0.0381 S12: -0.5041 S13: 0.1604 REMARK 3 S21: 0.0715 S22: -0.0933 S23: 0.2353 REMARK 3 S31: 0.3014 S32: -0.6083 S33: 0.0172 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' REMARK 3 ORIGIN FOR THE GROUP (A): 45.2416 -14.5341 -15.3797 REMARK 3 T TENSOR REMARK 3 T11: 1.4534 T22: 0.9635 REMARK 3 T33: 0.9436 T12: 0.2667 REMARK 3 T13: 0.1108 T23: -0.0017 REMARK 3 L TENSOR REMARK 3 L11: 3.4657 L22: 3.0411 REMARK 3 L33: 9.4296 L12: -2.8465 REMARK 3 L13: -3.6948 L23: 1.0739 REMARK 3 S TENSOR REMARK 3 S11: -0.8467 S12: 1.1760 S13: -1.0250 REMARK 3 S21: -1.0647 S22: -0.5748 S23: -0.1318 REMARK 3 S31: 1.4105 S32: 0.1863 S33: 1.0948 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 4I67 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1000076354. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6-7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99997 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS (VERSION MARCH 15 REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5963 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.330 REMARK 200 RESOLUTION RANGE LOW (A) : 44.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.760 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : 0.05200 REMARK 200 FOR THE DATA SET : 19.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 9.90 REMARK 200 R MERGE FOR SHELL (I) : 0.86800 REMARK 200 R SYM FOR SHELL (I) : 0.86800 REMARK 200 FOR SHELL : 1.200 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 3I31 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.06 M SODIUM MALONATE, PH 6.0, 0.1 M REMARK 280 TRIS-HCL, PH 7.5, 0.13 M POTASSIUM/SODIUM PHOSPHATE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 9.64767 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 19.29533 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.47150 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 24.11917 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 4.82383 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 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 ILE A 500 REMARK 465 PRO A 501 REMARK 465 SER A 502 REMARK 465 ARG A 503 REMARK 465 THR A 504 REMARK 465 ARG A 505 REMARK 465 ARG A 506 REMARK 465 PRO A 507 REMARK 465 ALA A 508 REMARK 465 ARG A 509 REMARK 465 ALA A 510 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 GLU A 425 108.52 -164.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3I31 RELATED DB: PDB REMARK 900 RELATED ID: 4I68 RELATED DB: PDB REMARK 900 RELATED ID: 4I69 RELATED DB: PDB DBREF 4I67 A 424 510 UNP Q72GF3 Q72GF3_THET2 431 517 DBREF 4I67 B 1 4 PDB 4I67 4I67 1 4 SEQRES 1 A 87 ALA GLU ARG SER LEU LEU THR GLY GLU GLU GLY TRP ARG SEQRES 2 A 87 THR TYR LYS ALA THR GLY PRO ARG LEU SER LEU PRO ARG SEQRES 3 A 87 LEU VAL ALA LEU LEU LYS GLY GLN GLY LEU GLU VAL GLY SEQRES 4 A 87 LYS VAL ALA GLU ALA GLU GLY GLY PHE TYR VAL ASP LEU SEQRES 5 A 87 ARG PRO GLU ALA ARG PRO GLU VAL ALA GLY LEU ARG LEU SEQRES 6 A 87 GLU PRO ALA ARG ARG VAL GLU GLY LEU LEU GLU ILE PRO SEQRES 7 A 87 SER ARG THR ARG ARG PRO ALA ARG ALA SEQRES 1 B 4 G G G RPC MODRES 4I67 RPC B 4 C HET RPC B 4 24 HETNAM RPC CYTIDINE 3',5'-BIS(DIHYDROGEN PHOSPHATE) FORMUL 2 RPC C9 H15 N3 O11 P2 FORMUL 3 HOH *11(H2 O) HELIX 1 1 SER A 446 GLN A 457 1 12 SHEET 1 A 4 VAL A 461 ALA A 467 0 SHEET 2 A 4 GLY A 470 LEU A 475 -1 O GLY A 470 N ALA A 467 SHEET 3 A 4 ARG A 436 THR A 441 -1 N ALA A 440 O PHE A 471 SHEET 4 A 4 ARG A 487 PRO A 490 -1 O GLU A 489 N LYS A 439 LINK O3' G B 3 P RPC B 4 1555 1555 1.59 CRYST1 88.435 88.435 28.943 90.00 90.00 120.00 P 61 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 0.011308 0.006529 0.000000 0.00000 SCALE2 0.000000 0.013057 0.000000 0.00000 SCALE3 0.000000 0.000000 0.034551 0.00000