HEADER RNA BINDING PROTEIN,HYDROLASE 30-JUN-09 3I31 TITLE HERA HELICASE RNA BINDING DOMAIN IS AN RRM FOLD COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAT RESISTANT RNA DEPENDENT ATPASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 431-517; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 262724; SOURCE 4 STRAIN: HB27; SOURCE 5 GENE: TT_C1895; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNA HELICASE, RNA RECOGNITION MOTIF, ATP-BINDING, HELICASE, KEYWDS 2 NUCLEOTIDE-BINDING, RNA BINDING PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.G.RUDOLPH,D.KLOSTERMEIER REVDAT 5 21-FEB-24 3I31 1 REMARK SEQADV LINK REVDAT 4 01-NOV-17 3I31 1 REMARK REVDAT 3 13-JUL-11 3I31 1 VERSN REVDAT 2 03-NOV-09 3I31 1 JRNL REVDAT 1 22-SEP-09 3I31 0 JRNL AUTH M.G.RUDOLPH,D.KLOSTERMEIER JRNL TITL THE THERMUS THERMOPHILUS DEAD BOX HELICASE HERA CONTAINS A JRNL TITL 2 MODIFIED RNA RECOGNITION MOTIF DOMAIN LOOSELY CONNECTED TO JRNL TITL 3 THE HELICASE CORE. JRNL REF RNA V. 15 1993 2009 JRNL REFN ISSN 1355-8382 JRNL PMID 19710183 JRNL DOI 10.1261/RNA.1820009 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 34.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.060 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 8882 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 427 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 34.2287 - 2.5958 0.99 3253 144 0.2028 0.2079 REMARK 3 2 2.5958 - 2.0605 0.94 2856 143 0.1778 0.2480 REMARK 3 3 2.0605 - 1.8000 0.79 2346 140 0.2245 0.2728 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 : 0.36 REMARK 3 B_SOL : 59.72 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.42300 REMARK 3 B22 (A**2) : 6.42300 REMARK 3 B33 (A**2) : -12.84600 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 : 0.008 597 REMARK 3 ANGLE : 1.202 805 REMARK 3 CHIRALITY : 0.068 88 REMARK 3 PLANARITY : 0.007 105 REMARK 3 DIHEDRAL : 17.462 230 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 6.2174 19.7902 23.2016 REMARK 3 T TENSOR REMARK 3 T11: 0.2971 T22: 0.1741 REMARK 3 T33: 0.2421 T12: -0.0126 REMARK 3 T13: -0.0511 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 1.3984 L22: 0.7800 REMARK 3 L33: 0.6232 L12: 0.0797 REMARK 3 L13: -0.9918 L23: 0.8351 REMARK 3 S TENSOR REMARK 3 S11: 0.0127 S12: -0.1116 S13: -0.1361 REMARK 3 S21: -0.0477 S22: 0.0318 S23: 0.1596 REMARK 3 S31: 0.2014 S32: -0.2157 S33: 0.0000 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 3I31 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000053900. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-09; 05-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SLS; SLS REMARK 200 BEAMLINE : X06SA; X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0; 1.8 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL; CCD REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M; MARMOSAIC 225 MM REMARK 200 CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9812 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 36.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12200 REMARK 200 FOR THE DATA SET : 7.5000 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) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.70600 REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NACAC PH 6.5, 16-18% P8000, 0.3 REMARK 280 -0.4M ZN(OAC)2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.44500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 18.75800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 18.75800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.22250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 18.75800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 18.75800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 102.66750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 18.75800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 18.75800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 34.22250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 18.75800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 18.75800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 102.66750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 68.44500 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 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 GLU A 499 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 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 468 OE2 REMARK 620 2 HOH A 515 O 116.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 3 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 466 OE1 REMARK 620 2 GLU A 466 OE2 48.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 511 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3I32 RELATED DB: PDB DBREF 3I31 A 424 510 UNP Q72GF3 Q72GF3_THET2 431 517 SEQADV 3I31 ALA A 423 UNP Q72GF3 EXPRESSION TAG SEQRES 1 A 88 ALA ALA GLU ARG SER LEU LEU THR GLY GLU GLU GLY TRP SEQRES 2 A 88 ARG THR TYR LYS ALA THR GLY PRO ARG LEU SER LEU PRO SEQRES 3 A 88 ARG LEU VAL ALA LEU LEU LYS GLY GLN GLY LEU GLU VAL SEQRES 4 A 88 GLY LYS VAL ALA GLU ALA GLU GLY GLY PHE TYR VAL ASP SEQRES 5 A 88 LEU ARG PRO GLU ALA ARG PRO GLU VAL ALA GLY LEU ARG SEQRES 6 A 88 LEU GLU PRO ALA ARG ARG VAL GLU GLY LEU LEU GLU ILE SEQRES 7 A 88 PRO SER ARG THR ARG ARG PRO ALA ARG ALA HET ZN A 1 1 HET NA A 2 1 HET NA A 3 1 HET NA A 4 1 HET TRS A 511 8 HETNAM ZN ZINC ION HETNAM NA SODIUM ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 ZN ZN 2+ FORMUL 3 NA 3(NA 1+) FORMUL 6 TRS C4 H12 N O3 1+ FORMUL 7 HOH *39(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 ASP A 474 N GLY A 462 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 ZN ZN A 1 OE2 GLU A 468 1555 1555 1.87 LINK ZN ZN A 1 O HOH A 515 1555 1555 2.07 LINK NA NA A 2 OE1 GLU A 433 1555 1555 2.89 LINK NA NA A 3 OE1 GLU A 466 1555 1555 2.77 LINK NA NA A 3 OE2 GLU A 466 1555 1555 2.69 LINK NA NA A 4 O HOH A 515 1555 1555 2.13 SITE 1 AC1 5 HOH A 23 GLU A 460 GLU A 468 TRS A 511 SITE 2 AC1 5 HOH A 515 SITE 1 AC2 3 HOH A 37 ARG A 426 GLU A 433 SITE 1 AC3 2 NA A 4 GLU A 466 SITE 1 AC4 2 NA A 3 HOH A 515 SITE 1 AC5 5 ZN A 1 TRP A 435 GLU A 460 VAL A 461 SITE 2 AC5 5 GLU A 468 CRYST1 37.516 37.516 136.890 90.00 90.00 90.00 P 41 21 2 8 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 0.026655 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026655 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007305 0.00000