HEADER HYDROLASE 11-FEB-06 2G0C TITLE STRUCTURE OF THE RNA BINDING DOMAIN (RESIDUES 404-479) OF THE BACILLUS TITLE 2 SUBTILIS YXIN PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT RNA HELICASE DBPA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RNA BINDING DOMAIN; COMPND 5 EC: 3.6.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: DBPA, DEAD; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNA RECOGNITION MOTIF, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.B.MCKAY REVDAT 6 14-FEB-24 2G0C 1 REMARK REVDAT 5 18-OCT-17 2G0C 1 REMARK REVDAT 4 13-JUL-11 2G0C 1 VERSN REVDAT 3 24-FEB-09 2G0C 1 VERSN REVDAT 2 06-JUN-06 2G0C 1 JRNL REVDAT 1 18-APR-06 2G0C 0 JRNL AUTH S.WANG,Y.HU,M.T.OVERGAARD,F.V.KARGINOV,O.C.UHLENBECK, JRNL AUTH 2 D.B.MCKAY JRNL TITL THE DOMAIN OF THE BACILLUS SUBTILIS DEAD-BOX HELICASE YXIN JRNL TITL 2 THAT IS RESPONSIBLE FOR SPECIFIC BINDING OF 23S RRNA HAS AN JRNL TITL 3 RNA RECOGNITION MOTIF FOLD. JRNL REF RNA V. 12 959 2006 JRNL REFN ISSN 1355-8382 JRNL PMID 16611943 JRNL DOI 10.1261/RNA.5906 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 9484 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.253 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.100 REMARK 3 FREE R VALUE TEST SET COUNT : 579 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 11 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 728 REMARK 3 BIN R VALUE (WORKING SET) : 0.3330 REMARK 3 BIN FREE R VALUE : 0.3830 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 48 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 511 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 48 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.39000 REMARK 3 B22 (A**2) : 0.39000 REMARK 3 B33 (A**2) : -0.77000 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.17 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) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.450 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.060 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2G0C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1000036528. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 10.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97858, 0.97910, 0.94643 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : WIGGLER REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9790 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.02600 REMARK 200 R SYM (I) : 0.02600 REMARK 200 FOR THE DATA SET : 20.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.32300 REMARK 200 R SYM FOR SHELL (I) : 0.32300 REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: DE NOVO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PRECIPITANT OF 3.2-3.6 M (NH4)2SO4 REMARK 280 BUFFERED WITH 0.1 M GLYCINE, PH 10.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K 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 32.13000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.50500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.50500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 16.06500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.50500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.50500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 48.19500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.50500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.50500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 16.06500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.50500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.50500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 48.19500 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 32.13000 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: PQS 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL 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 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 64.26000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1006 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1008 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1025 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1026 LIES ON A SPECIAL POSITION. 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 LYS A 414 REMARK 465 LYS A 415 REMARK 465 ILE A 416 REMARK 465 ARG A 417 REMARK 465 LYS A 468 REMARK 465 GLY A 469 REMARK 465 LYS A 470 REMARK 465 LYS A 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 GLY A 423 CA - C - N ANGL. DEV. = 21.9 DEGREES REMARK 500 GLY A 423 O - C - N ANGL. DEV. = -24.0 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 ALA A 477 -72.92 -63.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2003 DBREF 2G0C A 404 479 UNP P42305 DBPA_BACSU 404 479 SEQRES 1 A 76 MET LYS LEU TYR PHE ASN GLY GLY LYS LYS LYS LYS ILE SEQRES 2 A 76 ARG ALA VAL ASP PHE VAL GLY THR ILE ALA LYS ILE ASP SEQRES 3 A 76 GLY VAL SER ALA ASP ASP ILE GLY ILE ILE THR ILE MET SEQRES 4 A 76 ASP ASN ALA SER TYR VAL GLU ILE LEU ASN GLY LYS GLY SEQRES 5 A 76 PRO HIS VAL LEU LYS VAL MET LYS ASN THR THR VAL LYS SEQRES 6 A 76 GLY LYS GLN LEU LYS VAL ASN LYS ALA ASN LYS HET SO4 A2001 5 HET SO4 A2003 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *48(H2 O) HELIX 1 1 ALA A 418 LYS A 427 1 10 HELIX 2 2 SER A 432 ASP A 434 5 3 HELIX 3 3 LYS A 454 LYS A 463 1 10 SHEET 1 A 4 ILE A 436 ILE A 441 0 SHEET 2 A 4 SER A 446 ILE A 450 -1 O GLU A 449 N GLY A 437 SHEET 3 A 4 LYS A 405 PHE A 408 -1 N LEU A 406 O VAL A 448 SHEET 4 A 4 VAL A 474 LYS A 476 -1 O ASN A 475 N TYR A 407 SITE 1 AC1 5 THR A 424 LYS A 427 VAL A 467 HOH A1022 SITE 2 AC1 5 HOH A1035 SITE 1 AC2 5 LYS A 427 LYS A 454 ASN A 478 HOH A1017 SITE 2 AC2 5 HOH A1020 CRYST1 51.010 51.010 64.260 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 0.019600 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019600 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015560 0.00000