HEADER HYDROLASE 10-NOV-06 2E29 TITLE SOLUTION STRUCTURE OF THE GUCT DOMAIN FROM HUMAN ATP-DEPENDENT RNA TITLE 2 HELICASE DDX50, DEAD BOX PROTEIN 50 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT RNA HELICASE DDX50; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GUCT DOMAIN, RESIDUES 8-92; COMPND 5 SYNONYM: DEAD BOX PROTEIN 50, NUCLEOLAR PROTEIN GU2, GU-BETA; COMPND 6 EC: 3.6.1.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DDX50; SOURCE 6 EXPRESSION_SYSTEM: CELL-FREE PROTEIN SYNTHESIS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: P060403-01 KEYWDS ATP BINDING, HELICASE, HYDROLASE, NUCLEAR PROTEIN, NUCLEOTIDE- KEYWDS 2 BINDING, RNA-BINDING, GUCT DOMAIN, STRUCTURAL GENOMICS, NPPSFA, KEYWDS 3 NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, KEYWDS 4 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.OHNISHI,K.PAAKKONEN,P.GUNTERT,M.SATO,S.KOSHIBA,T.HARADA,S.WATANABE, AUTHOR 2 T.KIGAWA,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE AUTHOR 3 (RSGI) REVDAT 4 29-MAY-24 2E29 1 REMARK REVDAT 3 09-MAR-22 2E29 1 REMARK SEQADV REVDAT 2 02-DEC-08 2E29 1 JRNL VERSN REVDAT 1 15-MAY-07 2E29 0 JRNL AUTH S.OHNISHI,K.PAAKKONEN,S.KOSHIBA,N.TOCHIO,M.SATO,N.KOBAYASHI, JRNL AUTH 2 T.HARADA,S.WATANABE,Y.MUTO,P.GUNTERT,A.TANAKA,T.KIGAWA, JRNL AUTH 3 S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE GUCT DOMAIN FROM HUMAN RNA JRNL TITL 2 HELICASE II/GUBETA REVEALS THE RRM FOLD, BUT IMPLAUSIBLE RNA JRNL TITL 3 INTERACTIONS JRNL REF PROTEINS V. 74 133 2008 JRNL REFN ISSN 0887-3585 JRNL PMID 18615715 JRNL DOI 10.1002/PROT.22138 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, OPALP REMARK 3 AUTHORS : BRUKER (XWINNMR), KORADI, R. (OPALP) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HNN AND CACO RDC DATA, OBTAINED FROM REMARK 3 THE PF1 PHAGE SYSTEM, WERE USED IN THE TORSION ANGLE DYNAMICS REMARK 3 CALCULATION. REMARK 4 REMARK 4 2E29 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000026135. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.9MM PROTEIN U-15N,13C; 20MM D REMARK 210 -TRIS-HCL(PH7.0); 100MM NACL; REMARK 210 1MM D-DTT; 0.02% NAN3; 10% D2O, REMARK 210 90% H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20030801, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9816, CYANA 2.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 RESTRAINED MOLECULAR DYNAMICS 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 OE2 GLU A 40 HG SER A 84 1.54 REMARK 500 REMARK 500 REMARK: NULL 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 10 ARG A 55 NE - CZ - NH2 ANGL. DEV. = -3.2 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 1 PHE A 8 -174.31 57.19 REMARK 500 1 SER A 16 -76.13 -153.68 REMARK 500 1 ASN A 62 17.20 56.47 REMARK 500 2 GLU A 9 82.87 -155.08 REMARK 500 2 LEU A 13 -11.83 -152.27 REMARK 500 2 THR A 15 20.06 -144.33 REMARK 500 2 LYS A 18 -61.89 -142.91 REMARK 500 2 PRO A 91 -157.63 -79.12 REMARK 500 3 GLU A 9 75.96 44.87 REMARK 500 4 SER A 2 -90.82 -77.30 REMARK 500 4 SER A 3 -160.78 50.31 REMARK 500 4 ARG A 11 -153.96 47.45 REMARK 500 5 SER A 2 173.61 61.63 REMARK 500 5 ILE A 14 -143.64 -118.35 REMARK 500 5 ASN A 62 19.65 54.46 REMARK 500 6 SER A 3 88.15 -159.00 REMARK 500 6 SER A 5 -75.18 -155.51 REMARK 500 6 SER A 6 -120.39 44.12 REMARK 500 6 SER A 16 -70.90 -147.67 REMARK 500 6 ASN A 62 17.23 57.05 REMARK 500 7 SER A 16 -59.49 -135.96 REMARK 500 7 ASN A 62 15.87 52.88 REMARK 500 7 MET A 63 30.50 -82.34 REMARK 500 7 ASP A 83 -4.36 56.58 REMARK 500 8 SER A 2 72.33 42.81 REMARK 500 8 PHE A 8 27.71 -79.52 REMARK 500 8 ARG A 11 24.95 48.81 REMARK 500 8 SER A 16 177.02 76.22 REMARK 500 8 ARG A 55 63.10 35.22 REMARK 500 8 ASN A 62 6.25 54.89 REMARK 500 8 ASP A 83 3.25 55.29 REMARK 500 8 PRO A 91 -179.69 -66.97 REMARK 500 9 SER A 6 -179.65 58.30 REMARK 500 9 LEU A 13 -40.44 -149.65 REMARK 500 9 ASN A 62 10.16 57.87 REMARK 500 9 MET A 63 38.95 -79.34 REMARK 500 10 THR A 15 -32.97 -161.80 REMARK 500 10 ASN A 62 24.61 45.24 REMARK 500 11 PHE A 8 73.96 53.98 REMARK 500 11 ASP A 17 19.09 -146.40 REMARK 500 11 ASP A 83 16.15 57.49 REMARK 500 12 SER A 2 152.93 73.21 REMARK 500 12 ARG A 11 88.26 -152.97 REMARK 500 12 SER A 12 95.16 -164.81 REMARK 500 12 SER A 16 -39.97 158.98 REMARK 500 12 ASP A 33 -177.78 -177.41 REMARK 500 12 ASN A 62 9.17 57.54 REMARK 500 13 SER A 5 -7.59 -150.99 REMARK 500 13 PHE A 8 81.48 70.77 REMARK 500 13 LYS A 18 54.67 35.43 REMARK 500 REMARK 500 THIS ENTRY HAS 96 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 3 ARG A 11 0.08 SIDE CHAIN REMARK 500 6 ARG A 43 0.08 SIDE CHAIN REMARK 500 7 ARG A 55 0.13 SIDE CHAIN REMARK 500 17 ARG A 43 0.08 SIDE CHAIN REMARK 500 18 ARG A 55 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSI002004504.1 RELATED DB: TARGETDB DBREF 2E29 A 8 92 UNP Q9BQ39 DDX50_HUMAN 575 659 SEQADV 2E29 GLY A 1 UNP Q9BQ39 EXPRESSION TAG SEQADV 2E29 SER A 2 UNP Q9BQ39 EXPRESSION TAG SEQADV 2E29 SER A 3 UNP Q9BQ39 EXPRESSION TAG SEQADV 2E29 GLY A 4 UNP Q9BQ39 EXPRESSION TAG SEQADV 2E29 SER A 5 UNP Q9BQ39 EXPRESSION TAG SEQADV 2E29 SER A 6 UNP Q9BQ39 EXPRESSION TAG SEQADV 2E29 GLY A 7 UNP Q9BQ39 EXPRESSION TAG SEQRES 1 A 92 GLY SER SER GLY SER SER GLY PHE GLU PRO ARG SER LEU SEQRES 2 A 92 ILE THR SER ASP LYS GLY PHE VAL THR MET THR LEU GLU SEQRES 3 A 92 SER LEU GLU GLU ILE GLN ASP VAL SER CYS ALA TRP LYS SEQRES 4 A 92 GLU LEU ASN ARG LYS LEU SER SER ASN ALA VAL SER GLN SEQRES 5 A 92 ILE THR ARG MET CYS LEU LEU LYS GLY ASN MET GLY VAL SEQRES 6 A 92 CYS PHE ASP VAL PRO THR THR GLU SER GLU ARG LEU GLN SEQRES 7 A 92 ALA GLU TRP HIS ASP SER ASP TRP ILE LEU SER VAL PRO SEQRES 8 A 92 ALA HELIX 1 1 VAL A 34 LEU A 45 1 12 HELIX 2 2 SER A 46 SER A 51 1 6 HELIX 3 3 THR A 71 TRP A 81 1 11 SHEET 1 A 4 THR A 54 LEU A 58 0 SHEET 2 A 4 GLY A 64 PRO A 70 -1 O ASP A 68 N THR A 54 SHEET 3 A 4 PHE A 20 GLU A 26 -1 N MET A 23 O PHE A 67 SHEET 4 A 4 ILE A 87 SER A 89 -1 O SER A 89 N THR A 24 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