HEADER HYDROLASE 27-NOV-08 2KBE TITLE SOLUTION STRUCTURE OF AMINO-TERMINAL DOMAIN OF DBP5P COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT RNA HELICASE DBP5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: AMINO-TERMINAL DOMAIN; COMPND 5 SYNONYM: DEAD BOX PROTEIN 5, HELICASE CA5/6, RIBONUCLEIC ACID- COMPND 6 TRAFFICKING PROTEIN 8; COMPND 7 EC: 3.6.1.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: DBP5, RAT8, YOR046C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PETM KEYWDS DBP5P, ATP-BINDING, CYTOPLASM, HELICASE, HYDROLASE, MEMBRANE, MRNA KEYWDS 2 TRANSPORT, NUCLEAR PORE COMPLEX, NUCLEOTIDE-BINDING, NUCLEUS, KEYWDS 3 PHOSPHOPROTEIN, PROTEIN TRANSPORT, RNA-BINDING, TRANSLOCATION, KEYWDS 4 TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.S.FAN,J.ZHANG,D.YANG REVDAT 2 16-MAR-22 2KBE 1 REMARK REVDAT 1 13-OCT-09 2KBE 0 JRNL AUTH J.S.FAN,Z.CHENG,J.ZHANG,C.NOBLE,Z.ZHOU,H.SONG,D.YANG JRNL TITL SOLUTION AND CRYSTAL STRUCTURES OF MRNA EXPORTER DBP5P AND JRNL TITL 2 ITS INTERACTION WITH NUCLEOTIDES. JRNL REF J.MOL.BIOL. V. 388 1 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19281819 JRNL DOI 10.1016/J.JMB.2009.03.004 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.21, X-PLOR NIH 2.21 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA, CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA, CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KBE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-DEC-08. REMARK 100 THE DEPOSITION ID IS D_1000100910. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.7 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 20 MM MES, 100 MM POTASSIUM REMARK 210 ACETATE, 0.6 MM [U-13C; U-15N] REMARK 210 DBP5P, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HCCH-TOCSY; 3D HNCA; 4D 15N, REMARK 210 13C-EDITED 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 : NULL REMARK 210 METHOD USED : TORSION ANGLE 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 O THR A 142 H ALA A 146 1.53 REMARK 500 O GLY A 186 H THR A 189 1.57 REMARK 500 OE1 GLU A 240 H ASN A 243 1.60 REMARK 500 O LEU A 123 N LEU A 125 2.07 REMARK 500 O VAL A 286 N ASN A 288 2.12 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 GLU A 72 80.90 52.09 REMARK 500 1 LYS A 74 -106.27 -86.24 REMARK 500 1 VAL A 75 -118.83 50.67 REMARK 500 1 LYS A 76 -76.19 60.88 REMARK 500 1 ALA A 78 -55.29 -151.92 REMARK 500 1 ASP A 79 36.31 -166.61 REMARK 500 1 ASN A 85 20.90 -153.27 REMARK 500 1 SER A 86 153.53 -39.81 REMARK 500 1 LYS A 92 21.95 -142.17 REMARK 500 1 SER A 93 -163.25 -62.83 REMARK 500 1 ALA A 100 150.97 -48.70 REMARK 500 1 MET A 110 -79.41 -109.63 REMARK 500 1 LYS A 111 -153.63 -95.47 REMARK 500 1 PHE A 112 -152.40 -69.56 REMARK 500 1 LYS A 114 146.65 -173.48 REMARK 500 1 SER A 116 -176.08 48.18 REMARK 500 1 ILE A 118 164.20 -41.58 REMARK 500 1 GLU A 120 89.12 42.60 REMARK 500 1 ALA A 122 93.32 28.27 REMARK 500 1 LEU A 123 91.00 54.96 REMARK 500 1 PRO A 124 59.46 -25.14 REMARK 500 1 LEU A 125 -5.40 156.94 REMARK 500 1 ASN A 129 159.66 170.44 REMARK 500 1 PRO A 130 157.79 -37.69 REMARK 500 1 PRO A 131 121.39 -39.56 REMARK 500 1 ARG A 132 108.04 -172.19 REMARK 500 1 SER A 138 -144.47 -169.56 REMARK 500 1 SER A 140 87.18 -35.79 REMARK 500 1 THR A 142 -50.77 -154.09 REMARK 500 1 ARG A 155 -9.10 -58.01 REMARK 500 1 ASP A 160 19.49 -168.12 REMARK 500 1 ALA A 161 34.01 33.64 REMARK 500 1 PHE A 188 1.55 56.16 REMARK 500 1 THR A 189 158.63 -34.32 REMARK 500 1 LYS A 190 0.40 -61.89 REMARK 500 1 SER A 193 134.15 151.57 REMARK 500 1 PRO A 198 107.67 -46.48 REMARK 500 1 ASP A 199 12.62 59.63 REMARK 500 1 PHE A 201 -111.50 -99.38 REMARK 500 1 GLU A 202 -95.14 -132.93 REMARK 500 1 LYS A 203 -99.50 -151.50 REMARK 500 1 ASN A 204 34.61 -156.64 REMARK 500 1 LYS A 205 -79.84 -99.68 REMARK 500 1 GLN A 210 -39.05 -35.68 REMARK 500 1 MET A 228 98.27 -160.14 REMARK 500 1 LEU A 230 0.34 -69.56 REMARK 500 1 ILE A 233 170.80 -49.18 REMARK 500 1 LYS A 234 -3.97 -144.26 REMARK 500 1 GLU A 240 76.54 73.42 REMARK 500 1 GLN A 247 72.34 -111.78 REMARK 500 REMARK 500 THIS ENTRY HAS 1070 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KBF RELATED DB: PDB DBREF 2KBE A 71 296 UNP P20449 DBP5_YEAST 71 296 SEQRES 1 A 226 TYR GLU VAL LYS VAL LYS LEU ALA ASP ILE GLN ALA ASP SEQRES 2 A 226 PRO ASN SER PRO LEU TYR SER ALA LYS SER PHE ASP GLU SEQRES 3 A 226 LEU GLY LEU ALA PRO GLU LEU LEU LYS GLY ILE TYR ALA SEQRES 4 A 226 MET LYS PHE GLN LYS PRO SER LYS ILE GLN GLU ARG ALA SEQRES 5 A 226 LEU PRO LEU LEU LEU HIS ASN PRO PRO ARG ASN MET ILE SEQRES 6 A 226 ALA GLN SER GLN SER GLY THR GLY LYS THR ALA ALA PHE SEQRES 7 A 226 SER LEU THR MET LEU THR ARG VAL ASN PRO GLU ASP ALA SEQRES 8 A 226 SER PRO GLN ALA ILE CYS LEU ALA PRO SER ARG GLU LEU SEQRES 9 A 226 ALA ARG GLN THR LEU GLU VAL VAL GLN GLU MET GLY LYS SEQRES 10 A 226 PHE THR LYS ILE THR SER GLN LEU ILE VAL PRO ASP SER SEQRES 11 A 226 PHE GLU LYS ASN LYS GLN ILE ASN ALA GLN VAL ILE VAL SEQRES 12 A 226 GLY THR PRO GLY THR VAL LEU ASP LEU MET ARG ARG LYS SEQRES 13 A 226 LEU MET GLN LEU GLN LYS ILE LYS ILE PHE VAL LEU ASP SEQRES 14 A 226 GLU ALA ASP ASN MET LEU ASP GLN GLN GLY LEU GLY ASP SEQRES 15 A 226 GLN CYS ILE ARG VAL LYS ARG PHE LEU PRO LYS ASP THR SEQRES 16 A 226 GLN LEU VAL LEU PHE SER ALA THR PHE ALA ASP ALA VAL SEQRES 17 A 226 ARG GLN TYR ALA LYS LYS ILE VAL PRO ASN ALA ASN THR SEQRES 18 A 226 LEU GLU LEU GLN THR HELIX 1 1 ALA A 82 ASN A 85 5 4 HELIX 2 2 SER A 86 ALA A 91 1 6 HELIX 3 3 SER A 93 GLY A 98 1 6 HELIX 4 4 ALA A 100 MET A 110 1 11 HELIX 5 5 LYS A 117 LEU A 126 1 10 HELIX 6 6 THR A 142 VAL A 156 1 15 HELIX 7 7 SER A 171 GLY A 186 1 16 HELIX 8 8 THR A 218 ARG A 225 1 8 HELIX 9 9 GLU A 240 GLN A 247 1 8 HELIX 10 10 GLY A 249 LEU A 261 1 13 HELIX 11 11 ALA A 275 VAL A 286 1 12 SHEET 1 A 7 GLN A 194 ILE A 196 0 SHEET 2 A 7 VAL A 211 GLY A 214 1 O VAL A 213 N GLN A 194 SHEET 3 A 7 ALA A 165 LEU A 168 1 N ALA A 165 O ILE A 212 SHEET 4 A 7 ILE A 235 ASP A 239 1 O ASP A 239 N LEU A 168 SHEET 5 A 7 LEU A 267 PHE A 270 1 O VAL A 268 N LEU A 238 SHEET 6 A 7 MET A 134 GLN A 137 1 N MET A 134 O LEU A 269 SHEET 7 A 7 ASN A 290 GLU A 293 1 O ASN A 290 N ILE A 135 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