HEADER HYDROLASE 28-NOV-08 2KBF TITLE SOLUTION STRUCTURE OF CARBOXYL-TERMINAL DOMAIN OF DBP5P COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT RNA HELICASE DBP5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 296-482; 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: PET-M 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 2KBF 1 REMARK REVDAT 1 13-OCT-09 2KBF 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 2KBF 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_1000100911. 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 : 0.7 MM [U-13C; U-15N] PROTEIN, REMARK 210 20 MM MES, 100 MM POTASSIUM REMARK 210 ACETATE, 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 : NMRPIPE 2.3 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 HG21 VAL A 403 H ILE A 437 1.30 REMARK 500 HE22 GLN A 453 H GLU A 460 1.35 REMARK 500 O ASP A 442 H SER A 445 1.37 REMARK 500 O THR A 419 H ARG A 423 1.40 REMARK 500 O GLN A 453 H ASP A 458 1.44 REMARK 500 O LYS A 351 H HIS A 355 1.47 REMARK 500 HB VAL A 403 O ILE A 437 1.51 REMARK 500 O TYR A 325 H MET A 328 1.54 REMARK 500 O MET A 328 HG1 THR A 329 1.55 REMARK 500 CG2 VAL A 403 H ILE A 437 1.60 REMARK 500 OG1 THR A 339 OG1 THR A 342 2.05 REMARK 500 OG1 THR A 386 O VAL A 389 2.06 REMARK 500 OG SER A 332 O SER A 381 2.07 REMARK 500 O THR A 409 OD2 ASP A 416 2.09 REMARK 500 O ARG A 392 N ILE A 394 2.11 REMARK 500 O ASN A 300 N ASP A 302 2.11 REMARK 500 O ASP A 442 N SER A 445 2.11 REMARK 500 OH TYR A 308 OD2 ASP A 310 2.13 REMARK 500 OG1 THR A 398 N GLY A 428 2.13 REMARK 500 OD1 ASN A 404 N ASP A 406 2.13 REMARK 500 O ILE A 424 N ARG A 426 2.13 REMARK 500 O TYR A 325 N LEU A 327 2.13 REMARK 500 O LYS A 351 N HIS A 355 2.14 REMARK 500 O THR A 419 N ARG A 423 2.18 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 298 12.58 -141.43 REMARK 500 1 VAL A 299 -32.92 -164.61 REMARK 500 1 ASN A 300 76.58 58.68 REMARK 500 1 VAL A 301 -5.98 -41.65 REMARK 500 1 ASP A 302 21.81 -66.01 REMARK 500 1 ALA A 303 -35.71 -142.86 REMARK 500 1 LYS A 305 88.71 -45.58 REMARK 500 1 CYS A 311 -160.32 -47.02 REMARK 500 1 LYS A 312 -39.50 -134.82 REMARK 500 1 THR A 329 119.81 51.42 REMARK 500 1 ILE A 330 -33.28 -145.48 REMARK 500 1 SER A 332 176.08 158.57 REMARK 500 1 ALA A 338 19.06 -63.34 REMARK 500 1 LEU A 350 -17.00 -49.57 REMARK 500 1 HIS A 355 -168.76 35.80 REMARK 500 1 GLU A 356 105.21 35.72 REMARK 500 1 ASP A 363 -96.86 -69.54 REMARK 500 1 LEU A 364 141.37 -20.61 REMARK 500 1 GLN A 365 176.38 -48.91 REMARK 500 1 ARG A 380 6.06 55.53 REMARK 500 1 SER A 381 120.99 54.68 REMARK 500 1 LYS A 382 -71.92 -98.97 REMARK 500 1 ASN A 388 34.72 32.16 REMARK 500 1 ILE A 394 71.89 0.65 REMARK 500 1 ASP A 395 36.93 -95.73 REMARK 500 1 PRO A 397 83.48 -47.12 REMARK 500 1 THR A 398 147.70 -33.03 REMARK 500 1 SER A 400 16.48 -64.43 REMARK 500 1 VAL A 403 -159.95 167.26 REMARK 500 1 ASN A 404 -178.43 -171.54 REMARK 500 1 LEU A 407 -158.60 -42.52 REMARK 500 1 PRO A 408 -151.95 -84.07 REMARK 500 1 LEU A 410 116.05 -29.14 REMARK 500 1 GLN A 414 137.07 178.64 REMARK 500 1 ALA A 415 123.19 -3.08 REMARK 500 1 ARG A 423 -76.13 -45.99 REMARK 500 1 THR A 427 -87.24 30.77 REMARK 500 1 PHE A 430 115.20 -37.45 REMARK 500 1 ARG A 432 -111.32 -139.15 REMARK 500 1 ASP A 458 65.50 62.93 REMARK 500 1 GLU A 460 -24.05 116.36 REMARK 500 1 MET A 461 107.91 -4.28 REMARK 500 1 THR A 466 33.55 -98.04 REMARK 500 1 ASP A 467 17.95 -69.36 REMARK 500 2 GLU A 298 14.03 -144.59 REMARK 500 2 VAL A 299 -34.42 -155.37 REMARK 500 2 ASN A 300 106.81 41.16 REMARK 500 2 VAL A 301 -0.03 -53.93 REMARK 500 2 ASP A 302 21.81 -69.27 REMARK 500 2 ALA A 303 -34.83 -144.90 REMARK 500 REMARK 500 THIS ENTRY HAS 916 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KBE RELATED DB: PDB DBREF 2KBF A 296 482 UNP P20449 DBP5_YEAST 296 482 SEQRES 1 A 187 THR ASN GLU VAL ASN VAL ASP ALA ILE LYS GLN LEU TYR SEQRES 2 A 187 MET ASP CYS LYS ASN GLU ALA ASP LYS PHE ASP VAL LEU SEQRES 3 A 187 THR GLU LEU TYR GLY LEU MET THR ILE GLY SER SER ILE SEQRES 4 A 187 ILE PHE VAL ALA THR LYS LYS THR ALA ASN VAL LEU TYR SEQRES 5 A 187 GLY LYS LEU LYS SER GLU GLY HIS GLU VAL SER ILE LEU SEQRES 6 A 187 HIS GLY ASP LEU GLN THR GLN GLU ARG ASP ARG LEU ILE SEQRES 7 A 187 ASP ASP PHE ARG GLU GLY ARG SER LYS VAL LEU ILE THR SEQRES 8 A 187 THR ASN VAL LEU ALA ARG GLY ILE ASP ILE PRO THR VAL SEQRES 9 A 187 SER MET VAL VAL ASN TYR ASP LEU PRO THR LEU ALA ASN SEQRES 10 A 187 GLY GLN ALA ASP PRO ALA THR TYR ILE HIS ARG ILE GLY SEQRES 11 A 187 ARG THR GLY ARG PHE GLY ARG LYS GLY VAL ALA ILE SER SEQRES 12 A 187 PHE VAL HIS ASP LYS ASN SER PHE ASN ILE LEU SER ALA SEQRES 13 A 187 ILE GLN LYS TYR PHE GLY ASP ILE GLU MET THR ARG VAL SEQRES 14 A 187 PRO THR ASP ASP TRP ASP GLU VAL GLU LYS ILE VAL LYS SEQRES 15 A 187 LYS VAL LEU LYS ASP HELIX 1 1 ASN A 313 GLY A 326 1 14 HELIX 2 2 THR A 339 GLU A 353 1 15 HELIX 3 3 GLN A 365 GLU A 378 1 14 HELIX 4 4 ALA A 391 ASP A 395 5 5 HELIX 5 5 ASP A 416 ARG A 426 1 11 HELIX 6 6 ASP A 442 GLY A 457 1 16 HELIX 7 7 TRP A 469 VAL A 479 1 11 SHEET 1 A 7 SER A 358 LEU A 360 0 SHEET 2 A 7 VAL A 383 THR A 386 1 O ILE A 385 N LEU A 360 SHEET 3 A 7 SER A 333 PHE A 336 1 N SER A 333 O LEU A 384 SHEET 4 A 7 VAL A 402 ASN A 404 1 O VAL A 403 N ILE A 334 SHEET 5 A 7 ALA A 436 PHE A 439 1 O ILE A 437 N ASN A 404 SHEET 6 A 7 LEU A 307 MET A 309 1 N MET A 309 O SER A 438 SHEET 7 A 7 THR A 462 VAL A 464 1 O THR A 462 N TYR A 308 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