10 20 30 40 50 60 70 80 1Q1V - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA BINDING PROTEIN 22-JUL-03 1Q1V
TITLE STRUCTURE OF THE ONCOPROTEIN DEK: A PUTATIVE DNA-BINDING TITLE 2 DOMAIN RELATED TO THE WINGED HELIX MOTIF
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEK PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 309-378; COMPND 5 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: DEK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28C
KEYWDS WINGED-HELIX MOTIF, DNA BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR M.DEVANY,N.P.KOTHARU,H.MATSUO
REVDAT 2 24-FEB-09 1Q1V 1 VERSN REVDAT 1 10-AUG-04 1Q1V 0
JRNL AUTH M.DEVANY,N.P.KOTHARU,H.MATSUO JRNL TITL SOLUTION NMR STRUCTURE OF THE C-TERMINAL DOMAIN OF JRNL TITL 2 THE HUMAN PROTEIN DEK JRNL REF PROTEIN SCI. V. 13 2252 2004 JRNL REFN ISSN 0961-8368 JRNL PMID 15238633 JRNL DOI 10.1110/PS.04797104
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE BASED ON 1456 NON- REMARK 3 REDUNDANT NOES, 33 HYDROGEN BOND RESTRAINTS DERIVED FROM REMARK 3 DEUTERIUM EXCHANG EXPERIMENTS, AND 46 DIHEDRAL-ANGLE REMARK 3 RESTRAINTS DERIVED FROM CA CHEMICAL SHIFTS.
REMARK 4 REMARK 4 1Q1V COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUL-03. REMARK 100 THE RCSB ID CODE IS RCSB019811.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.75 REMARK 210 IONIC STRENGTH : 50MM NAPO4, 100MM KCL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0MM DEK C-TERMINAL DOMAIN REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, 3D_ REMARK 210 13C-SEPARATED_NOESY, 3D_ REMARK 210 HCCHTOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 TOTAL ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: DISTANCE RESTRAINTS COLLECTED FROM A NOESY SPECTRUM REMARK 210 WITH 150MS MIXING TIME.
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 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 310 -59.28 -177.64 REMARK 500 1 ILE A 313 -55.57 -137.92 REMARK 500 1 LYS A 314 104.60 59.54 REMARK 500 1 LYS A 317 71.14 -164.01 REMARK 500 1 ASP A 358 54.53 -100.74 REMARK 500 1 LEU A 359 97.54 -57.23 REMARK 500 1 GLU A 377 32.78 -163.67 REMARK 500 2 LYS A 314 30.10 -158.68 REMARK 500 2 LYS A 317 -163.04 -66.43 REMARK 500 2 LYS A 331 -70.98 -78.64 REMARK 500 2 LYS A 348 -70.24 -71.82 REMARK 500 2 ASP A 358 48.81 -91.86 REMARK 500 2 LEU A 359 108.93 -38.79 REMARK 500 3 LEU A 312 -58.88 66.67 REMARK 500 3 ILE A 313 168.80 54.35 REMARK 500 3 LYS A 314 155.25 177.62 REMARK 500 3 LEU A 316 -77.40 -66.93 REMARK 500 3 THR A 321 156.02 -40.97 REMARK 500 3 ASP A 358 52.53 -93.92 REMARK 500 3 LEU A 359 103.42 -47.45 REMARK 500 3 GLU A 377 35.60 -173.92 REMARK 500 4 ILE A 313 76.37 -108.71 REMARK 500 4 LYS A 314 39.92 -153.25 REMARK 500 4 LEU A 316 -87.86 -72.64 REMARK 500 4 LYS A 348 -75.68 -66.64 REMARK 500 4 ASP A 358 42.98 -86.22 REMARK 500 4 LEU A 359 99.32 -43.13 REMARK 500 5 ILE A 313 98.26 60.53 REMARK 500 5 LYS A 314 -165.67 -119.54 REMARK 500 5 LYS A 317 -178.80 -52.46 REMARK 500 5 ASP A 358 51.19 -90.50 REMARK 500 5 GLU A 377 43.30 -148.54 REMARK 500 6 LEU A 312 61.46 -112.12 REMARK 500 6 LYS A 314 104.69 -50.25 REMARK 500 6 LEU A 316 47.64 -146.37 REMARK 500 6 LYS A 317 -163.93 -103.45 REMARK 500 6 THR A 321 159.34 -49.49 REMARK 500 6 ALA A 336 -159.76 -151.63 REMARK 500 6 ASP A 358 51.26 -94.86 REMARK 500 6 LEU A 359 112.98 -39.32 REMARK 500 6 ILE A 366 -70.11 -59.51 REMARK 500 6 GLU A 377 26.19 -159.16 REMARK 500 7 LEU A 316 56.34 -110.80 REMARK 500 7 LYS A 318 55.64 -151.05 REMARK 500 7 THR A 321 161.43 -43.19 REMARK 500 7 THR A 356 46.72 -82.43 REMARK 500 7 THR A 360 -59.60 -120.22 REMARK 500 7 GLU A 377 38.48 173.01 REMARK 500 8 LYS A 317 -159.85 58.99 REMARK 500 8 LYS A 349 -71.03 -70.60 REMARK 500 8 ASP A 358 47.56 -95.09 REMARK 500 8 GLU A 377 40.43 -171.58 REMARK 500 9 LEU A 332 -70.12 -72.40 REMARK 500 9 ASP A 358 48.00 -91.83 REMARK 500 9 LEU A 359 107.13 -38.98 REMARK 500 9 ILE A 366 -71.33 -47.51 REMARK 500 10 ILE A 313 -86.93 55.82 REMARK 500 10 LYS A 314 168.89 61.21 REMARK 500 10 ASP A 358 52.64 -93.32 REMARK 500 10 LEU A 359 110.87 -39.12 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 1 ARG A 362 0.29 SIDE_CHAIN REMARK 500 2 ARG A 362 0.32 SIDE_CHAIN REMARK 500 3 ARG A 362 0.31 SIDE_CHAIN REMARK 500 4 ARG A 362 0.16 SIDE_CHAIN REMARK 500 5 ARG A 362 0.27 SIDE_CHAIN REMARK 500 6 ARG A 362 0.31 SIDE_CHAIN REMARK 500 7 ARG A 362 0.21 SIDE_CHAIN REMARK 500 8 ARG A 362 0.11 SIDE_CHAIN REMARK 500 9 ARG A 362 0.08 SIDE_CHAIN REMARK 500 10 ARG A 362 0.27 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 1Q1V A 309 375 UNP P35659 DEK_HUMAN 309 375
SEQADV 1Q1V LEU A 376 UNP P35659 CLONING ARTIFACT SEQADV 1Q1V GLU A 377 UNP P35659 CLONING ARTIFACT SEQADV 1Q1V HIS A 378 UNP P35659 CLONING ARTIFACT
SEQRES 1 A 70 ASP GLU PRO LEU ILE LYS LYS LEU LYS LYS PRO PRO THR SEQRES 2 A 70 ASP GLU GLU LEU LYS GLU THR ILE LYS LYS LEU LEU ALA SEQRES 3 A 70 SER ALA ASN LEU GLU GLU VAL THR MET LYS GLN ILE CYS SEQRES 4 A 70 LYS LYS VAL TYR GLU ASN TYR PRO THR TYR ASP LEU THR SEQRES 5 A 70 GLU ARG LYS ASP PHE ILE LYS THR THR VAL LYS GLU LEU SEQRES 6 A 70 ILE SER LEU GLU HIS
HELIX 1 1 THR A 321 ALA A 334 1 14 HELIX 2 2 SER A 335 ALA A 336 5 2 HELIX 3 3 ASN A 337 VAL A 341 5 5 HELIX 4 4 THR A 342 TYR A 354 1 13 HELIX 5 5 THR A 360 LEU A 376 1 17
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 309
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