PDB Short entry for 2JX3 HEADER DNA BINDING PROTEIN 02-NOV-07 2JX3 TITLE NMR SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DEK COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN DEK; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SAP DOMAIN; 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET28A KEYWDS ALPHA HELIX, SAF/SAP MOTIF, DNA BINDING, CHROMOSOMAL REARRANGEMENT, KEYWDS 2 DNA-BINDING, NUCLEUS, PHOSPHORYLATION, PROTO-ONCOGENE, DNA BINDING KEYWDS 3 PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR H.MATSUO,M.DEVANY REVDAT 3 16-MAR-22 2JX3 1 REMARK REVDAT 2 24-FEB-09 2JX3 1 VERSN REVDAT 1 12-FEB-08 2JX3 0 JRNL AUTH M.DEVANY,F.KAPPES,K.M.CHEN,D.M.MARKOVITZ,H.MATSUO JRNL TITL SOLUTION NMR STRUCTURE OF THE N-TERMINAL DOMAIN OF THE HUMAN JRNL TITL 2 DEK PROTEIN JRNL REF PROTEIN SCI. V. 17 205 2008 JRNL REFN ISSN 0961-8368 JRNL PMID 18227428 JRNL DOI 10.1110/PS.073244108 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: INITIAL TEMP=2000, COOLING STEPS= 60000 REMARK 4 REMARK 4 2JX3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000100399. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 100MM KCL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.65 MM [U-100% 13C; U-100% 15N] REMARK 210 DEK78-208, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 PRO A 111 REMARK 465 SER A 112 REMARK 465 GLY A 113 REMARK 465 LYS A 114 REMARK 465 PRO A 115 REMARK 465 LEU A 116 REMARK 465 PRO A 117 REMARK 465 LYS A 118 REMARK 465 SER A 119 REMARK 465 LYS A 120 REMARK 465 LYS A 121 REMARK 465 THR A 122 REMARK 465 CYS A 123 REMARK 465 SER A 124 REMARK 465 LYS A 125 REMARK 465 GLY A 126 REMARK 465 SER A 127 REMARK 465 LYS A 128 REMARK 465 LYS A 129 REMARK 465 GLU A 130 REMARK 465 ARG A 131 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 2 HE22 GLN A 5 1.52 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 THR A 2 52.98 -164.03 REMARK 500 1 GLN A 5 27.97 -153.79 REMARK 500 1 LYS A 10 -177.22 -61.02 REMARK 500 1 ILE A 14 98.96 -42.83 REMARK 500 1 PHE A 19 -71.70 -62.09 REMARK 500 1 LYS A 23 44.82 -96.02 REMARK 500 1 PRO A 40 79.42 -69.65 REMARK 500 1 THR A 42 -111.23 -104.87 REMARK 500 1 PHE A 53 -81.75 -78.87 REMARK 500 1 SER A 54 -43.26 -134.05 REMARK 500 1 PRO A 57 56.71 -69.38 REMARK 500 1 PHE A 58 -142.98 -94.24 REMARK 500 1 LYS A 60 -166.93 -115.22 REMARK 500 1 ARG A 91 88.96 66.73 REMARK 500 1 HIS A 108 76.21 178.29 REMARK 500 1 PRO A 109 -93.46 -70.68 REMARK 500 2 THR A 2 51.12 -162.79 REMARK 500 2 ALA A 4 99.32 -162.96 REMARK 500 2 LYS A 10 -167.83 -52.23 REMARK 500 2 ILE A 14 100.36 -43.08 REMARK 500 2 SER A 22 60.99 -65.11 REMARK 500 2 LYS A 24 97.29 57.26 REMARK 500 2 LYS A 25 -163.34 -121.75 REMARK 500 2 THR A 26 -54.67 -121.53 REMARK 500 2 ARG A 30 -75.30 -48.78 REMARK 500 2 LEU A 32 -74.71 -68.14 REMARK 500 2 VAL A 50 -76.12 -43.62 REMARK 500 2 GLN A 52 77.94 -104.43 REMARK 500 2 PHE A 53 -87.21 -96.83 REMARK 500 2 GLU A 59 -147.61 179.47 REMARK 500 2 LYS A 60 -33.23 -173.75 REMARK 500 2 ARG A 91 91.72 54.28 REMARK 500 2 SER A 92 110.24 177.05 REMARK 500 2 PHE A 105 -72.95 -108.00 REMARK 500 2 HIS A 108 74.89 171.88 REMARK 500 2 PRO A 109 -90.69 -72.31 REMARK 500 3 THR A 2 -43.81 -146.46 REMARK 500 3 ILE A 3 -60.90 -149.89 REMARK 500 3 ALA A 4 86.41 -156.13 REMARK 500 3 GLN A 9 79.63 -104.65 REMARK 500 3 LYS A 10 -143.84 -60.67 REMARK 500 3 ILE A 14 86.35 -55.53 REMARK 500 3 SER A 22 59.55 -65.24 REMARK 500 3 LYS A 24 101.67 68.45 REMARK 500 3 ARG A 30 -82.25 -71.95 REMARK 500 3 LEU A 32 -70.28 -67.38 REMARK 500 3 ARG A 39 87.87 -167.88 REMARK 500 3 THR A 42 -140.09 -128.29 REMARK 500 3 SER A 54 116.32 63.68 REMARK 500 3 PHE A 56 -73.42 -53.44 REMARK 500 REMARK 500 THIS ENTRY HAS 205 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 1 ARG A 16 0.28 SIDE CHAIN REMARK 500 1 ARG A 30 0.28 SIDE CHAIN REMARK 500 1 ARG A 39 0.32 SIDE CHAIN REMARK 500 1 ARG A 76 0.09 SIDE CHAIN REMARK 500 1 ARG A 91 0.32 SIDE CHAIN REMARK 500 1 ARG A 101 0.19 SIDE CHAIN REMARK 500 2 ARG A 16 0.31 SIDE CHAIN REMARK 500 2 ARG A 30 0.31 SIDE CHAIN REMARK 500 2 ARG A 39 0.32 SIDE CHAIN REMARK 500 2 ARG A 76 0.14 SIDE CHAIN REMARK 500 2 ARG A 91 0.30 SIDE CHAIN REMARK 500 2 ARG A 101 0.18 SIDE CHAIN REMARK 500 3 ARG A 16 0.29 SIDE CHAIN REMARK 500 3 ARG A 30 0.27 SIDE CHAIN REMARK 500 3 ARG A 39 0.29 SIDE CHAIN REMARK 500 3 ARG A 91 0.20 SIDE CHAIN REMARK 500 3 ARG A 101 0.28 SIDE CHAIN REMARK 500 4 ARG A 16 0.23 SIDE CHAIN REMARK 500 4 ARG A 30 0.21 SIDE CHAIN REMARK 500 4 ARG A 39 0.29 SIDE CHAIN REMARK 500 4 ARG A 76 0.30 SIDE CHAIN REMARK 500 4 ARG A 91 0.25 SIDE CHAIN REMARK 500 4 ARG A 101 0.29 SIDE CHAIN REMARK 500 5 ARG A 16 0.32 SIDE CHAIN REMARK 500 5 ARG A 30 0.20 SIDE CHAIN REMARK 500 5 ARG A 39 0.18 SIDE CHAIN REMARK 500 5 ARG A 76 0.18 SIDE CHAIN REMARK 500 5 ARG A 91 0.32 SIDE CHAIN REMARK 500 5 ARG A 101 0.27 SIDE CHAIN REMARK 500 6 ARG A 16 0.25 SIDE CHAIN REMARK 500 6 ARG A 30 0.26 SIDE CHAIN REMARK 500 6 ARG A 39 0.24 SIDE CHAIN REMARK 500 6 ARG A 76 0.31 SIDE CHAIN REMARK 500 6 ARG A 91 0.30 SIDE CHAIN REMARK 500 6 ARG A 101 0.31 SIDE CHAIN REMARK 500 7 ARG A 16 0.16 SIDE CHAIN REMARK 500 7 ARG A 30 0.25 SIDE CHAIN REMARK 500 7 ARG A 39 0.32 SIDE CHAIN REMARK 500 7 ARG A 76 0.30 SIDE CHAIN REMARK 500 7 ARG A 91 0.17 SIDE CHAIN REMARK 500 7 ARG A 101 0.31 SIDE CHAIN REMARK 500 8 ARG A 16 0.22 SIDE CHAIN REMARK 500 8 ARG A 30 0.13 SIDE CHAIN REMARK 500 8 ARG A 39 0.25 SIDE CHAIN REMARK 500 8 ARG A 76 0.15 SIDE CHAIN REMARK 500 8 ARG A 91 0.24 SIDE CHAIN REMARK 500 8 ARG A 101 0.20 SIDE CHAIN REMARK 500 9 ARG A 16 0.28 SIDE CHAIN REMARK 500 9 ARG A 30 0.16 SIDE CHAIN REMARK 500 9 ARG A 39 0.24 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 59 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2JX3 A 1 131 UNP P35659 DEK_HUMAN 78 208 SEQRES 1 A 131 PHE THR ILE ALA GLN GLY LYS GLY GLN LYS LEU CYS GLU SEQRES 2 A 131 ILE GLU ARG ILE HIS PHE PHE LEU SER LYS LYS LYS THR SEQRES 3 A 131 ASP GLU LEU ARG ASN LEU HIS LYS LEU LEU TYR ASN ARG SEQRES 4 A 131 PRO GLY THR VAL SER SER LEU LYS LYS ASN VAL GLY GLN SEQRES 5 A 131 PHE SER GLY PHE PRO PHE GLU LYS GLY SER VAL GLN TYR SEQRES 6 A 131 LYS LYS LYS GLU GLU MET LEU LYS LYS PHE ARG ASN ALA SEQRES 7 A 131 MET LEU LYS SER ILE CYS GLU VAL LEU ASP LEU GLU ARG SEQRES 8 A 131 SER GLY VAL ASN SER GLU LEU VAL LYS ARG ILE LEU ASN SEQRES 9 A 131 PHE LEU MET HIS PRO LYS PRO SER GLY LYS PRO LEU PRO SEQRES 10 A 131 LYS SER LYS LYS THR CYS SER LYS GLY SER LYS LYS GLU SEQRES 11 A 131 ARG HELIX 1 1 ILE A 14 LYS A 23 1 10 HELIX 2 2 LYS A 25 LEU A 36 1 12 HELIX 3 3 VAL A 43 GLN A 52 1 10 HELIX 4 4 SER A 62 VAL A 86 1 25 HELIX 5 5 VAL A 94 PHE A 105 1 12 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