HEADER DNA BINDING PROTEIN 15-DEC-03 1RW2 TITLE THREE-DIMENSIONAL STRUCTURE OF KU80 CTD COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT DNA HELICASE II, 80 KDA SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KU80 C-TERMINAL DOMAIN; COMPND 5 SYNONYM: LUPUS KU AUTOANTIGEN PROTEIN P86, KU86, KU80, 86 KDA SUBUNIT COMPND 6 OF KU ANTIGEN, THYROID- LUPUS AUTOANTIGEN, TLAA, CTC BOX BINDING COMPND 7 FACTOR 85 KDA SUBUNIT, CTCBF, CTC85, NUCLEAR FACTOR IV, DNA-REPAIR COMPND 8 PROTEIN XRCC5; COMPND 9 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: KU80 (566-710); 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: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS KU80, NHEJ, DNA-PK, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Z.ZHANG,W.HU,L.CANO,T.D.LEE,D.J.CHEN,Y.CHEN REVDAT 4 02-MAR-22 1RW2 1 REMARK SEQADV REVDAT 3 24-FEB-09 1RW2 1 VERSN REVDAT 2 18-MAY-04 1RW2 1 AUTHOR JRNL REVDAT 1 30-DEC-03 1RW2 0 JRNL AUTH Z.ZHANG,W.HU,L.CANO,T.D.LEE,D.J.CHEN,Y.CHEN JRNL TITL SOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF KU80 SUGGESTS JRNL TITL 2 IMPORTANT SITES FOR PROTEIN-PROTEIN INTERACTIONS. JRNL REF STRUCTURE V. 12 495 2004 JRNL REFN ISSN 0969-2126 JRNL PMID 15016365 JRNL DOI 10.1016/J.STR.2004.02.007 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1, ARIA 1.2 REMARK 3 AUTHORS : VARIAN (VNMR), JENS LINGE, MICHAEL NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 2449 RESTRAINTS, 2180 ARE REMARK 3 NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 201 DIHEDRAL ANGLE RESTRAINTS,68 RESIDUE REMARK 3 DIPOLAR COUPLING REMARK 4 REMARK 4 1RW2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000021079. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 100 MM PHOSPHATE BUFFER REMARK 210 PRESSURE : 1 ATMOSPHERE REMARK 210 SAMPLE CONTENTS : APPROXIMATELY 1 MM N-15/C-13 REMARK 210 LABELED PROTEIN IN 100 MM REMARK 210 PHOSPHATE BUFFER, PH 6.0, AND 5 REMARK 210 MM DTT; APPROXIMATELY 1 MM N-15/ REMARK 210 C-13 LABELED PROTEIN IN 100 MM REMARK 210 PHOSPHATE BUFFER, PH 6.0, AND 5 REMARK 210 MM DTT; APPROXIMATELY 1 MM N-15 REMARK 210 LABELED PROTEIN IN 100 MM REMARK 210 PHOSPHATE BUFFER, PH 6.0, AN REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; HCCH REMARK 210 -TOCSY; HNCACB, C(CO)NH, HNCO, REMARK 210 HN(CA)CO, H(CCO)NH, HBHA(CO)NH; REMARK 210 3D_15N-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 98, 2000, DIANA 1.5 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,TARGET REMARK 210 FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 2 PHE A 74 CE1 PHE A 74 CZ 0.193 REMARK 500 2 PHE A 74 CZ PHE A 74 CE2 -0.166 REMARK 500 2 PHE A 100 CE1 PHE A 100 CZ 0.180 REMARK 500 2 PHE A 100 CZ PHE A 100 CE2 -0.164 REMARK 500 3 PHE A 74 CE1 PHE A 74 CZ 0.198 REMARK 500 3 PHE A 74 CZ PHE A 74 CE2 -0.172 REMARK 500 3 PHE A 84 CE1 PHE A 84 CZ 0.118 REMARK 500 4 PHE A 74 CE1 PHE A 74 CZ 0.208 REMARK 500 4 PHE A 74 CZ PHE A 74 CE2 -0.180 REMARK 500 6 PHE A 100 CZ PHE A 100 CE2 0.127 REMARK 500 7 PHE A 74 CE1 PHE A 74 CZ 0.238 REMARK 500 7 PHE A 74 CZ PHE A 74 CE2 -0.208 REMARK 500 8 PHE A 74 CE1 PHE A 74 CZ 0.200 REMARK 500 8 PHE A 74 CZ PHE A 74 CE2 -0.173 REMARK 500 9 PHE A 74 CE1 PHE A 74 CZ 0.194 REMARK 500 9 PHE A 74 CZ PHE A 74 CE2 -0.166 REMARK 500 9 PHE A 100 CE1 PHE A 100 CZ 0.171 REMARK 500 9 PHE A 100 CZ PHE A 100 CE2 -0.146 REMARK 500 9 PHE A 146 CE1 PHE A 146 CZ 0.187 REMARK 500 9 PHE A 146 CZ PHE A 146 CE2 -0.168 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 HIS A 5 -170.29 59.05 REMARK 500 1 LYS A 8 98.75 58.93 REMARK 500 1 GLN A 13 -87.72 58.41 REMARK 500 1 PHE A 18 -165.07 -170.04 REMARK 500 1 SER A 21 -85.16 60.90 REMARK 500 1 LEU A 23 -67.86 -92.76 REMARK 500 1 GLU A 25 -73.99 -97.29 REMARK 500 1 SER A 27 -78.65 -71.62 REMARK 500 1 VAL A 28 -92.47 50.92 REMARK 500 1 VAL A 31 130.38 65.36 REMARK 500 1 VAL A 34 172.10 50.74 REMARK 500 1 ASN A 35 107.84 61.34 REMARK 500 1 LYS A 48 -72.66 -46.10 REMARK 500 1 THR A 68 -177.60 -66.59 REMARK 500 1 LYS A 111 -157.62 -107.59 REMARK 500 1 GLN A 112 -122.68 -91.66 REMARK 500 1 ILE A 125 50.82 -104.35 REMARK 500 1 LEU A 127 167.15 53.80 REMARK 500 1 GLU A 131 53.13 170.66 REMARK 500 1 LYS A 150 -160.03 -121.75 REMARK 500 1 ASP A 151 -166.05 47.59 REMARK 500 2 HIS A 2 -158.71 -80.65 REMARK 500 2 LYS A 10 -39.17 -145.30 REMARK 500 2 GLU A 12 30.61 -145.47 REMARK 500 2 GLN A 13 148.39 65.31 REMARK 500 2 HIS A 17 107.84 64.77 REMARK 500 2 SER A 21 -58.49 -125.70 REMARK 500 2 SER A 22 13.97 59.60 REMARK 500 2 SER A 33 -1.97 -161.70 REMARK 500 2 LYS A 48 -156.32 -64.11 REMARK 500 2 ALA A 49 167.62 -48.55 REMARK 500 2 THR A 68 -178.71 -65.38 REMARK 500 2 SER A 92 77.51 45.02 REMARK 500 2 LYS A 111 -164.36 -108.48 REMARK 500 2 GLN A 112 51.47 -101.72 REMARK 500 2 ILE A 125 61.14 -115.18 REMARK 500 2 LEU A 127 -166.03 35.54 REMARK 500 2 LYS A 130 -56.16 168.23 REMARK 500 2 GLU A 131 -80.05 176.88 REMARK 500 2 ALA A 133 -152.69 -85.24 REMARK 500 2 SER A 136 -179.30 57.38 REMARK 500 3 HIS A 7 -14.71 -164.87 REMARK 500 3 LYS A 8 106.13 63.16 REMARK 500 3 HIS A 17 -11.88 -140.46 REMARK 500 3 GLU A 25 -36.37 -152.61 REMARK 500 3 SER A 27 -71.45 -150.61 REMARK 500 3 VAL A 28 176.84 52.99 REMARK 500 3 SER A 33 -173.65 -172.26 REMARK 500 3 VAL A 34 -152.56 40.36 REMARK 500 3 LYS A 48 -82.05 -46.34 REMARK 500 REMARK 500 THIS ENTRY HAS 204 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1RW2 A 8 152 UNP P13010 KU86_HUMAN 565 709 SEQADV 1RW2 MET A 1 UNP P13010 CLONING ARTIFACT SEQADV 1RW2 HIS A 2 UNP P13010 EXPRESSION TAG SEQADV 1RW2 HIS A 3 UNP P13010 EXPRESSION TAG SEQADV 1RW2 HIS A 4 UNP P13010 EXPRESSION TAG SEQADV 1RW2 HIS A 5 UNP P13010 EXPRESSION TAG SEQADV 1RW2 HIS A 6 UNP P13010 EXPRESSION TAG SEQADV 1RW2 HIS A 7 UNP P13010 EXPRESSION TAG SEQRES 1 A 152 MET HIS HIS HIS HIS HIS HIS LYS LEU LYS THR GLU GLN SEQRES 2 A 152 GLY GLY ALA HIS PHE SER VAL SER SER LEU ALA GLU GLY SEQRES 3 A 152 SER VAL THR SER VAL GLY SER VAL ASN PRO ALA GLU ASN SEQRES 4 A 152 PHE ARG VAL LEU VAL LYS GLN LYS LYS ALA SER PHE GLU SEQRES 5 A 152 GLU ALA SER ASN GLN LEU ILE ASN HIS ILE GLU GLN PHE SEQRES 6 A 152 LEU ASP THR ASN GLU THR PRO TYR PHE MET LYS SER ILE SEQRES 7 A 152 ASP CYS ILE ARG ALA PHE ARG GLU GLU ALA ILE LYS PHE SEQRES 8 A 152 SER GLU GLU GLN ARG PHE ASN ASN PHE LEU LYS ALA LEU SEQRES 9 A 152 GLN GLU LYS VAL GLU ILE LYS GLN LEU ASN HIS PHE TRP SEQRES 10 A 152 GLU ILE VAL VAL GLN ASP GLY ILE THR LEU ILE THR LYS SEQRES 11 A 152 GLU GLU ALA SER GLY SER SER VAL THR ALA GLU GLU ALA SEQRES 12 A 152 LYS LYS PHE LEU ALA PRO LYS ASP LYS HELIX 1 1 ALA A 37 GLN A 46 1 10 HELIX 2 2 SER A 50 THR A 68 1 19 HELIX 3 3 THR A 71 SER A 92 1 22 HELIX 4 4 GLU A 94 LYS A 111 1 18 HELIX 5 5 LEU A 113 GLY A 124 1 12 HELIX 6 6 ALA A 140 LEU A 147 1 8 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