HEADER HYDROLASE 18-DEC-07 2VKC TITLE SOLUTION STRUCTURE OF THE B3BP SMR DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEDD4-BINDING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1666-1770; COMPND 5 SYNONYM: N4BP2, BCL-3-BINDING PROTEIN, B3BP SMR DOMAIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HUMAN BCL3 BINDING PROTEIN, ALTERNATIVE SPLICING, KEYWDS 2 HOMOLOGOUS RECOMBINATION, MISMATCH REPAIR, SMALL MUTS KEYWDS 3 RELATED, NUCLEOTIDE-BINDING, ATP-BINDING, UBL CONJUGATION, KEYWDS 4 PHOSPHORYLATION, SMR, B3BP, HYDROLASE, CYTOPLASM, COILED KEYWDS 5 COIL EXPDTA SOLUTION NMR NUMMDL 28 AUTHOR T.DIERCKS,E.AB,M.A.DANIELS,R.N.DEJONG,R.BESSELING,R.KAPTEIN, AUTHOR 2 G.E.FOLKERS REVDAT 3 24-MAR-09 2VKC 1 ATOM REVDAT 2 24-FEB-09 2VKC 1 VERSN REVDAT 1 14-OCT-08 2VKC 0 JRNL AUTH T.DIERCKS,E.AB,M.A.DANIELS,R.N.DE JONG,R.BESSELING, JRNL AUTH 2 R.KAPTEIN,G.E.FOLKERS JRNL TITL SOLUTION STRUCTURE AND CHARACTERIZATION OF THE JRNL TITL 2 DNA- BINDING ACTIVITY OF THE B3BP-SMR DOMAIN. JRNL REF J.MOL.BIOL. V. 383 1156 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18804481 JRNL DOI 10.1016/J.JMB.2008.09.005 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- REMARK 3 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, REMARK 3 RICE,SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RECORD PROTOCOL REMARK 4 REMARK 4 2VKC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-DEC-07. REMARK 100 THE PDBE ID CODE IS EBI-34814. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308.0 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 200 MM REMARK 210 PRESSURE : 1.0 REMARK 210 SAMPLE CONTENTS : 95% WATER/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HCH-NOESY; HNH-NOESY;CNH- REMARK 210 NOESY; 2D-NON-NOESY; 2D- REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA REMARK 210 METHOD USED : CANDID,PROXIES REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 250 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 28 REMARK 210 CONFORMERS, SELECTION CRITERIA : QUALITY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NONE 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 HZ3 LYS A 1743 - OE1 GLU A 1759 1.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 26 PRO A1762 C - N - CA ANGL. DEV. = 9.3 DEGREES 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 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 LEU A1693 45.38 -143.53 REMARK 500 1 HIS A1734 -60.71 168.96 REMARK 500 1 ILE A1760 -72.96 -71.69 REMARK 500 1 LYS A1761 -154.41 -150.88 REMARK 500 2 ASN A1689 52.78 74.67 REMARK 500 2 LEU A1693 39.52 -149.20 REMARK 500 2 HIS A1734 -59.87 -173.40 REMARK 500 2 ILE A1760 -73.13 -78.71 REMARK 500 2 LYS A1761 -146.52 -163.20 REMARK 500 3 PRO A1723 26.53 -75.27 REMARK 500 3 HIS A1734 -74.24 -154.79 REMARK 500 3 SER A1735 -77.65 -131.00 REMARK 500 3 VAL A1739 32.46 -89.39 REMARK 500 3 LYS A1761 -145.47 178.78 REMARK 500 4 ASN A1689 61.33 64.14 REMARK 500 4 LEU A1693 41.25 -158.54 REMARK 500 4 SER A1735 -161.82 -171.03 REMARK 500 4 LYS A1761 -145.25 -178.65 REMARK 500 5 ASN A1689 73.36 59.30 REMARK 500 5 LEU A1693 40.07 -142.28 REMARK 500 5 ASN A1733 106.97 -19.80 REMARK 500 5 HIS A1734 -49.91 108.52 REMARK 500 5 SER A1735 -47.44 171.95 REMARK 500 5 VAL A1739 -73.02 67.10 REMARK 500 5 ALA A1740 77.54 47.38 REMARK 500 5 ILE A1760 -71.47 -89.84 REMARK 500 5 LYS A1761 -147.67 -151.50 REMARK 500 6 PRO A1723 23.48 -74.02 REMARK 500 6 ARG A1741 -40.04 68.60 REMARK 500 6 LYS A1761 -146.37 172.37 REMARK 500 7 ASN A1689 47.30 80.81 REMARK 500 7 LEU A1693 43.26 -159.42 REMARK 500 7 SER A1735 41.68 -154.27 REMARK 500 7 VAL A1739 -70.77 -99.78 REMARK 500 7 ALA A1740 73.61 12.93 REMARK 500 7 ILE A1760 -77.44 -87.90 REMARK 500 7 LYS A1761 -148.11 -153.55 REMARK 500 8 PRO A1723 20.40 -74.65 REMARK 500 8 SER A1735 -158.09 -117.37 REMARK 500 8 VAL A1739 -67.43 -95.97 REMARK 500 8 ALA A1740 73.48 53.13 REMARK 500 8 SER A1754 61.78 61.00 REMARK 500 8 LYS A1761 -149.21 -171.51 REMARK 500 9 HIS A1734 -74.04 -123.91 REMARK 500 9 ILE A1760 -71.37 -76.66 REMARK 500 9 LYS A1761 -148.35 -169.53 REMARK 500 10 LEU A1693 43.23 -149.26 REMARK 500 10 HIS A1734 -50.81 -155.93 REMARK 500 10 LYS A1761 -146.23 174.23 REMARK 500 11 LEU A1693 34.40 -153.25 REMARK 500 11 HIS A1734 -48.53 -167.29 REMARK 500 11 SER A1735 -64.70 -174.82 REMARK 500 11 LYS A1761 -145.05 178.57 REMARK 500 12 SER A1735 -34.24 -175.67 REMARK 500 12 VAL A1739 72.47 55.38 REMARK 500 12 ALA A1740 68.62 -102.23 REMARK 500 12 ILE A1760 -75.24 -66.31 REMARK 500 12 LYS A1761 -147.82 -156.42 REMARK 500 13 VAL A1739 92.43 67.53 REMARK 500 13 ILE A1760 -73.67 -74.96 REMARK 500 13 LYS A1761 -147.65 -154.12 REMARK 500 14 ASN A1733 105.63 -43.27 REMARK 500 14 HIS A1734 -81.76 31.49 REMARK 500 14 LYS A1761 -147.42 -174.02 REMARK 500 15 LEU A1693 36.93 -150.21 REMARK 500 15 HIS A1734 -57.81 -163.49 REMARK 500 15 SER A1735 -31.00 -135.23 REMARK 500 15 ALA A1740 2.10 59.51 REMARK 500 15 ILE A1760 -78.78 -76.91 REMARK 500 15 LYS A1761 -147.73 -153.87 REMARK 500 16 LEU A1693 36.69 -141.06 REMARK 500 16 PRO A1723 21.74 -76.27 REMARK 500 16 HIS A1734 -37.75 96.73 REMARK 500 16 LYS A1761 -144.76 174.80 REMARK 500 17 HIS A1734 -66.84 -177.38 REMARK 500 17 LYS A1761 -144.70 -174.64 REMARK 500 18 PRO A1723 20.66 -78.76 REMARK 500 18 ASN A1733 123.04 -23.84 REMARK 500 18 ALA A1740 63.52 26.71 REMARK 500 18 ILE A1760 -72.68 -68.45 REMARK 500 18 LYS A1761 -147.42 -170.04 REMARK 500 19 LEU A1693 35.81 -153.77 REMARK 500 19 HIS A1734 -68.87 -170.57 REMARK 500 19 SER A1735 28.26 -145.86 REMARK 500 19 LYS A1761 -144.69 178.21 REMARK 500 20 LEU A1693 41.87 -140.88 REMARK 500 20 ASN A1733 106.48 -51.35 REMARK 500 20 ARG A1741 -42.62 75.76 REMARK 500 20 ILE A1760 -72.97 -67.34 REMARK 500 20 LYS A1761 -151.25 -158.85 REMARK 500 21 PRO A1687 6.44 -67.95 REMARK 500 21 LEU A1693 36.18 -142.69 REMARK 500 21 ASN A1733 111.61 -31.94 REMARK 500 21 HIS A1734 -82.87 64.26 REMARK 500 21 SER A1735 95.61 -161.09 REMARK 500 21 LYS A1761 -145.63 -174.65 REMARK 500 22 ASN A1689 49.51 70.19 REMARK 500 22 LEU A1693 35.27 -145.48 REMARK 500 22 ILE A1760 -76.04 -78.53 REMARK 500 22 LYS A1761 -147.98 -153.74 REMARK 500 23 ASN A1733 151.52 -45.87 REMARK 500 23 SER A1735 -170.27 -173.92 REMARK 500 23 LYS A1761 -148.92 -160.56 REMARK 500 24 ASN A1689 34.55 71.58 REMARK 500 24 LEU A1693 23.25 -140.95 REMARK 500 24 HIS A1734 -69.05 57.16 REMARK 500 24 SER A1735 16.68 -177.11 REMARK 500 24 ILE A1760 -73.44 -83.71 REMARK 500 24 LYS A1761 -148.82 -153.54 REMARK 500 25 LYS A1667 3.60 -69.62 REMARK 500 25 PRO A1723 22.84 -76.83 REMARK 500 25 LYS A1761 -146.89 -171.17 REMARK 500 26 SER A1735 -69.76 -171.07 REMARK 500 26 VAL A1739 -71.29 -81.89 REMARK 500 26 ALA A1740 80.96 41.48 REMARK 500 26 ILE A1760 -74.96 -78.26 REMARK 500 26 LYS A1761 -152.64 -155.59 REMARK 500 27 ASN A1733 105.25 -21.22 REMARK 500 27 HIS A1734 -92.45 41.17 REMARK 500 27 VAL A1739 -76.91 -76.91 REMARK 500 27 ALA A1740 74.24 22.51 REMARK 500 27 LYS A1761 -148.26 172.23 REMARK 500 28 ASN A1733 103.20 -23.08 REMARK 500 28 ALA A1740 74.79 59.29 REMARK 500 28 LYS A1761 -146.61 -168.66 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 A1707 0.09 SIDE CHAIN REMARK 500 3 ARG A1707 0.11 SIDE CHAIN REMARK 500 4 ARG A1707 0.08 SIDE CHAIN REMARK 500 5 ARG A1731 0.07 SIDE CHAIN REMARK 500 9 ARG A1707 0.10 SIDE CHAIN REMARK 500 18 ARG A1707 0.08 SIDE CHAIN REMARK 500 19 ARG A1707 0.07 SIDE CHAIN REMARK 500 22 ARG A1707 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2D9I RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE SMR DOMAIN OF REMARK 900 NEDD4-BINDINGPROTEIN 2 DBREF 2VKC A 1666 1770 UNP Q86UW6 N4BP2_HUMAN 1666 1770 SEQRES 1 A 135 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER HIS SEQRES 2 A 135 MET LEU VAL PRO ARG GLY SER LEU GLN GLN GLY THR LEU SEQRES 3 A 135 HIS GLU GLN LYS MET LYS GLU ALA ASN HIS LEU ALA ALA SEQRES 4 A 135 ILE GLU ILE PHE GLU LYS VAL ASN ALA SER LEU LEU PRO SEQRES 5 A 135 GLN ASN VAL LEU ASP LEU HIS GLY LEU HIS VAL ASP GLU SEQRES 6 A 135 ALA LEU GLU HIS LEU MET ARG VAL LEU GLU LYS LYS THR SEQRES 7 A 135 GLU GLU PHE LYS GLN ASN GLY GLY LYS PRO TYR LEU SER SEQRES 8 A 135 VAL ILE THR GLY ARG GLY ASN HIS SER GLN GLY GLY VAL SEQRES 9 A 135 ALA ARG ILE LYS PRO ALA VAL ILE LYS TYR LEU ILE SER SEQRES 10 A 135 HIS SER PHE ARG PHE SER GLU ILE LYS PRO GLY CYS LEU SEQRES 11 A 135 LYS VAL MET LEU LYS HELIX 1 1 GLU A 1668 LEU A 1686 1 19 HELIX 2 2 HIS A 1697 GLN A 1718 1 22 HELIX 3 3 ARG A 1741 SER A 1752 1 12 SHEET 1 AA 4 VAL A1690 ASP A1692 0 SHEET 2 AA 4 TYR A1724 ILE A1728 1 O SER A1726 N LEU A1691 SHEET 3 AA 4 CYS A1764 MET A1768 -1 O LEU A1765 N VAL A1727 SHEET 4 AA 4 ARG A1756 GLU A1759 -1 O ARG A1756 N MET A1768 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