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, HOMOLOGOUS KEYWDS 2 RECOMBINATION, MISMATCH REPAIR, SMALL MUTS RELATED, NUCLEOTIDE- KEYWDS 3 BINDING, ATP-BINDING, UBL CONJUGATION, PHOSPHORYLATION, SMR, B3BP, KEYWDS 4 HYDROLASE, CYTOPLASM, COILED 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 4 15-MAY-24 2VKC 1 ATOM 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 DNA- BINDING JRNL TITL 2 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, RICE, REMARK 3 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 18-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1290034814. 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 REMARK 210 PRESSURE : 1.0 ATM 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- NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ 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 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 1-28 REMARK 465 RES C SSSEQI REMARK 465 MET A 1636 REMARK 465 GLY A 1637 REMARK 465 SER A 1638 REMARK 465 SER A 1639 REMARK 465 HIS A 1640 REMARK 465 HIS A 1641 REMARK 465 HIS A 1642 REMARK 465 HIS A 1643 REMARK 465 HIS A 1644 REMARK 465 HIS A 1645 REMARK 465 SER A 1646 REMARK 465 SER A 1647 REMARK 465 HIS A 1648 REMARK 465 MET A 1649 REMARK 465 LEU A 1650 REMARK 465 VAL A 1651 REMARK 465 PRO A 1652 REMARK 465 ARG A 1653 REMARK 465 GLY A 1654 REMARK 465 SER A 1655 REMARK 465 LEU A 1656 REMARK 465 GLN A 1657 REMARK 465 GLN A 1658 REMARK 465 GLY A 1659 REMARK 465 THR A 1660 REMARK 465 LEU A 1661 REMARK 465 HIS A 1662 REMARK 465 GLU A 1663 REMARK 465 GLN A 1664 REMARK 465 LYS A 1665 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 HZ3 LYS A 1743 OE2 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 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 LEU A1693 45.38 -143.53 REMARK 500 1 HIS A1734 -60.71 168.96 REMARK 500 1 ILE A1760 -72.96 -71.68 REMARK 500 1 LYS A1761 -154.41 -150.88 REMARK 500 1 PRO A1762 99.88 -48.71 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 2 PRO A1762 67.27 -11.25 REMARK 500 3 PRO A1723 26.53 -75.27 REMARK 500 3 ARG A1731 -167.10 76.16 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 3 PRO A1762 53.16 -9.51 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 4 PRO A1762 88.53 -22.15 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 5 PRO A1762 73.37 -23.74 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 6 PRO A1762 48.58 -3.70 REMARK 500 7 ASN A1689 47.30 80.81 REMARK 500 7 LEU A1693 43.26 -159.42 REMARK 500 7 ARG A1731 -39.70 74.91 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 7 PRO A1762 84.06 -30.02 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 REMARK 500 THIS ENTRY HAS 166 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 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 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