HEADER MEMBRANE PROTEIN 01-JUL-09 2KLE TITLE ISIC REFINED SOLUTION STRUCTURE OF THE CALCIUM BINDING DOMAIN OF THE TITLE 2 C-TERMINAL CYTOSOLIC DOMAIN OF POLYCYSTIN-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYCYSTIN-2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 680-796; COMPND 5 SYNONYM: POLYCYSTIC KIDNEY DISEASE 2 PROTEIN, AUTOSOMAL DOMINANT COMPND 6 POLYCYSTIC KIDNEY DISEASE TYPE II PROTEIN, POLYCYSTWIN, R48321; COMPND 7 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: PKD2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET41A KEYWDS PC2, PKD2, CALCIUM BINDING DOMAIN, EF HAND, CYTOSOLIC, CALCIUM, KEYWDS 2 COILED COIL, DISEASE MUTATION, GLYCOPROTEIN, ION TRANSPORT, IONIC KEYWDS 3 CHANNEL, MEMBRANE, PHOSPHOPROTEIN, POLYMORPHISM, TRANSMEMBRANE, KEYWDS 4 TRANSPORT, MEMBRANE PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR H.R.KALBITZER REVDAT 4 16-MAR-22 2KLE 1 REMARK SEQADV REVDAT 3 06-OCT-09 2KLE 1 JRNL REVDAT 2 29-SEP-09 2KLE 1 REMARK REVDAT 1 28-JUL-09 2KLE 0 JRNL AUTH F.H.SCHUMANN,H.HOFFMEISTER,M.SCHMIDT,R.BADER,E.BESL, JRNL AUTH 2 R.WITZGALL,H.R.KALBITZER JRNL TITL NMR-ASSIGNMENTS OF A CYTOSOLIC DOMAIN OF THE C-TERMINUS OF JRNL TITL 2 POLYCYSTIN-2 JRNL REF BIOMOL.NMR ASSIGN. V. 3 141 2009 JRNL REFN ISSN 1874-2718 JRNL PMID 19636966 JRNL DOI 10.1007/S12104-009-9160-X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.SCHUMANN,H.HOFFMEISTER,R.BADER,M.SCHMIDT,R.WITZGALL, REMARK 1 AUTH 2 H.R.KALBITZER REMARK 1 TITL CA2+-DEPENDENT CONFORMATIONAL CHANGES IN A C-TERMINAL REMARK 1 TITL 2 CYTOSOLIC DOMAIN OF POLYCYSTIN-2 REMARK 1 REF J.BIOL.CHEM. V. 284 24372 2009 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 19546223 REMARK 1 DOI 10.1074/JBC.M109.025635 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AUREMOL, CNS 1.1, AUREMOL-ISIC REMARK 3 AUTHORS : BRUKER BIOSPIN (AUREMOL), REMARK 3 BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE, REMARK 3 JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON, REMARK 3 WARREN (CNS), BRUNNER, K., GRONWALD, W., TRENNER, REMARK 3 J.M., NEIDIG, K.P., AND KALBITZER, H.R. (AUREMOL- REMARK 3 ISIC) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES WERE FIRST REFINED WITH REMARK 3 AUREMOL-ISUC AND THEN REFINED WITH CNS IN EXPLICIT WATER; REMARK 3 BRUNNER, K., GRONWALD, W., TRENNER, J.M., NEIDIG, K.P., AND REMARK 3 KALBITZER, H.R. (2006) BMC STRUCT. BIOL. 6, 14, FOR WATERRE REMARK 3 FINEMENT; LINGE, J.P., WILLIAMS, M.A., SPRONK, C.A.E.M., BONVIN, REMARK 3 A.M.J.J. & NILGES, M. (2003). REFINEMENT OF PROTEIN STRUCTURES REMARK 3 IN EXPLICIT SOLVENT. PROTEINS: STRUCT. FUNCT. GENET. 50, 496-506 REMARK 3 FOR EXPLICIT WATER REFINEMENT REMARK 4 REMARK 4 2KLE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000101265. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0.51 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5MM [U-100% 13C; U-100% 15N] REMARK 210 POLYCYSTIN-2 POLYPEPTIDE-1, 5MM REMARK 210 CA2+-2, 0.1MM DSS-3, 10MM REMARK 210 POTASSIUM PHOSPHATE BUFFER-4, REMARK 210 500MM NACL-5, 2MM DTE-6, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HNCANNH; 3D HNCO; 2D 15N-TOCSY- REMARK 210 HSQC; 3D HCCH-TOCSY; 2D 1H-1H REMARK 210 NOESY; 3D 1H-15N-NOESY-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.1 REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 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 GLY A 674 REMARK 465 SER A 675 REMARK 465 THR A 676 REMARK 465 ALA A 677 REMARK 465 ILE A 678 REMARK 465 GLY A 679 REMARK 465 ILE A 680 REMARK 465 ASN A 681 REMARK 465 ASP A 682 REMARK 465 THR A 683 REMARK 465 TYR A 684 REMARK 465 SER A 685 REMARK 465 GLU A 686 REMARK 465 VAL A 687 REMARK 465 LYS A 688 REMARK 465 SER A 689 REMARK 465 ASP A 690 REMARK 465 LEU A 691 REMARK 465 ALA A 692 REMARK 465 GLN A 693 REMARK 465 GLN A 694 REMARK 465 LYS A 695 REMARK 465 ALA A 696 REMARK 465 GLU A 697 REMARK 465 MET A 698 REMARK 465 GLU A 699 REMARK 465 LEU A 700 REMARK 465 SER A 701 REMARK 465 ASP A 702 REMARK 465 LEU A 703 REMARK 465 ILE A 704 REMARK 465 ARG A 705 REMARK 465 LYS A 706 REMARK 465 GLY A 707 REMARK 465 TYR A 708 REMARK 465 HIS A 709 REMARK 465 LYS A 710 REMARK 465 ALA A 711 REMARK 465 LEU A 712 REMARK 465 VAL A 713 REMARK 465 LYS A 714 REMARK 465 LEU A 715 REMARK 465 LYS A 716 REMARK 465 LEU A 717 REMARK 465 LYS A 718 REMARK 465 LYS A 719 REMARK 465 ASN A 720 REMARK 465 THR A 721 REMARK 465 VAL A 722 REMARK 465 ASP A 723 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-10 REMARK 470 RES CSSEQI ATOMS REMARK 470 LEU A 796 O 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 ASN A 737 H LEU A 741 1.52 REMARK 500 HG1 THR A 751 OE1 GLU A 754 1.59 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 1 ASN A 737 C ASN A 737 O -0.205 REMARK 500 1 ARG A 742 C ARG A 742 O -0.152 REMARK 500 2 ASN A 737 C ASN A 737 O -0.206 REMARK 500 2 ARG A 742 C ARG A 742 O -0.167 REMARK 500 3 ASN A 737 C ASN A 737 O -0.207 REMARK 500 3 ARG A 742 C ARG A 742 O -0.155 REMARK 500 4 ASN A 737 C ASN A 737 O -0.199 REMARK 500 4 ARG A 742 C ARG A 742 O -0.147 REMARK 500 5 ASN A 737 C ASN A 737 O -0.210 REMARK 500 5 ARG A 742 C ARG A 742 O -0.157 REMARK 500 6 ASN A 737 C ASN A 737 O -0.209 REMARK 500 6 ARG A 742 C ARG A 742 O -0.157 REMARK 500 7 ASN A 737 C ASN A 737 O -0.210 REMARK 500 7 ARG A 742 C ARG A 742 O -0.158 REMARK 500 8 ASN A 737 C ASN A 737 O -0.209 REMARK 500 8 ARG A 742 C ARG A 742 O -0.159 REMARK 500 9 ASN A 737 C ASN A 737 O -0.201 REMARK 500 9 ARG A 742 C ARG A 742 O -0.157 REMARK 500 10 ASN A 737 C ASN A 737 O -0.215 REMARK 500 10 ARG A 742 C ARG A 742 O -0.162 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 SER A 728 -73.54 -49.64 REMARK 500 1 LEU A 729 -72.52 171.82 REMARK 500 1 LYS A 746 105.64 -59.46 REMARK 500 1 LYS A 748 -38.07 -156.12 REMARK 500 1 HIS A 750 -76.38 -90.89 REMARK 500 1 ASP A 767 -63.32 -104.48 REMARK 500 1 GLN A 768 82.22 39.49 REMARK 500 1 GLU A 769 19.74 156.98 REMARK 500 1 MET A 778 -82.68 -78.01 REMARK 500 1 GLU A 785 142.71 -174.48 REMARK 500 1 ASP A 792 -76.25 -159.31 REMARK 500 1 SER A 794 40.19 -168.80 REMARK 500 2 GLU A 727 -94.46 -121.17 REMARK 500 2 SER A 728 -72.56 -58.42 REMARK 500 2 LEU A 729 -81.06 173.33 REMARK 500 2 LYS A 748 -33.57 -171.88 REMARK 500 2 HIS A 750 -78.37 -86.44 REMARK 500 2 GLN A 768 84.83 40.63 REMARK 500 2 GLU A 769 21.31 155.75 REMARK 500 2 MET A 778 -85.92 -80.24 REMARK 500 2 ASP A 792 -75.83 -156.33 REMARK 500 2 SER A 794 30.81 -166.69 REMARK 500 3 SER A 728 -73.13 -56.63 REMARK 500 3 LEU A 729 -89.32 -173.54 REMARK 500 3 LYS A 748 -28.47 -168.91 REMARK 500 3 HIS A 750 -75.80 -84.88 REMARK 500 3 ASP A 767 -60.00 -104.08 REMARK 500 3 GLN A 768 83.08 39.35 REMARK 500 3 GLU A 769 18.36 156.54 REMARK 500 3 ARG A 779 159.78 97.83 REMARK 500 3 ASP A 792 -64.57 -149.68 REMARK 500 3 HIS A 793 -132.05 -136.54 REMARK 500 3 SER A 794 51.56 -159.31 REMARK 500 4 GLU A 727 175.92 62.62 REMARK 500 4 SER A 728 -71.81 -57.32 REMARK 500 4 LEU A 729 -86.02 170.98 REMARK 500 4 LYS A 746 103.53 -55.56 REMARK 500 4 LYS A 748 -31.57 -152.42 REMARK 500 4 HIS A 750 -78.62 -89.55 REMARK 500 4 GLN A 768 87.30 41.15 REMARK 500 4 GLU A 769 15.79 155.80 REMARK 500 4 MET A 778 -84.43 -83.95 REMARK 500 4 GLU A 785 134.90 -171.46 REMARK 500 4 LEU A 791 -62.96 -109.21 REMARK 500 4 ASP A 792 -76.76 -131.56 REMARK 500 4 SER A 794 29.54 -167.30 REMARK 500 5 LEU A 729 -97.70 -177.36 REMARK 500 5 LYS A 748 -40.93 -162.70 REMARK 500 5 HIS A 750 -73.22 -93.33 REMARK 500 5 ASP A 767 -63.91 -103.03 REMARK 500 REMARK 500 THIS ENTRY HAS 111 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 779 0.08 SIDE CHAIN REMARK 500 2 ARG A 779 0.08 SIDE CHAIN REMARK 500 5 ARG A 742 0.07 SIDE CHAIN REMARK 500 5 ARG A 779 0.08 SIDE CHAIN REMARK 500 8 ARG A 779 0.10 SIDE CHAIN REMARK 500 9 ARG A 779 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KLD RELATED DB: PDB REMARK 900 THE SAME STRUCTURE REFINED BY ANOTHER REFINEMENT METHOD DBREF 2KLE A 680 796 UNP Q13563 PKD2_HUMAN 680 796 SEQADV 2KLE GLY A 674 UNP Q13563 EXPRESSION TAG SEQADV 2KLE SER A 675 UNP Q13563 EXPRESSION TAG SEQADV 2KLE THR A 676 UNP Q13563 EXPRESSION TAG SEQADV 2KLE ALA A 677 UNP Q13563 EXPRESSION TAG SEQADV 2KLE ILE A 678 UNP Q13563 EXPRESSION TAG SEQADV 2KLE GLY A 679 UNP Q13563 EXPRESSION TAG SEQRES 1 A 123 GLY SER THR ALA ILE GLY ILE ASN ASP THR TYR SER GLU SEQRES 2 A 123 VAL LYS SER ASP LEU ALA GLN GLN LYS ALA GLU MET GLU SEQRES 3 A 123 LEU SER ASP LEU ILE ARG LYS GLY TYR HIS LYS ALA LEU SEQRES 4 A 123 VAL LYS LEU LYS LEU LYS LYS ASN THR VAL ASP ASP ILE SEQRES 5 A 123 SER GLU SER LEU ARG GLN GLY GLY GLY LYS LEU ASN PHE SEQRES 6 A 123 ASP GLU LEU ARG GLN ASP LEU LYS GLY LYS GLY HIS THR SEQRES 7 A 123 ASP ALA GLU ILE GLU ALA ILE PHE THR LYS TYR ASP GLN SEQRES 8 A 123 ASP GLY ASP GLN GLU LEU THR GLU HIS GLU HIS GLN GLN SEQRES 9 A 123 MET ARG ASP ASP LEU GLU LYS GLU ARG GLU ASP LEU ASP SEQRES 10 A 123 LEU ASP HIS SER SER LEU HELIX 1 1 PHE A 738 LYS A 746 1 9 HELIX 2 2 THR A 751 ASP A 763 1 13 HELIX 3 3 THR A 771 MET A 778 1 8 HELIX 4 4 ASP A 781 GLU A 785 5 5 SHEET 1 A 2 LEU A 736 ASN A 737 0 SHEET 2 A 2 GLU A 769 LEU A 770 -1 O LEU A 770 N LEU A 736 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