PDB Short entry for 2Y4Q HEADER TRANSPORT PROTEIN 07-JAN-11 2Y4Q TITLE SOLUTION STRUCTURE OF THE EF-HAND DOMAIN OF HUMAN POLYCYSTIN 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYCYSTIN-2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 717-792; COMPND 5 SYNONYM: AUTOSOMAL DOMINANT POLYCYSTIC KIDNEY DISEASE TYPE II COMPND 6 PROTEIN, POLYCYSTIC KIDNEY DISEASE 2 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PRSETA KEYWDS TRANSPORT PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.D.ALLEN,S.QAMAR,R.N.SANDFORD REVDAT 4 24-JAN-18 2Y4Q 1 SOURCE REMARK REVDAT 3 27-AUG-14 2Y4Q 1 JRNL REVDAT 2 16-JUL-14 2Y4Q 1 COMPND SOURCE JRNL REMARK REVDAT 1 21-DEC-11 2Y4Q 0 JRNL AUTH M.D.ALLEN,S.QAMAR,M.K.VADIVELU,R.N.SANDFORD,M.BYCROFT JRNL TITL A HIGH-RESOLUTION STRUCTURE OF THE EF-HAND DOMAIN OF HUMAN JRNL TITL 2 POLYCYSTIN-2. JRNL REF PROTEIN SCI. V. 23 1301 2014 JRNL REFN ISSN 0961-8368 JRNL PMID 24990821 JRNL DOI 10.1002/PRO.2513 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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: NULL REMARK 4 REMARK 4 2Y4Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1290046948. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 95% WATER / 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL 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 : CNS REMARK 210 METHOD USED : ANNEAL.INP REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 25 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : NO VIOLATIONS > 0.25A 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 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: 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 716 -53.16 -130.63 REMARK 500 1 ASP A 763 62.26 -69.49 REMARK 500 1 ASP A 788 -2.09 73.96 REMARK 500 1 ASP A 790 -81.11 -160.28 REMARK 500 2 ASP A 763 62.22 -68.89 REMARK 500 2 LEU A 789 160.58 59.69 REMARK 500 3 SER A 716 -59.83 -161.55 REMARK 500 3 ASP A 763 62.18 -69.31 REMARK 500 3 GLU A 787 75.85 -103.36 REMARK 500 3 ASP A 788 -36.99 178.49 REMARK 500 4 LEU A 717 162.83 55.61 REMARK 500 4 ASP A 763 62.22 -68.11 REMARK 500 4 ASP A 788 68.14 -167.13 REMARK 500 4 LEU A 791 69.63 32.82 REMARK 500 5 ASP A 763 62.42 -67.31 REMARK 500 5 LEU A 789 -84.08 60.40 REMARK 500 5 ASP A 790 -54.77 178.50 REMARK 500 5 LEU A 791 68.16 62.30 REMARK 500 6 SER A 716 -71.01 62.70 REMARK 500 6 ASP A 788 -35.78 -134.75 REMARK 500 7 ASP A 763 62.35 -67.70 REMARK 500 7 ARG A 786 -75.50 -112.92 REMARK 500 7 GLU A 787 176.63 -58.85 REMARK 500 7 ASP A 788 -77.33 -173.34 REMARK 500 8 ASP A 763 62.29 -68.21 REMARK 500 8 GLU A 787 24.41 -150.79 REMARK 500 8 ASP A 790 -78.09 -65.92 REMARK 500 8 LEU A 791 78.95 62.64 REMARK 500 9 SER A 716 -31.56 -164.23 REMARK 500 9 ASP A 763 62.29 -69.40 REMARK 500 9 GLN A 768 28.74 46.92 REMARK 500 9 ASP A 788 -47.29 -161.55 REMARK 500 9 LEU A 789 71.88 -103.95 REMARK 500 9 LEU A 791 87.57 -150.14 REMARK 500 10 ASP A 763 62.21 -68.62 REMARK 500 10 ASP A 788 -36.79 178.07 REMARK 500 11 SER A 716 -171.27 62.75 REMARK 500 11 ASP A 763 62.24 -68.87 REMARK 500 11 ASP A 788 46.09 -159.50 REMARK 500 12 SER A 716 -63.57 70.60 REMARK 500 12 LEU A 717 175.47 90.04 REMARK 500 12 GLN A 768 27.29 49.17 REMARK 500 12 ASP A 788 -38.29 -144.64 REMARK 500 12 LEU A 789 97.03 -41.55 REMARK 500 12 ASP A 790 -45.66 -158.44 REMARK 500 13 SER A 716 -175.33 61.43 REMARK 500 13 ASP A 763 62.24 -69.67 REMARK 500 13 ARG A 786 -80.24 -124.33 REMARK 500 13 GLU A 787 96.59 75.00 REMARK 500 13 LEU A 789 100.09 -160.90 REMARK 500 REMARK 500 THIS ENTRY HAS 87 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 800 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 765 OD1 REMARK 620 2 ASP A 767 OD1 68.2 REMARK 620 3 ASP A 767 OD2 71.2 46.3 REMARK 620 4 ASP A 763 OD2 88.2 68.6 115.0 REMARK 620 5 GLU A 769 O 139.7 72.3 87.6 69.8 REMARK 620 6 ASP A 765 OD2 55.8 91.3 53.4 143.7 134.2 REMARK 620 7 GLU A 774 OE1 132.2 147.1 151.8 84.9 80.6 121.3 REMARK 620 8 GLU A 774 OE2 132.4 137.5 99.5 134.5 83.7 80.7 53.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 800 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17621 RELATED DB: BMRB REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 714 TO 716 WERE PART OF THE TEV CLEAVAGE SITE DBREF 2Y4Q A 717 792 UNP Q13563 PKD2_HUMAN 717 792 SEQADV 2Y4Q GLY A 714 UNP Q13563 EXPRESSION TAG SEQADV 2Y4Q GLY A 715 UNP Q13563 EXPRESSION TAG SEQADV 2Y4Q SER A 716 UNP Q13563 EXPRESSION TAG SEQRES 1 A 79 GLY GLY SER LEU LYS LYS ASN THR VAL ASP ASP ILE SER SEQRES 2 A 79 GLU SER LEU ARG GLN GLY GLY GLY LYS LEU ASN PHE ASP SEQRES 3 A 79 GLU LEU ARG GLN ASP LEU LYS GLY LYS GLY HIS THR ASP SEQRES 4 A 79 ALA GLU ILE GLU ALA ILE PHE THR LYS TYR ASP GLN ASP SEQRES 5 A 79 GLY ASP GLN GLU LEU THR GLU HIS GLU HIS GLN GLN MET SEQRES 6 A 79 ARG ASP ASP LEU GLU LYS GLU ARG GLU ASP LEU ASP LEU SEQRES 7 A 79 ASP HET CA A 800 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ HELIX 1 1 LYS A 718 GLY A 733 1 16 HELIX 2 2 PHE A 738 GLY A 747 1 10 HELIX 3 3 THR A 751 ASP A 763 1 13 HELIX 4 4 GLU A 772 GLU A 787 1 16 SHEET 1 AA 2 LYS A 735 ASN A 737 0 SHEET 2 AA 2 GLU A 769 THR A 771 -1 O LEU A 770 N LEU A 736 LINK CA CA A 800 OD1 ASP A 765 1555 1555 2.32 LINK CA CA A 800 OD1 ASP A 767 1555 1555 2.33 LINK CA CA A 800 OD2 ASP A 767 1555 1555 3.02 LINK CA CA A 800 OD2 ASP A 763 1555 1555 2.42 LINK CA CA A 800 O GLU A 769 1555 1555 2.33 LINK CA CA A 800 OD2 ASP A 765 1555 1555 2.38 LINK CA CA A 800 OE1 GLU A 774 1555 1555 2.32 LINK CA CA A 800 OE2 GLU A 774 1555 1555 2.51 SITE 1 AC1 5 ASP A 763 ASP A 765 ASP A 767 GLU A 769 SITE 2 AC1 5 GLU A 774 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