HEADER TRANSPORT PROTEIN, RNA BINDING PROTEIN 24-MAY-05 2CTK TITLE SOLUTION STRUCTURE OF THE 12TH KH TYPE I DOMAIN FROM HUMAN VIGILIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: VIGILIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KH DOMAIN; COMPND 5 SYNONYM: HIGH DENSITY LIPOPROTEIN-BINDING PROTEIN, HDL-BINDING COMPND 6 PROTEIN; 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: HDLBP; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P050131-01; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS K HOMOLOGY TYPE I DOMAIN, RNA-BINDING, CELL STEROL METABOLISM, BETA- KEYWDS 2 ALPHA-ALPHA-BETA-BETA-ALPHA STRUCTURE, STRUCTURAL GENOMICS, NPPSFA, KEYWDS 3 NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, KEYWDS 4 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, TRANSPORT KEYWDS 5 PROTEIN, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.TOMIZAWA,T.KIGAWA,S.KOSHIBA,M.INOUE,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2CTK 1 REMARK SEQADV REVDAT 2 24-FEB-09 2CTK 1 VERSN REVDAT 1 24-NOV-05 2CTK 0 JRNL AUTH T.TOMIZAWA,T.KIGAWA,S.KOSHIBA,M.INOUE,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE 12TH KH TYPE I DOMAIN FROM HUMAN JRNL TITL 2 VIGILIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, CYANA 2.0.17 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2CTK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000024604. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.28MM KH DOMAIN U-15N, 13C; REMARK 210 20MM D-TRIS-HCL(PH 7.0); 100MM REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3; 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20030801, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9295, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 RESTRAINTED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION, STRUCTURES WITH REMARK 210 THE LOWEST ENERGY, STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS 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 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 PRO A 16 -178.93 -69.76 REMARK 500 1 ARG A 29 -35.63 -39.85 REMARK 500 1 ALA A 68 -34.08 -39.87 REMARK 500 1 ARG A 95 75.77 -66.61 REMARK 500 1 PHE A 97 99.72 -45.95 REMARK 500 2 SER A 2 78.49 -69.80 REMARK 500 2 LEU A 11 -176.28 -171.70 REMARK 500 2 GLU A 12 112.51 -165.17 REMARK 500 2 SER A 37 -62.66 -96.68 REMARK 500 2 GLU A 88 -70.07 -90.27 REMARK 500 3 ALA A 10 107.49 -170.50 REMARK 500 3 ALA A 68 -36.49 -36.65 REMARK 500 3 ARG A 95 138.66 -36.34 REMARK 500 3 SER A 96 85.03 -66.04 REMARK 500 3 PHE A 97 141.50 -36.68 REMARK 500 3 LYS A 98 108.43 -167.76 REMARK 500 3 SER A 102 41.52 38.64 REMARK 500 4 ALA A 68 -36.39 -36.63 REMARK 500 4 LEU A 94 -38.55 -37.86 REMARK 500 5 ALA A 10 119.09 -164.36 REMARK 500 6 PRO A 16 -179.20 -69.70 REMARK 500 6 ARG A 29 -38.30 -39.42 REMARK 500 6 PHE A 97 155.00 -45.90 REMARK 500 7 SER A 2 125.86 -173.10 REMARK 500 7 ALA A 10 108.24 -171.56 REMARK 500 7 GLN A 34 179.18 -49.98 REMARK 500 7 LYS A 35 89.39 -46.69 REMARK 500 7 GLU A 47 53.86 36.83 REMARK 500 7 GLU A 88 -65.57 -92.78 REMARK 500 7 SER A 99 96.07 -53.30 REMARK 500 8 ALA A 13 142.34 -170.38 REMARK 500 8 ALA A 68 -34.90 -36.16 REMARK 500 9 SER A 2 111.14 -161.01 REMARK 500 9 GLU A 9 136.91 -170.63 REMARK 500 9 ALA A 10 115.39 -161.45 REMARK 500 9 LYS A 35 50.13 38.40 REMARK 500 9 PHE A 97 136.86 -39.00 REMARK 500 9 PRO A 101 2.20 -69.77 REMARK 500 10 ALA A 10 120.16 -175.01 REMARK 500 10 PRO A 16 -178.17 -69.73 REMARK 500 10 LYS A 35 -53.50 -126.03 REMARK 500 10 ALA A 68 -26.33 -39.26 REMARK 500 10 ARG A 95 39.90 70.77 REMARK 500 10 PHE A 97 121.76 -34.99 REMARK 500 10 PRO A 101 0.88 -69.77 REMARK 500 11 SER A 3 177.70 -52.44 REMARK 500 11 PRO A 16 -178.76 -69.75 REMARK 500 11 SER A 99 139.88 -173.75 REMARK 500 12 SER A 3 95.91 -47.34 REMARK 500 12 ALA A 10 108.92 -167.66 REMARK 500 REMARK 500 THIS ENTRY HAS 102 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSO002000906.1 RELATED DB: TARGETDB DBREF 2CTK A 8 98 UNP Q00341 VIGLN_HUMAN 964 1054 SEQADV 2CTK GLY A 1 UNP Q00341 CLONING ARTIFACT SEQADV 2CTK SER A 2 UNP Q00341 CLONING ARTIFACT SEQADV 2CTK SER A 3 UNP Q00341 CLONING ARTIFACT SEQADV 2CTK GLY A 4 UNP Q00341 CLONING ARTIFACT SEQADV 2CTK SER A 5 UNP Q00341 CLONING ARTIFACT SEQADV 2CTK SER A 6 UNP Q00341 CLONING ARTIFACT SEQADV 2CTK GLY A 7 UNP Q00341 CLONING ARTIFACT SEQADV 2CTK SER A 99 UNP Q00341 CLONING ARTIFACT SEQADV 2CTK GLY A 100 UNP Q00341 CLONING ARTIFACT SEQADV 2CTK PRO A 101 UNP Q00341 CLONING ARTIFACT SEQADV 2CTK SER A 102 UNP Q00341 CLONING ARTIFACT SEQADV 2CTK SER A 103 UNP Q00341 CLONING ARTIFACT SEQADV 2CTK GLY A 104 UNP Q00341 CLONING ARTIFACT SEQRES 1 A 104 GLY SER SER GLY SER SER GLY LYS GLU ALA LEU GLU ALA SEQRES 2 A 104 LEU VAL PRO VAL THR ILE GLU VAL GLU VAL PRO PHE ASP SEQRES 3 A 104 LEU HIS ARG TYR VAL ILE GLY GLN LYS GLY SER GLY ILE SEQRES 4 A 104 ARG LYS MET MET ASP GLU PHE GLU VAL ASN ILE HIS VAL SEQRES 5 A 104 PRO ALA PRO GLU LEU GLN SER ASP ILE ILE ALA ILE THR SEQRES 6 A 104 GLY LEU ALA ALA ASN LEU ASP ARG ALA LYS ALA GLY LEU SEQRES 7 A 104 LEU GLU ARG VAL LYS GLU LEU GLN ALA GLU GLN GLU ASP SEQRES 8 A 104 ARG ALA LEU ARG SER PHE LYS SER GLY PRO SER SER GLY HELIX 1 1 HIS A 28 GLY A 33 1 6 HELIX 2 2 GLY A 36 PHE A 46 1 11 HELIX 3 3 LEU A 67 ARG A 95 1 29 SHEET 1 A 3 VAL A 17 GLU A 22 0 SHEET 2 A 3 ILE A 61 GLY A 66 -1 O GLY A 66 N VAL A 17 SHEET 3 A 3 ASN A 49 HIS A 51 -1 N ASN A 49 O THR A 65 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