PDB Short entry for 2CTF HEADER TRANSPORT PROTEIN 24-MAY-05 2CTF TITLE SOLUTION STRUCTURE OF THE 4TH 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 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: P050131-13; 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 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 10-NOV-21 2CTF 1 REMARK SEQADV REVDAT 2 24-FEB-09 2CTF 1 VERSN REVDAT 1 24-NOV-05 2CTF 0 JRNL AUTH T.TOMIZAWA,T.KIGAWA,S.KOSHIBA,M.INOUE,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE 4TH 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 2CTF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000024602. 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 : 1.16MM KH DOMAIN U-15N, 13C; REMARK 210 20MM D-TRIS-HCL; 100MM NACL; 1MM REMARK 210 D-DTT; 0.02% NAN3; 10% 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 GLU A 8 54.36 34.63 REMARK 500 1 PRO A 9 -175.20 -69.78 REMARK 500 1 ALA A 23 120.86 -173.14 REMARK 500 1 ASN A 24 89.47 -69.47 REMARK 500 1 ALA A 32 106.76 -58.63 REMARK 500 2 SER A 2 -62.44 -98.97 REMARK 500 2 PRO A 9 -169.16 -69.77 REMARK 500 2 GLU A 18 116.01 -173.34 REMARK 500 2 ALA A 23 135.00 -39.46 REMARK 500 2 ALA A 32 105.42 -59.63 REMARK 500 3 VAL A 19 171.85 -47.50 REMARK 500 3 LYS A 45 35.93 35.34 REMARK 500 3 GLU A 65 -68.56 -95.87 REMARK 500 3 ARG A 96 39.40 -82.62 REMARK 500 4 LEU A 12 132.66 -174.56 REMARK 500 4 LEU A 16 77.59 -116.50 REMARK 500 4 LYS A 22 37.11 -97.97 REMARK 500 4 ALA A 32 102.83 -50.15 REMARK 500 4 MET A 56 78.22 -115.38 REMARK 500 5 LEU A 16 98.00 -64.23 REMARK 500 5 GLU A 18 136.27 -172.12 REMARK 500 5 PHE A 26 136.57 -36.27 REMARK 500 5 ALA A 32 102.75 -50.71 REMARK 500 5 THR A 76 -27.46 -39.98 REMARK 500 6 LYS A 11 38.75 -91.76 REMARK 500 6 ALA A 21 41.83 -108.90 REMARK 500 6 ALA A 23 49.04 -87.35 REMARK 500 6 ALA A 32 104.04 -56.06 REMARK 500 6 PRO A 34 -179.90 -69.85 REMARK 500 6 GLU A 65 -74.99 -66.40 REMARK 500 6 GLU A 67 -27.01 -39.66 REMARK 500 7 PRO A 9 -172.28 -69.78 REMARK 500 8 SER A 5 116.91 -173.63 REMARK 500 8 LYS A 11 44.17 -95.22 REMARK 500 8 LEU A 12 51.26 37.31 REMARK 500 8 GLN A 14 120.24 -170.50 REMARK 500 8 ALA A 15 110.33 -160.49 REMARK 500 8 GLU A 18 110.31 -174.45 REMARK 500 8 PRO A 34 -172.41 -69.69 REMARK 500 8 MET A 56 75.92 -118.83 REMARK 500 8 SER A 97 41.39 -91.38 REMARK 500 9 LYS A 11 143.57 -174.94 REMARK 500 9 LEU A 16 101.06 -35.23 REMARK 500 9 GLU A 18 -176.18 -65.27 REMARK 500 9 ALA A 21 76.81 -62.44 REMARK 500 9 PRO A 34 -176.37 -69.65 REMARK 500 9 LYS A 44 97.59 -61.75 REMARK 500 9 ARG A 96 48.12 -96.30 REMARK 500 9 SER A 100 100.32 -36.61 REMARK 500 10 PRO A 9 -170.32 -69.71 REMARK 500 REMARK 500 THIS ENTRY HAS 110 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSO002000906.6 RELATED DB: TARGETDB DBREF 2CTF A 8 96 UNP Q00341 VIGLN_HUMAN 346 434 SEQADV 2CTF GLY A 1 UNP Q00341 CLONING ARTIFACT SEQADV 2CTF SER A 2 UNP Q00341 CLONING ARTIFACT SEQADV 2CTF SER A 3 UNP Q00341 CLONING ARTIFACT SEQADV 2CTF GLY A 4 UNP Q00341 CLONING ARTIFACT SEQADV 2CTF SER A 5 UNP Q00341 CLONING ARTIFACT SEQADV 2CTF SER A 6 UNP Q00341 CLONING ARTIFACT SEQADV 2CTF GLY A 7 UNP Q00341 CLONING ARTIFACT SEQADV 2CTF SER A 80 UNP Q00341 ASN 418 ENGINEERED MUTATION SEQADV 2CTF SER A 97 UNP Q00341 CLONING ARTIFACT SEQADV 2CTF GLY A 98 UNP Q00341 CLONING ARTIFACT SEQADV 2CTF PRO A 99 UNP Q00341 CLONING ARTIFACT SEQADV 2CTF SER A 100 UNP Q00341 CLONING ARTIFACT SEQADV 2CTF SER A 101 UNP Q00341 CLONING ARTIFACT SEQADV 2CTF GLY A 102 UNP Q00341 CLONING ARTIFACT SEQRES 1 A 102 GLY SER SER GLY SER SER GLY GLU PRO GLU LYS LEU GLY SEQRES 2 A 102 GLN ALA LEU THR GLU VAL TYR ALA LYS ALA ASN SER PHE SEQRES 3 A 102 THR VAL SER SER VAL ALA ALA PRO SER TRP LEU HIS ARG SEQRES 4 A 102 PHE ILE ILE GLY LYS LYS GLY GLN ASN LEU ALA LYS ILE SEQRES 5 A 102 THR GLN GLN MET PRO LYS VAL HIS ILE GLU PHE THR GLU SEQRES 6 A 102 GLY GLU ASP LYS ILE THR LEU GLU GLY PRO THR GLU ASP SEQRES 7 A 102 VAL SER VAL ALA GLN GLU GLN ILE GLU GLY MET VAL LYS SEQRES 8 A 102 ASP LEU ILE ASN ARG SER GLY PRO SER SER GLY HELIX 1 1 HIS A 38 GLY A 43 1 6 HELIX 2 2 GLN A 47 MET A 56 1 10 HELIX 3 3 PRO A 75 SER A 97 1 23 SHEET 1 A 3 THR A 27 ALA A 32 0 SHEET 2 A 3 LYS A 69 GLY A 74 -1 O LEU A 72 N SER A 29 SHEET 3 A 3 HIS A 60 PHE A 63 -1 N HIS A 60 O GLU A 73 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