HEADER NEUROPEPTIDE 29-NOV-18 6IB6 TITLE SOLUTION STRUCTURE OF THE WATER-SOLUBLE LU-DOMAIN OF HUMAN LYPD6 TITLE 2 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: LY6/PLAUR DOMAIN-CONTAINING PROTEIN 6; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: N-TERMINAL MET WAS ADDED DUE TO RECOMBINANT PRODUCTION SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: UBIQUITOUS. HIGHLY EXPRESSED IN BRAIN AND HEART; SOURCE 6 GENE: LYPD6, UNQ3023/PRO9821; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET22B(+); SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B(+)/LYPD6 KEYWDS LYPD6, LY6/UPAR, NICOTINIC ACETYLCHOLINE RECEPTOR, THREE-FINGER KEYWDS 2 PROTEINS, SIGNALING PROTEIN, NEUROPEPTIDE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.V.TSAREV,D.S.KULBATSKII,A.S.PARAMONOV,E.N.LYUKMANOVA,Z.O.SHENKAREV REVDAT 2 13-JAN-21 6IB6 1 JRNL SSBOND REVDAT 1 18-DEC-19 6IB6 0 JRNL AUTH A.S.PARAMONOV,M.V.KOCHAROVSKAYA,A.V.TSAREV,D.S.KULBATSKII, JRNL AUTH 2 E.V.LOKTYUSHOV,M.A.SHULEPKO,M.P.KIRPICHNIKOV,E.N.LYUKMANOVA, JRNL AUTH 3 Z.O.SHENKAREV JRNL TITL STRUCTURAL DIVERSITY AND DYNAMICS OF HUMAN THREE-FINGER JRNL TITL 2 PROTEINS ACTING ON NICOTINIC ACETYLCHOLINE RECEPTORS. JRNL REF INT J MOL SCI V. 21 2020 JRNL REFN ESSN 1422-0067 JRNL PMID 33019770 JRNL DOI 10.3390/IJMS21197280 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.97 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6IB6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1200011973. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : AMBIENT PA REMARK 210 SAMPLE CONTENTS : 0.1 MM [U-99% 13C; U-99% 15N] REMARK 210 LYPD6SH, 95% H2O/5% D2O; 0.1 MM REMARK 210 [U-99% 15N] LYPD6SH, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D HNCA; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 2D 1H-15N REMARK 210 HSQC; 2D 1H-13C HSQC ALIPHATIC; REMARK 210 3D HNCO; 3D HCCH-TOCSY; 2D 1H-1H REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.97, CARA REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 PHE A 101 -168.69 -116.68 REMARK 500 1 TYR A 113 -70.45 -54.64 REMARK 500 1 ALA A 119 74.37 50.72 REMARK 500 1 PRO A 125 -171.68 -69.76 REMARK 500 1 GLU A 127 41.20 39.07 REMARK 500 1 GLU A 177 13.41 -146.13 REMARK 500 1 CYS A 181 31.35 -93.55 REMARK 500 1 PRO A 186 -170.71 -69.79 REMARK 500 1 PHE A 194 44.10 37.35 REMARK 500 2 GLU A 107 124.49 -174.84 REMARK 500 2 TRP A 118 -75.47 -89.62 REMARK 500 2 ALA A 119 74.55 54.22 REMARK 500 2 ARG A 129 -41.97 -133.38 REMARK 500 2 SER A 158 62.14 -110.22 REMARK 500 2 HIS A 166 -177.63 -64.09 REMARK 500 2 ILE A 180 43.39 37.59 REMARK 500 2 ASN A 182 48.83 -88.45 REMARK 500 2 PRO A 184 -171.60 -69.84 REMARK 500 2 GLU A 189 112.32 -176.84 REMARK 500 3 GLU A 107 123.64 -174.81 REMARK 500 3 ALA A 119 74.96 51.01 REMARK 500 3 PRO A 120 109.22 -52.29 REMARK 500 3 PRO A 125 -176.93 -69.77 REMARK 500 3 ARG A 129 -40.91 -132.08 REMARK 500 3 GLU A 165 -41.77 -138.88 REMARK 500 3 HIS A 166 -73.71 -50.53 REMARK 500 3 ILE A 180 51.27 35.96 REMARK 500 4 TRP A 118 -75.59 -93.29 REMARK 500 4 ALA A 119 73.86 55.60 REMARK 500 4 PRO A 125 -174.68 -69.79 REMARK 500 4 ARG A 129 -41.64 -138.66 REMARK 500 4 ASP A 163 -78.51 -85.12 REMARK 500 4 ILE A 180 42.06 38.52 REMARK 500 4 PRO A 186 -170.41 -69.73 REMARK 500 4 ASN A 188 -169.78 -129.60 REMARK 500 5 GLU A 107 105.10 -162.72 REMARK 500 5 TRP A 118 -73.33 -89.80 REMARK 500 5 ALA A 119 76.85 52.30 REMARK 500 5 ARG A 126 179.11 -56.43 REMARK 500 5 ARG A 129 -48.26 -141.73 REMARK 500 5 THR A 140 -74.96 -69.10 REMARK 500 5 SER A 158 68.67 -104.32 REMARK 500 5 SER A 164 -77.42 -130.99 REMARK 500 5 HIS A 166 42.80 -93.01 REMARK 500 5 ILE A 180 45.61 37.23 REMARK 500 5 PRO A 186 -170.88 -69.79 REMARK 500 5 ARG A 187 50.43 -109.40 REMARK 500 6 ALA A 119 74.07 52.35 REMARK 500 6 PRO A 125 -170.75 -69.76 REMARK 500 7 TRP A 118 -75.91 -90.10 REMARK 500 REMARK 500 THIS ENTRY HAS 172 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34333 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE WATER-SOLUBLE LU-DOMAIN OF HUMAN LYPD6 REMARK 900 PROTEIN DBREF 6IB6 A 101 195 UNP Q86Y78 LYPD6_HUMAN 47 141 SEQADV 6IB6 MET A 100 UNP Q86Y78 INITIATING METHIONINE SEQRES 1 A 96 MET PHE LYS CYS PHE THR CYS GLU LYS ALA ALA ASP ASN SEQRES 2 A 96 TYR GLU CYS ASN ARG TRP ALA PRO ASP ILE TYR CYS PRO SEQRES 3 A 96 ARG GLU THR ARG TYR CYS TYR THR GLN HIS THR MET GLU SEQRES 4 A 96 VAL THR GLY ASN SER ILE SER VAL THR LYS ARG CYS VAL SEQRES 5 A 96 PRO LEU GLU GLU CYS LEU SER THR GLY CYS ARG ASP SER SEQRES 6 A 96 GLU HIS GLU GLY HIS LYS VAL CYS THR SER CYS CYS GLU SEQRES 7 A 96 GLY ASN ILE CYS ASN LEU PRO LEU PRO ARG ASN GLU THR SEQRES 8 A 96 ASP ALA THR PHE ALA HELIX 1 AA1 ASP A 111 ALA A 119 1 9 SHEET 1 AA1 3 SER A 143 VAL A 151 0 SHEET 2 AA1 3 TYR A 130 MET A 137 -1 N GLN A 134 O THR A 147 SHEET 3 AA1 3 LYS A 170 CYS A 175 -1 O LYS A 170 N MET A 137 SSBOND 1 CYS A 103 CYS A 131 1555 1555 2.10 SSBOND 2 CYS A 103 CYS A 181 1555 1555 2.64 SSBOND 3 CYS A 106 CYS A 115 1555 1555 1.96 SSBOND 4 CYS A 124 CYS A 150 1555 1555 1.99 SSBOND 5 CYS A 156 CYS A 175 1555 1555 2.06 SSBOND 6 CYS A 161 CYS A 172 1555 1555 2.16 SSBOND 7 CYS A 176 CYS A 181 1555 1555 2.15 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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