HEADER LIGAND BINDING PROTEIN 14-AUG-06 2I1P TITLE SOLUTION STRUCTURE OF THE TWELFTH CYSTEINE-RICH LIGAND-BINDING REPEAT TITLE 2 IN RAT MEGALIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MEG-A12; COMPND 5 SYNONYM: MEGALIN, GLYCOPROTEIN 330, GP330; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PKM263 KEYWDS LOW DENSITY LIPOPROTEIN RECEPTOR, CYSTEINE-RICH REPEAT, LIGAND KEYWDS 2 BINDING DOMAIN, CALCIUM CAGE, LIGAND BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.A.WOLF,F.DANCEA,M.SHI,V.BADE-NOSKOVA,H.RUETERJANS,D.KERJASCHKI, AUTHOR 2 C.LUECKE REVDAT 6 13-NOV-24 2I1P 1 REMARK REVDAT 5 14-JUN-23 2I1P 1 REMARK LINK REVDAT 4 19-FEB-20 2I1P 1 REMARK SEQADV REVDAT 3 24-FEB-09 2I1P 1 VERSN REVDAT 2 20-MAR-07 2I1P 1 JRNL REVDAT 1 13-FEB-07 2I1P 0 JRNL AUTH C.A.WOLF,F.DANCEA,M.SHI,V.BADE-NOSKOVA,H.RUETERJANS, JRNL AUTH 2 D.KERJASCHKI,C.LUECKE JRNL TITL SOLUTION STRUCTURE OF THE TWELFTH CYSTEINE-RICH JRNL TITL 2 LIGAND-BINDING REPEAT IN RAT MEGALIN. JRNL REF J.BIOMOL.NMR V. 37 321 2007 JRNL REFN ISSN 0925-2738 JRNL PMID 17245526 JRNL DOI 10.1007/S10858-006-9129-3 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, ARIA 1.2 REMARK 3 AUTHORS : BRUKER (XWINNMR), LINGE ET AL. (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON 606 NON REMARK 3 -REDUNDANT NOE RESTRAINTS REMARK 4 REMARK 4 2I1P COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1000039025. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 10MM CACL2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5MM MEG-A12, 10MM CACL2, 90% REMARK 210 H20, 10% D20 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D TOCSY; 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AURELIA 2.5.9, ARIA 1.2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 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 MET A1184 76.03 60.77 REMARK 500 1 CYS A1208 82.42 69.90 REMARK 500 1 ASP A1216 -91.09 -106.90 REMARK 500 1 ASN A1217 24.57 -167.33 REMARK 500 1 ARG A1226 89.94 57.12 REMARK 500 2 SER A1199 -79.32 -106.97 REMARK 500 2 CYS A1208 90.02 68.06 REMARK 500 2 ASP A1209 -43.59 -145.79 REMARK 500 3 PRO A1228 90.70 -63.44 REMARK 500 4 THR A1189 -163.90 -119.38 REMARK 500 4 SER A1199 -76.81 -85.28 REMARK 500 4 CYS A1208 81.90 64.45 REMARK 500 4 ASP A1209 -34.82 -134.41 REMARK 500 5 ALA A1183 62.45 60.30 REMARK 500 5 SER A1199 -90.79 -79.64 REMARK 500 5 CYS A1208 71.58 56.98 REMARK 500 5 ASP A1216 -92.34 -116.44 REMARK 500 5 ASN A1217 25.20 -164.12 REMARK 500 6 CYS A1208 84.07 61.52 REMARK 500 7 CYS A1208 83.68 59.41 REMARK 500 7 ASP A1216 -96.70 -115.40 REMARK 500 7 ASN A1217 28.55 -156.52 REMARK 500 8 ASN A1187 37.37 -96.99 REMARK 500 9 CYS A1208 77.55 64.83 REMARK 500 10 CYS A1208 82.71 61.49 REMARK 500 11 ALA A1183 58.95 -90.30 REMARK 500 11 ASN A1187 108.61 -177.22 REMARK 500 11 THR A1189 -163.01 -105.93 REMARK 500 11 CYS A1208 72.43 62.87 REMARK 500 12 ALA A1183 72.72 57.42 REMARK 500 12 CYS A1208 89.97 66.20 REMARK 500 12 ASP A1209 -9.43 -151.58 REMARK 500 12 PRO A1224 99.70 -65.99 REMARK 500 13 CYS A1208 85.82 63.54 REMARK 500 13 ASP A1209 -37.07 -130.84 REMARK 500 14 ALA A1183 71.87 -105.19 REMARK 500 14 MET A1184 -175.85 65.40 REMARK 500 14 CYS A1208 83.24 69.90 REMARK 500 14 ASP A1216 -101.18 -102.25 REMARK 500 14 ASN A1217 23.61 -154.36 REMARK 500 15 CYS A1208 79.38 64.58 REMARK 500 15 ASP A1216 -86.51 -99.17 REMARK 500 15 ASN A1217 9.49 173.59 REMARK 500 16 CYS A1208 62.13 67.91 REMARK 500 16 ARG A1226 123.51 69.32 REMARK 500 17 CYS A1208 75.10 61.07 REMARK 500 17 ASP A1216 -95.27 -91.04 REMARK 500 17 ASN A1217 13.50 179.37 REMARK 500 17 ALA A1221 -77.14 -77.63 REMARK 500 18 ASN A1187 41.21 -94.70 REMARK 500 REMARK 500 THIS ENTRY HAS 59 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 A1230 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A1206 O REMARK 620 2 ASP A1209 OD1 105.5 REMARK 620 3 ASP A1209 OD2 66.8 40.8 REMARK 620 4 VAL A1211 O 171.3 69.0 109.0 REMARK 620 5 ASP A1213 OD2 83.7 77.6 85.9 88.4 REMARK 620 6 ASP A1219 OD2 108.5 144.0 175.2 75.8 94.3 REMARK 620 7 GLU A1220 OE1 97.9 109.6 102.2 90.5 171.7 77.5 REMARK 620 8 GLU A1220 OE2 122.1 68.3 80.3 63.0 141.3 102.4 43.7 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 1230 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7263 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFT ASSIGNMENTS OF MEG-A12 DBREF 2I1P A 1185 1229 UNP P98158 LRP2_RAT 1185 1229 SEQADV 2I1P GLY A 1182 UNP P98158 CLONING ARTIFACT SEQADV 2I1P ALA A 1183 UNP P98158 CLONING ARTIFACT SEQADV 2I1P MET A 1184 UNP P98158 CLONING ARTIFACT SEQRES 1 A 48 GLY ALA MET VAL LEU ASN CYS THR SER ALA GLN PHE LYS SEQRES 2 A 48 CYS ALA ASP GLY SER SER CYS ILE ASN SER ARG TYR ARG SEQRES 3 A 48 CYS ASP GLY VAL TYR ASP CYS ARG ASP ASN SER ASP GLU SEQRES 4 A 48 ALA GLY CYS PRO THR ARG PRO PRO GLY HET CA A1230 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ HELIX 1 1 ASN A 1203 ARG A 1207 5 5 HELIX 2 2 ASN A 1217 GLY A 1222 1 6 SHEET 1 A 2 PHE A1193 LYS A1194 0 SHEET 2 A 2 CYS A1201 ILE A1202 -1 O ILE A1202 N PHE A1193 SSBOND 1 CYS A 1188 CYS A 1201 1555 1555 2.03 SSBOND 2 CYS A 1195 CYS A 1214 1555 1555 2.03 SSBOND 3 CYS A 1208 CYS A 1223 1555 1555 2.03 LINK O TYR A1206 CA CA A1230 1555 1555 2.81 LINK OD1 ASP A1209 CA CA A1230 1555 1555 3.34 LINK OD2 ASP A1209 CA CA A1230 1555 1555 2.64 LINK O VAL A1211 CA CA A1230 1555 1555 2.82 LINK OD2 ASP A1213 CA CA A1230 1555 1555 2.66 LINK OD2 ASP A1219 CA CA A1230 1555 1555 2.51 LINK OE1 GLU A1220 CA CA A1230 1555 1555 2.67 LINK OE2 GLU A1220 CA CA A1230 1555 1555 3.08 SITE 1 AC1 6 TYR A1206 ASP A1209 VAL A1211 ASP A1213 SITE 2 AC1 6 ASP A1219 GLU A1220 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