PDB Short entry for 1D2J HEADER SIGNALING PROTEIN 23-SEP-99 1D2J TITLE LDL RECEPTOR LIGAND-BINDING MODULE 6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LOW-DENSITY LIPOPROTEIN RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND-BINDING DOMAIN, SIXTH REPEAT; COMPND 5 SYNONYM: LR6*; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMM-LR6* KEYWDS RECEPTOR, LDLR, CYSTEINE-RICH MODULE, CALCIUM LIGAND-BINDING, KEYWDS 2 FAMILIAL HYPERCHOLESTEROLEMIA, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.L.NORTH,S.C.BLACKLOW REVDAT 3 03-NOV-21 1D2J 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1D2J 1 VERSN REVDAT 1 22-MAR-00 1D2J 0 JRNL AUTH C.L.NORTH,S.C.BLACKLOW JRNL TITL SOLUTION STRUCTURE OF THE SIXTH LDL-A MODULE OF THE LDL JRNL TITL 2 RECEPTOR. JRNL REF BIOCHEMISTRY V. 39 2564 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10704205 JRNL DOI 10.1021/BI992087A REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.L.NORTH,S.C.BLACKLOW REMARK 1 TITL STRUCTURAL INDEPENDENCE OF LIGAND-BINDING MODULES FIVE AND REMARK 1 TITL 2 SIX OF THE LDL RECEPTOR REMARK 1 REF BIOCHEMISTRY V. 38 3926 1999 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI9821622 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 97.0, X-PLOR 3.8.1 REMARK 3 AUTHORS : MSI (FELIX), A. BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 541 UNIQUE NOE DISTANCES, 3 DISULFIDE REMARK 3 BONDS, 9 H-BONDS, 17 DISTANCES DEFINE THE CA++ BINDING SITE, 17 REMARK 3 PHI ANGLES DERIVED FROM J-HNHA MEASUREMENTS REMARK 4 REMARK 4 1D2J COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-SEP-99. REMARK 100 THE DEPOSITION ID IS D_1000009734. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298; 298; 298 REMARK 210 PH : 5.2; 5.2; 5.2; 5.2 REMARK 210 IONIC STRENGTH : 10 MM; 10 MM; 10 MM; 10 MM REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM LR6 U-15N; 10 MM CACL2; 1 REMARK 210 MM LR6 U-15N; 10 MM CACL2; 1 MM REMARK 210 LR6 UNLABELED; 10 MM CACL2; 1 MM REMARK 210 LR6 UNLABELED; 10 MM CACL2 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; HYDROGEN REMARK 210 EXCHANGE; 2D NOESY; HMQC-J REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 400 MHZ REMARK 210 SPECTROMETER MODEL : UNITY; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY 1.3.13, DYANA 1.5 REMARK 210 METHOD USED : SIMULATED ANNEALING IN TORSION REMARK 210 ANGLE SPACE FOLLOWED BY REMARK 210 SIMULATED ANNEALING REFINEMENT REMARK 210 IN 3D COORDINATE SPACE. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 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: 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 ALA A 213 36.54 -153.02 REMARK 500 1 THR A 214 -0.76 73.08 REMARK 500 1 CYS A 215 -78.02 -116.02 REMARK 500 1 ASP A 218 60.15 173.96 REMARK 500 1 GLU A 219 -150.44 -117.72 REMARK 500 1 CYS A 234 76.99 37.69 REMARK 500 1 ASP A 235 29.11 -140.68 REMARK 500 1 GLU A 237 76.75 -152.69 REMARK 500 1 TYR A 238 90.90 -34.22 REMARK 500 1 LYS A 241 -42.27 70.43 REMARK 500 1 LEU A 243 99.81 72.94 REMARK 500 1 SER A 244 -27.08 -171.48 REMARK 500 1 GLU A 246 -43.53 -141.96 REMARK 500 1 VAL A 247 89.38 -33.41 REMARK 500 1 CYS A 249 -146.73 -124.61 REMARK 500 2 ALA A 213 28.79 -148.29 REMARK 500 2 CYS A 215 -71.84 -113.41 REMARK 500 2 ASP A 218 12.18 -144.88 REMARK 500 2 GLU A 219 -150.77 -89.78 REMARK 500 2 CYS A 234 91.83 34.18 REMARK 500 2 ASP A 235 21.22 -150.16 REMARK 500 2 TYR A 238 87.23 -67.00 REMARK 500 2 LYS A 241 -42.25 69.50 REMARK 500 2 LEU A 243 98.36 69.77 REMARK 500 2 SER A 244 -31.04 -164.45 REMARK 500 2 GLU A 246 -75.12 -127.38 REMARK 500 2 VAL A 247 77.27 0.69 REMARK 500 2 CYS A 249 -135.70 -88.25 REMARK 500 3 ALA A 213 39.62 -155.20 REMARK 500 3 THR A 214 -2.47 74.08 REMARK 500 3 CYS A 215 -80.02 -123.45 REMARK 500 3 ASP A 218 67.77 167.55 REMARK 500 3 GLU A 219 -149.64 -132.00 REMARK 500 3 CYS A 234 84.70 28.04 REMARK 500 3 ASP A 235 33.36 -143.43 REMARK 500 3 TYR A 238 75.47 -54.36 REMARK 500 3 LYS A 241 -43.55 70.50 REMARK 500 3 LEU A 243 98.04 67.80 REMARK 500 3 SER A 244 -32.44 -163.51 REMARK 500 3 GLU A 246 -74.46 -111.05 REMARK 500 3 VAL A 247 94.61 -44.87 REMARK 500 3 VAL A 250 28.07 37.15 REMARK 500 4 ALA A 213 53.61 -111.50 REMARK 500 4 THR A 214 -61.57 66.01 REMARK 500 4 GLU A 219 -151.65 -91.89 REMARK 500 4 CYS A 234 85.47 28.77 REMARK 500 4 ASP A 235 33.37 -145.18 REMARK 500 4 TYR A 238 75.52 -53.71 REMARK 500 4 LYS A 241 -42.88 70.82 REMARK 500 4 LEU A 243 95.93 67.94 REMARK 500 REMARK 500 THIS ENTRY HAS 273 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 216 0.26 SIDE CHAIN REMARK 500 1 ARG A 232 0.22 SIDE CHAIN REMARK 500 1 ARG A 236 0.20 SIDE CHAIN REMARK 500 2 ARG A 216 0.23 SIDE CHAIN REMARK 500 2 ARG A 232 0.20 SIDE CHAIN REMARK 500 2 ARG A 236 0.29 SIDE CHAIN REMARK 500 3 ARG A 216 0.21 SIDE CHAIN REMARK 500 3 ARG A 232 0.28 SIDE CHAIN REMARK 500 3 ARG A 236 0.31 SIDE CHAIN REMARK 500 4 ARG A 216 0.19 SIDE CHAIN REMARK 500 4 ARG A 232 0.24 SIDE CHAIN REMARK 500 4 ARG A 236 0.22 SIDE CHAIN REMARK 500 5 ARG A 216 0.28 SIDE CHAIN REMARK 500 5 ARG A 232 0.26 SIDE CHAIN REMARK 500 5 ARG A 236 0.23 SIDE CHAIN REMARK 500 6 ARG A 216 0.31 SIDE CHAIN REMARK 500 6 ARG A 232 0.13 SIDE CHAIN REMARK 500 6 ARG A 236 0.23 SIDE CHAIN REMARK 500 7 ARG A 216 0.29 SIDE CHAIN REMARK 500 7 ARG A 236 0.24 SIDE CHAIN REMARK 500 8 ARG A 216 0.26 SIDE CHAIN REMARK 500 8 ARG A 232 0.28 SIDE CHAIN REMARK 500 8 ARG A 236 0.32 SIDE CHAIN REMARK 500 9 ARG A 216 0.22 SIDE CHAIN REMARK 500 9 ARG A 232 0.32 SIDE CHAIN REMARK 500 9 ARG A 236 0.17 SIDE CHAIN REMARK 500 10 ARG A 216 0.31 SIDE CHAIN REMARK 500 10 ARG A 232 0.21 SIDE CHAIN REMARK 500 10 ARG A 236 0.20 SIDE CHAIN REMARK 500 11 ARG A 216 0.11 SIDE CHAIN REMARK 500 11 ARG A 232 0.26 SIDE CHAIN REMARK 500 11 ARG A 236 0.20 SIDE CHAIN REMARK 500 12 ARG A 216 0.28 SIDE CHAIN REMARK 500 12 ARG A 232 0.11 SIDE CHAIN REMARK 500 12 ARG A 236 0.18 SIDE CHAIN REMARK 500 13 ARG A 216 0.29 SIDE CHAIN REMARK 500 13 ARG A 232 0.14 SIDE CHAIN REMARK 500 13 ARG A 236 0.30 SIDE CHAIN REMARK 500 14 ARG A 216 0.25 SIDE CHAIN REMARK 500 14 ARG A 232 0.31 SIDE CHAIN REMARK 500 14 ARG A 236 0.23 SIDE CHAIN REMARK 500 15 ARG A 216 0.29 SIDE CHAIN REMARK 500 15 ARG A 232 0.14 SIDE CHAIN REMARK 500 15 ARG A 236 0.27 SIDE CHAIN REMARK 500 16 ARG A 232 0.31 SIDE CHAIN REMARK 500 16 ARG A 236 0.17 SIDE CHAIN REMARK 500 17 ARG A 216 0.14 SIDE CHAIN REMARK 500 17 ARG A 232 0.29 SIDE CHAIN REMARK 500 17 ARG A 236 0.21 SIDE CHAIN REMARK 500 18 ARG A 216 0.22 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 58 PLANE DEVIATIONS. 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 1 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 232 O REMARK 620 2 ASP A 235 OD2 79.6 REMARK 620 3 GLU A 237 O 173.6 94.0 REMARK 620 4 ASP A 239 OD2 93.5 99.1 87.6 REMARK 620 5 ASP A 245 OD2 92.1 161.7 94.0 97.7 REMARK 620 6 GLU A 246 OE2 131.5 121.0 52.0 121.5 54.0 REMARK 620 7 GLU A 246 OE1 96.5 79.2 82.0 169.3 85.7 52.9 REMARK 620 N 1 2 3 4 5 6 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 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AJJ RELATED DB: PDB REMARK 900 MODULE PRECEEDING THIS ENTRY IN THE LDL RECEPTOR DBREF 1D2J A 212 251 UNP P01130 LDLR_HUMAN 233 272 SEQADV 1D2J LEU A 243 UNP P01130 MET 264 ENGINEERED MUTATION SEQRES 1 A 40 VAL ALA THR CYS ARG PRO ASP GLU PHE GLN CYS SER ASP SEQRES 2 A 40 GLY ASN CYS ILE HIS GLY SER ARG GLN CYS ASP ARG GLU SEQRES 3 A 40 TYR ASP CYS LYS ASP LEU SER ASP GLU VAL GLY CYS VAL SEQRES 4 A 40 ASN HET CA A 1 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ HELIX 1 1 HIS A 229 GLN A 233 5 5 SHEET 1 A 2 PHE A 220 CYS A 222 0 SHEET 2 A 2 ASN A 226 ILE A 228 -1 O ASN A 226 N CYS A 222 SSBOND 1 CYS A 215 CYS A 227 1555 1555 2.02 SSBOND 2 CYS A 222 CYS A 240 1555 1555 2.02 SSBOND 3 CYS A 234 CYS A 249 1555 1555 2.03 LINK CA CA A 1 O ARG A 232 1555 1555 2.55 LINK CA CA A 1 OD2 ASP A 235 1555 1555 2.53 LINK CA CA A 1 O GLU A 237 1555 1555 2.63 LINK CA CA A 1 OD2 ASP A 239 1555 1555 2.40 LINK CA CA A 1 OD2 ASP A 245 1555 1555 2.60 LINK CA CA A 1 OE2 GLU A 246 1555 1555 2.40 LINK CA CA A 1 OE1 GLU A 246 1555 1555 2.43 SITE 1 AC1 6 ARG A 232 ASP A 235 GLU A 237 ASP A 239 SITE 2 AC1 6 ASP A 245 GLU A 246 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