HEADER LIPID BINDING PROTEIN 05-JUL-00 1F8Z TITLE NMR STRUCTURE OF THE SIXTH LIGAND-BINDING MODULE OF THE LDL RECEPTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: LOW-DENSITY LIPOPROTEIN RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SIXTH LIGAND-BINDING MODULE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: PEPTIDE SYNTHESIS - BASED ON THE HUMAN SEQUENCE KEYWDS LDL RECEPTOR, LIGAND-BINDING DOMAIN, CALCIUM-BINDING, FAMILIAL KEYWDS 2 HYPERCHOLESTEROLEMIA, LIPID BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.J.CLAYTON,I.M.BRERETON,P.A.KROON,R.SMITH REVDAT 5 30-OCT-24 1F8Z 1 REMARK REVDAT 4 23-FEB-22 1F8Z 1 REMARK LINK REVDAT 3 24-FEB-09 1F8Z 1 VERSN REVDAT 2 01-APR-03 1F8Z 1 JRNL REVDAT 1 18-OCT-00 1F8Z 0 JRNL AUTH D.CLAYTON,I.M.BRERETON,P.A.KROON,R.SMITH JRNL TITL THREE-DIMENSIONAL NMR STRUCTURE OF THE SIXTH LIGAND-BINDING JRNL TITL 2 MODULE OF THE HUMAN LDL RECEPTOR: COMPARISON OF TWO ADJACENT JRNL TITL 3 MODULES WITH DIFFERENT LIGAND BINDING SPECIFICITIES. JRNL REF FEBS LETT. V. 479 118 2000 JRNL REFN ISSN 0014-5793 JRNL PMID 10981718 JRNL DOI 10.1016/S0014-5793(00)01842-1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR, X-PLOR 3.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), AXEL BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 STRUCTURES ARE BASED ON 552 DISTANCE CONSTRAINTS, 18 BACKBONE REMARK 3 ANGLE RESTRAINTS REMARK 3 AND 14 SIDECHAIN ANGLE RESTRAINTS REMARK 4 REMARK 4 1F8Z COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-00. REMARK 100 THE DEPOSITION ID IS D_1000011390. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.50 REMARK 210 IONIC STRENGTH : 10 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 3 MM LB6, 10 MM CACL2, 1 MM REMARK 210 3,3,3-TRIMETHYLSILYLPROPIONATE; REMARK 210 3 MM LB6, 10 MM CACL2, 1 MM 3,3, REMARK 210 3-TRIMETHYLSILYLPROPIONATE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; E-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AURELIA, XEASY, DYANA 1.5, X REMARK 210 -PLOR 3.1 REMARK 210 METHOD USED : STRUCTURE DETERMINATION BY REMARK 210 TORSION ANGLE DYNAMICS, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 CYS A 15 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 1 CYS A 22 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 2 CYS A 22 CA - CB - SG ANGL. DEV. = 7.8 DEGREES REMARK 500 3 CYS A 15 CA - CB - SG ANGL. DEV. = 6.8 DEGREES REMARK 500 3 CYS A 22 CA - CB - SG ANGL. DEV. = 7.2 DEGREES REMARK 500 4 CYS A 22 CA - CB - SG ANGL. DEV. = 6.8 DEGREES REMARK 500 6 ARG A 20 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 7 CYS A 22 CA - CB - SG ANGL. DEV. = 7.8 DEGREES REMARK 500 8 CYS A 22 CA - CB - SG ANGL. DEV. = 7.5 DEGREES REMARK 500 9 CYS A 22 CA - CB - SG ANGL. DEV. = 7.3 DEGREES REMARK 500 11 CYS A 22 CA - CB - SG ANGL. DEV. = 7.5 DEGREES REMARK 500 12 CYS A 22 CA - CB - SG ANGL. DEV. = 7.3 DEGREES REMARK 500 13 CYS A 15 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 13 CYS A 22 CA - CB - SG ANGL. DEV. = 6.9 DEGREES REMARK 500 14 CYS A 22 CA - CB - SG ANGL. DEV. = 7.8 DEGREES REMARK 500 15 CYS A 15 CA - CB - SG ANGL. DEV. = 7.2 DEGREES REMARK 500 15 CYS A 22 CA - CB - SG ANGL. DEV. = 8.3 DEGREES REMARK 500 16 CYS A 22 CA - CB - SG ANGL. DEV. = 7.5 DEGREES REMARK 500 17 CYS A 22 CA - CB - SG ANGL. DEV. = 8.3 DEGREES REMARK 500 18 CYS A 22 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 19 CYS A 15 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 19 CYS A 22 CA - CB - SG ANGL. DEV. = 7.3 DEGREES REMARK 500 20 CYS A 22 CA - CB - SG ANGL. DEV. = 7.7 DEGREES 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 ASP A 23 3.39 -150.33 REMARK 500 1 GLU A 25 38.03 -92.60 REMARK 500 1 TYR A 26 75.85 -2.20 REMARK 500 1 MET A 31 17.15 56.81 REMARK 500 2 CYS A 22 63.86 68.06 REMARK 500 2 ASP A 23 9.97 -150.42 REMARK 500 2 ARG A 24 28.23 43.10 REMARK 500 2 GLU A 25 41.38 -101.65 REMARK 500 2 TYR A 26 80.39 1.07 REMARK 500 2 MET A 31 17.41 55.80 REMARK 500 3 ASP A 23 3.64 -150.61 REMARK 500 3 GLU A 25 39.82 -93.95 REMARK 500 3 TYR A 26 79.06 -3.96 REMARK 500 3 MET A 31 11.17 51.23 REMARK 500 4 ASP A 23 -5.07 -141.70 REMARK 500 4 GLU A 25 44.71 -98.48 REMARK 500 4 TYR A 26 82.95 -2.60 REMARK 500 4 MET A 31 16.46 46.11 REMARK 500 5 CYS A 22 65.00 67.67 REMARK 500 5 ASP A 23 1.11 -150.48 REMARK 500 5 GLU A 25 40.48 -89.99 REMARK 500 5 TYR A 26 76.31 1.40 REMARK 500 5 MET A 31 12.54 57.51 REMARK 500 5 VAL A 38 46.80 -102.93 REMARK 500 6 ASP A 23 2.49 -150.18 REMARK 500 6 GLU A 25 43.65 -98.37 REMARK 500 6 TYR A 26 83.97 -3.66 REMARK 500 6 MET A 31 14.48 53.72 REMARK 500 6 CYS A 37 -75.50 -52.57 REMARK 500 7 ASP A 23 6.44 -150.45 REMARK 500 7 ARG A 24 29.96 48.95 REMARK 500 7 GLU A 25 41.92 -92.29 REMARK 500 7 TYR A 26 79.79 -5.74 REMARK 500 7 MET A 31 15.90 59.42 REMARK 500 8 ASP A 23 6.64 -150.60 REMARK 500 8 GLU A 25 41.76 -92.12 REMARK 500 8 TYR A 26 76.96 -6.52 REMARK 500 8 MET A 31 13.40 54.65 REMARK 500 8 VAL A 38 43.16 -95.19 REMARK 500 9 ASP A 23 9.32 -150.43 REMARK 500 9 GLU A 25 45.38 -97.83 REMARK 500 9 TYR A 26 85.73 -11.39 REMARK 500 9 MET A 31 15.65 52.17 REMARK 500 10 ASP A 23 12.17 -150.56 REMARK 500 10 ARG A 24 33.62 39.90 REMARK 500 10 GLU A 25 40.15 -96.73 REMARK 500 10 TYR A 26 76.82 1.36 REMARK 500 10 CYS A 37 -73.42 -68.87 REMARK 500 11 CYS A 22 61.59 63.48 REMARK 500 11 ASP A 23 -0.20 -143.53 REMARK 500 REMARK 500 THIS ENTRY HAS 97 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 A 40 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 20 O REMARK 620 2 ASP A 23 OD1 61.5 REMARK 620 3 GLU A 25 O 138.9 117.7 REMARK 620 4 GLU A 25 N 129.9 68.5 69.3 REMARK 620 5 TYR A 26 N 179.5 118.0 41.0 49.7 REMARK 620 6 ASP A 27 OD2 62.9 113.1 84.2 148.8 117.3 REMARK 620 7 ASP A 33 OD2 87.2 140.9 101.2 134.6 93.3 65.0 REMARK 620 8 GLU A 34 OE2 70.2 66.2 150.4 87.3 109.8 122.7 82.1 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 40 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LDL RELATED DB: PDB REMARK 900 1LDL CONTAINS THE FIRST LIGAND-BINDING MODULE OF THE LDL RECEPTOR REMARK 900 RELATED ID: 1LDR RELATED DB: PDB REMARK 900 1LDR CONTAINS THE SECOND LIGAND-BINDING MODULE OF THE LDL RECEPTOR DBREF 1F8Z A 1 39 UNP P01130 LDLR_HUMAN 234 272 SEQRES 1 A 39 ALA THR CYS ARG PRO ASP GLU PHE GLN CYS SER ASP GLY SEQRES 2 A 39 ASN CYS ILE HIS GLY SER ARG GLN CYS ASP ARG GLU TYR SEQRES 3 A 39 ASP CYS LYS ASP MET SER ASP GLU VAL GLY CYS VAL ASN HET CA A 40 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ HELIX 1 1 MET A 31 VAL A 35 5 5 SHEET 1 A 2 GLU A 7 GLN A 9 0 SHEET 2 A 2 CYS A 15 HIS A 17 -1 O ILE A 16 N PHE A 8 SSBOND 1 CYS A 3 CYS A 15 1555 1555 2.02 SSBOND 2 CYS A 10 CYS A 28 1555 1555 2.02 SSBOND 3 CYS A 22 CYS A 37 1555 1555 2.02 LINK O ARG A 20 CA CA A 40 1555 1555 2.79 LINK OD1 ASP A 23 CA CA A 40 1555 1555 2.65 LINK O GLU A 25 CA CA A 40 1555 1555 3.19 LINK N GLU A 25 CA CA A 40 1555 1555 3.02 LINK N TYR A 26 CA CA A 40 1555 1555 3.25 LINK OD2 ASP A 27 CA CA A 40 1555 1555 2.64 LINK OD2 ASP A 33 CA CA A 40 1555 1555 2.63 LINK OE2 GLU A 34 CA CA A 40 1555 1555 2.62 SITE 1 AC1 7 ARG A 20 ASP A 23 GLU A 25 TYR A 26 SITE 2 AC1 7 ASP A 27 ASP A 33 GLU A 34 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