PDB Short entry for 1I0U HEADER LIPID BINDING PROTEIN 29-JAN-01 1I0U TITLE SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF A CONCATEMER OF EGF- TITLE 2 HOMOLOGY MODULES OF THE HUMAN LOW DENSITY LIPOPROTEIN RECEPTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: LOW DENSITY LIPOPROTEIN RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EGF-AB CONCATEMER(RESIDUES 314-395); COMPND 5 SYNONYM: LDL RECEPTOR; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: LIVER; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DH5-ALPHA; BL21-DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-4T; PET-30A+ KEYWDS ANTI-PARALLEL BETA STRANDS, CALCIUM BINDING SITES, LIPID BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR AUTHOR N.D.KURNIAWAN,K.ALIABADIZADEH,I.M.BRERETON,P.A.KROON,R.SMITH REVDAT 4 23-FEB-22 1I0U 1 REMARK LINK REVDAT 3 24-FEB-09 1I0U 1 VERSN REVDAT 2 31-DEC-02 1I0U 1 REMARK REVDAT 1 15-AUG-01 1I0U 0 JRNL AUTH N.D.KURNIAWAN,K.ALIABADIZADEH,I.M.BRERETON,P.A.KROON,R.SMITH JRNL TITL NMR STRUCTURE AND BACKBONE DYNAMICS OF A CONCATEMER OF JRNL TITL 2 EPIDERMAL GROWTH FACTOR HOMOLOGY MODULES OF THE HUMAN JRNL TITL 3 LOW-DENSITY LIPOPROTEIN RECEPTOR. JRNL REF J.MOL.BIOL. V. 311 341 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11478865 JRNL DOI 10.1006/JMBI.2001.4867 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.D.KURNIAWAN,A.R.ATKINS,I.M.BRERETON,P.A.KROON,R.SMITH REMARK 1 TITL NMR STRUCTURE OF A CONCATEMER OF THE FIRST AND SECOND REMARK 1 TITL 2 LIGAND-BINDING MODULES OF THE HUMAN LOW-DENSITY LIPOPROTEIN REMARK 1 TITL 3 RECEPTOR REMARK 1 REF PROTEIN SCI. V. 9 1282 2000 REMARK 1 REFN ISSN 0961-8368 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.A.SPRINGER REMARK 1 TITL AN EXTRACELLULAR BETA-PROPELLER MODULE PREDICTED IN REMARK 1 TITL 2 LIPOPROTEIN AND SCAVENGER RECEPTORS, TYROSINE REMARK 1 TITL 3 KINASES,EPIDERMAL GROWTH FACTOR PRECURSOR, AND EXTRACELLULAR REMARK 1 TITL 4 MATRIX COMPONENTS. AN EXTRACELLULAR BETA-PROPELLER MODULE REMARK 1 TITL 5 PREDICTED IN LIPOPROTEIN AND SCAVENGER RECEPTORS, TYROSINE REMARK 1 TITL 6 KINASES,EPIDERMAL GROWTH FACTOR PRECURSOR, AND EXTRACELLULAR REMARK 1 TITL 7 MATRIX COMPONENTS REMARK 1 REF J.MOL.BIOL. V. 283 837 1998 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.1998.2115 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, X-PLOR 3.85 REMARK 3 AUTHORS : BRUKER (XWINNMR), A. BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON: 874 NOE REMARK 3 RESTRAINTS, 64 PHI DIHEDRAL ANGLES, 14 CHI1 DIHEDRAL ANGLES, 14 REMARK 3 HYDROGEN BONDS, 9 CALCIUM ION LIGAND RESTRAINTS REMARK 4 REMARK 4 1I0U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-FEB-01. REMARK 100 THE DEPOSITION ID IS D_1000012765. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310; 283; 295 REMARK 210 PH : 5.5; 5.5; 5.5 REMARK 210 IONIC STRENGTH : 0.060; 0.060; 0.060 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM EGF-AB, 20MM CACL2; 1MM EGF REMARK 210 -AB, 20MM CACL2; 1MM 15N-EGF-AB, REMARK 210 20MM CACL2; 1.5MM EGF-A, 20MM REMARK 210 CACL2; 1.5MM EGF-A, 20MM CACL2 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNHA; 2D NOESY; DQF-COSY; 3D_15N REMARK 210 -SEPARATED_NOESY 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 : SPARKY 3.95, DYANA 1.5, MOLMOL REMARK 210 2.6 REMARK 210 METHOD USED : 1. TORSION ANGLES DYNAMICS 2. REMARK 210 RESTRAINED MOLECULAR DYNAMICS REMARK 210 WITH CALCIUM 3. ENERGY REMARK 210 MINIMISATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : ENERGY MINIMISED AVERAGE REMARK 210 STRUCTURE FROM 30 SELECTED REMARK 210 STRUCTURE WITH LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: 15N T1, T2, AND NOE RELAXATIONS TO OBTAIN BACKBONE REMARK 210 DYNAMICS INFORMATION T1/T2 DATA WERE NOT USED FOR STRUCTURE REMARK 210 REFINEMENT 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 CYS A 55 CA - CB - SG ANGL. DEV. = 8.6 DEGREES REMARK 500 CYS A 64 CA - CB - SG ANGL. DEV. = 7.1 DEGREES REMARK 500 CYS A 66 CA - CB - SG ANGL. DEV. = 12.0 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 THR A 2 -172.40 -64.57 REMARK 500 ASN A 9 87.69 -41.75 REMARK 500 CYS A 12 -129.77 -105.01 REMARK 500 SER A 13 35.05 -159.98 REMARK 500 HIS A 14 -104.48 -109.78 REMARK 500 ASP A 18 86.55 -52.36 REMARK 500 TYR A 23 154.44 -34.32 REMARK 500 VAL A 34 -76.11 -79.74 REMARK 500 GLN A 36 -66.96 65.01 REMARK 500 ASP A 49 -40.84 -140.77 REMARK 500 THR A 50 -102.30 -75.57 REMARK 500 GLN A 53 -113.69 -111.79 REMARK 500 LEU A 58 -152.91 -176.35 REMARK 500 GLU A 68 -79.00 47.75 REMARK 500 THR A 76 -37.79 -140.05 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 83 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 2 O REMARK 620 2 GLU A 4 OE1 104.2 REMARK 620 3 GLU A 4 OE2 58.2 46.9 REMARK 620 4 GLU A 4 N 78.1 75.3 59.9 REMARK 620 5 ASP A 18 OD1 61.9 76.6 64.2 122.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 84 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 41 OD2 REMARK 620 2 ILE A 42 O 65.9 REMARK 620 3 GLU A 44 OE1 106.4 89.8 REMARK 620 4 GLU A 44 OE2 62.8 58.1 46.6 REMARK 620 5 ASN A 57 OD1 162.2 101.4 59.5 100.2 REMARK 620 6 LEU A 58 O 131.0 144.2 109.5 153.8 66.7 REMARK 620 N 1 2 3 4 5 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 83 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 84 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F5Y RELATED DB: PDB REMARK 900 1F5Y CONTAINS LIGAND BINDING MODULES (LB1-2) OF THE HUMAN LDL REMARK 900 RECEPTOR REMARK 900 RELATED ID: 1LRX RELATED DB: PDB REMARK 900 1LRX CONTAINS YWTD MODULES OF THE HUMAN LDL RECEPTOR REMARK 900 RELATED ID: 1HZ8 RELATED DB: PDB REMARK 900 1HZ8 IS THE ENSEMBLE OF 30 STRUCTURES DBREF 1I0U A 1 82 UNP P01130 LDLR_HUMAN 314 395 SEQRES 1 A 82 GLY THR ASN GLU CYS LEU ASP ASN ASN GLY GLY CYS SER SEQRES 2 A 82 HIS VAL CYS ASN ASP LEU LYS ILE GLY TYR GLU CYS LEU SEQRES 3 A 82 CYS PRO ASP GLY PHE GLN LEU VAL ALA GLN ARG ARG CYS SEQRES 4 A 82 GLU ASP ILE ASP GLU CYS GLN ASP PRO ASP THR CYS SER SEQRES 5 A 82 GLN LEU CYS VAL ASN LEU GLU GLY GLY TYR LYS CYS GLN SEQRES 6 A 82 CYS GLU GLU GLY PHE GLN LEU ASP PRO HIS THR LYS ALA SEQRES 7 A 82 CYS LYS ALA VAL HET CA A 83 1 HET CA A 84 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) HELIX 1 1 ASN A 8 CYS A 12 5 5 SHEET 1 A 2 VAL A 15 ASN A 17 0 SHEET 2 A 2 GLU A 24 LEU A 26 -1 N GLU A 24 O ASN A 17 SHEET 1 B 2 GLN A 32 ALA A 35 0 SHEET 2 B 2 ARG A 38 GLU A 40 -1 N ARG A 38 O ALA A 35 SHEET 1 C 2 CYS A 55 VAL A 56 0 SHEET 2 C 2 LYS A 63 CYS A 64 -1 O LYS A 63 N VAL A 56 SHEET 1 D 2 PHE A 70 LEU A 72 0 SHEET 2 D 2 CYS A 79 ALA A 81 -1 O LYS A 80 N GLN A 71 SSBOND 1 CYS A 5 CYS A 16 1555 1555 2.02 SSBOND 2 CYS A 12 CYS A 25 1555 1555 2.02 SSBOND 3 CYS A 27 CYS A 39 1555 1555 2.02 SSBOND 4 CYS A 45 CYS A 55 1555 1555 2.02 SSBOND 5 CYS A 51 CYS A 64 1555 1555 2.02 SSBOND 6 CYS A 66 CYS A 79 1555 1555 2.02 LINK O THR A 2 CA CA A 83 1555 1555 2.83 LINK OE1 GLU A 4 CA CA A 83 1555 1555 2.69 LINK OE2 GLU A 4 CA CA A 83 1555 1555 2.75 LINK N GLU A 4 CA CA A 83 1555 1555 3.17 LINK OD1 ASP A 18 CA CA A 83 1555 1555 2.71 LINK OD2 ASP A 41 CA CA A 84 1555 1555 2.72 LINK O ILE A 42 CA CA A 84 1555 1555 2.70 LINK OE1 GLU A 44 CA CA A 84 1555 1555 2.71 LINK OE2 GLU A 44 CA CA A 84 1555 1555 2.76 LINK OD1 ASN A 57 CA CA A 84 1555 1555 2.67 LINK O LEU A 58 CA CA A 84 1555 1555 2.76 SITE 1 AC1 4 THR A 2 ASN A 3 GLU A 4 ASP A 18 SITE 1 AC2 6 ASP A 41 ILE A 42 GLU A 44 ASN A 57 SITE 2 AC2 6 LEU A 58 GLY A 60 CRYST1 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