HEADER STRUCTURAL PROTEIN 21-DEC-17 6BYV TITLE SOLUTION NMR STRUCTURE OF CYSTEINE-RICH CALCIUM BOUND DOMAINS OF VERY TITLE 2 LOW DENSITY LIPOPROTEIN RECEPTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: VERY LOW-DENSITY LIPOPROTEIN RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VLDL-R; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: VLDLR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 3 MODULES, CALCIUM-BOUND DOMAINS, DISULFIDE BONDS, STRUCTURAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.BANERJEE,J.M.GRUSCHUS,N.TJANDRA,S.YAKOVLEV,L.MEDVED REVDAT 5 14-JUN-23 6BYV 1 REMARK REVDAT 4 17-APR-19 6BYV 1 REMARK REVDAT 3 08-AUG-18 6BYV 1 JRNL REVDAT 2 01-AUG-18 6BYV 1 JRNL REVDAT 1 18-JUL-18 6BYV 0 JRNL AUTH K.BANERJEE,S.YAKOVLEV,J.M.GRUSCHUS,L.MEDVED,N.TJANDRA JRNL TITL NUCLEAR MAGNETIC RESONANCE SOLUTION STRUCTURE OF THE JRNL TITL 2 RECOMBINANT FRAGMENT CONTAINING THREE FIBRIN-BINDING JRNL TITL 3 CYSTEINE-RICH DOMAINS OF THE VERY LOW DENSITY LIPOPROTEIN JRNL TITL 4 RECEPTOR. JRNL REF BIOCHEMISTRY V. 57 4395 2018 JRNL REFN ISSN 1520-4995 JRNL PMID 29965730 JRNL DOI 10.1021/ACS.BIOCHEM.8B00349 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6BYV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1000231406. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 306.5; 306.5 REMARK 210 PH : 6.2; 6.2 REMARK 210 IONIC STRENGTH : 100; 100 REMARK 210 PRESSURE : 760 MMHG; 760 MMHG REMARK 210 SAMPLE CONTENTS : 350 UM [U-99% 15N] VLDLR, 93% REMARK 210 H2O/7% D2O; 250 UM [U-99% 13C; U- REMARK 210 99% 15N] VLDLR, 93% H2O/7% D2O; REMARK 210 250 UM [U-99% 13C; U-99% 15N] REMARK 210 VLDLR, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HNCO; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRPIPE, ANALYSIS, REMARK 210 TALOS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 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 PRO A 17 155.51 -45.23 REMARK 500 1 SER A 18 -9.55 -47.63 REMARK 500 1 LYS A 21 172.32 -45.04 REMARK 500 1 CYS A 22 100.45 -45.58 REMARK 500 1 ASP A 23 17.12 -150.83 REMARK 500 1 PRO A 26 17.10 -64.69 REMARK 500 1 PRO A 36 -15.95 -44.72 REMARK 500 1 CYS A 39 35.32 -88.03 REMARK 500 1 HIS A 40 67.90 -57.52 REMARK 500 1 MET A 41 -25.17 169.18 REMARK 500 1 CYS A 44 -175.59 -54.16 REMARK 500 1 ILE A 46 135.30 68.33 REMARK 500 1 GLU A 48 130.29 -171.18 REMARK 500 1 VAL A 61 -19.60 -38.92 REMARK 500 1 CYS A 71 36.29 -59.72 REMARK 500 1 ASN A 82 -95.13 -55.03 REMARK 500 1 PRO A 87 -13.89 -42.51 REMARK 500 1 ARG A 100 -7.30 -59.34 REMARK 500 1 CYS A 104 98.72 -30.44 REMARK 500 1 ASP A 109 -54.88 -170.78 REMARK 500 1 CYS A 110 -74.81 -58.44 REMARK 500 1 SER A 111 -64.31 -106.50 REMARK 500 1 CYS A 119 44.41 -88.54 REMARK 500 2 PRO A 17 152.88 -44.62 REMARK 500 2 SER A 18 -10.49 -48.45 REMARK 500 2 LYS A 21 171.95 -44.23 REMARK 500 2 CYS A 22 101.22 -44.88 REMARK 500 2 ASP A 23 19.34 -154.06 REMARK 500 2 PRO A 26 18.35 -67.04 REMARK 500 2 PRO A 36 -15.89 -46.49 REMARK 500 2 CYS A 39 30.17 -89.25 REMARK 500 2 HIS A 40 71.02 -52.48 REMARK 500 2 MET A 41 -36.81 165.31 REMARK 500 2 CYS A 44 -178.04 -58.07 REMARK 500 2 ILE A 46 -67.48 77.06 REMARK 500 2 GLU A 48 150.81 176.90 REMARK 500 2 CYS A 71 33.86 -55.99 REMARK 500 2 ASN A 79 50.29 37.89 REMARK 500 2 ASN A 82 -86.91 -67.58 REMARK 500 2 CYS A 104 101.43 -25.05 REMARK 500 2 ASP A 109 -57.99 -135.74 REMARK 500 2 CYS A 110 -66.89 -103.88 REMARK 500 2 SER A 111 -64.92 -100.23 REMARK 500 2 ASP A 112 -36.46 -144.77 REMARK 500 2 LEU A 117 109.56 -53.48 REMARK 500 2 CYS A 119 36.36 -90.32 REMARK 500 3 ASP A 7 157.14 -35.68 REMARK 500 3 SER A 18 -11.12 -41.12 REMARK 500 3 LYS A 21 172.11 -43.38 REMARK 500 3 CYS A 22 101.16 -48.99 REMARK 500 REMARK 500 THIS ENTRY HAS 434 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 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A 20 O REMARK 620 2 ASP A 23 OD1 81.8 REMARK 620 3 ASP A 25 O 155.3 118.1 REMARK 620 4 ASP A 27 OD2 95.2 123.3 62.2 REMARK 620 5 ASP A 33 OD2 96.7 157.3 70.7 79.4 REMARK 620 6 GLU A 34 OE2 120.8 69.8 81.8 143.8 92.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A 63 O REMARK 620 2 ASP A 66 OD1 122.8 REMARK 620 3 GLU A 68 O 100.6 78.9 REMARK 620 4 ASP A 70 OD2 153.9 82.8 78.3 REMARK 620 5 ASP A 76 OD2 128.1 80.9 130.6 54.7 REMARK 620 6 GLU A 77 OE2 69.9 73.8 137.9 127.9 75.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 203 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 102 O REMARK 620 2 ASN A 105 OD1 109.8 REMARK 620 3 GLN A 107 O 141.2 71.6 REMARK 620 4 ASP A 109 OD2 78.6 92.0 62.7 REMARK 620 5 ASP A 115 OD2 99.8 146.6 75.8 79.0 REMARK 620 6 GLU A 116 OE2 155.8 80.1 62.4 124.1 78.9 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30388 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF CYSTEINE-RICH CALCIUM BOUND DOMAINS OF REMARK 900 VERY LOW DENSITY LIPOPROTEIN RECEPTOR DBREF 6BYV A 1 121 UNP P98155 VLDLR_HUMAN 70 190 SEQRES 1 A 121 LYS THR CYS ALA GLU SER ASP PHE VAL CYS ASN ASN GLY SEQRES 2 A 121 GLN CYS VAL PRO SER ARG TRP LYS CYS ASP GLY ASP PRO SEQRES 3 A 121 ASP CYS GLU ASP GLY SER ASP GLU SER PRO GLU GLN CYS SEQRES 4 A 121 HIS MET ARG THR CYS ARG ILE HIS GLU ILE SER CYS GLY SEQRES 5 A 121 ALA HIS SER THR GLN CYS ILE PRO VAL SER TRP ARG CYS SEQRES 6 A 121 ASP GLY GLU ASN ASP CYS ASP SER GLY GLU ASP GLU GLU SEQRES 7 A 121 ASN CYS GLY ASN ILE THR CYS SER PRO ASP GLU PHE THR SEQRES 8 A 121 CYS SER SER GLY ARG CYS ILE SER ARG ASN PHE VAL CYS SEQRES 9 A 121 ASN GLY GLN ASP ASP CYS SER ASP GLY SER ASP GLU LEU SEQRES 10 A 121 ASP CYS ALA PRO HET CA A 201 1 HET CA A 202 1 HET CA A 203 1 HETNAM CA CALCIUM ION FORMUL 2 CA 3(CA 2+) HELIX 1 AA1 PRO A 17 LYS A 21 5 5 HELIX 2 AA2 GLY A 31 SER A 35 5 5 HELIX 3 AA3 PRO A 60 ARG A 64 5 5 HELIX 4 AA4 SER A 99 VAL A 103 5 5 HELIX 5 AA5 GLY A 113 LEU A 117 5 5 SHEET 1 AA1 2 PHE A 8 VAL A 9 0 SHEET 2 AA1 2 CYS A 15 VAL A 16 -1 O VAL A 16 N PHE A 8 SHEET 1 AA2 2 ILE A 49 SER A 50 0 SHEET 2 AA2 2 CYS A 58 ILE A 59 -1 O ILE A 59 N ILE A 49 SHEET 1 AA3 2 PHE A 90 THR A 91 0 SHEET 2 AA3 2 CYS A 97 ILE A 98 -1 O ILE A 98 N PHE A 90 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 39 1555 1555 2.01 SSBOND 4 CYS A 44 CYS A 58 1555 1555 2.03 SSBOND 5 CYS A 51 CYS A 71 1555 1555 2.02 SSBOND 6 CYS A 65 CYS A 80 1555 1555 2.02 SSBOND 7 CYS A 85 CYS A 97 1555 1555 2.01 SSBOND 8 CYS A 92 CYS A 110 1555 1555 2.02 SSBOND 9 CYS A 104 CYS A 119 1555 1555 2.02 LINK O TRP A 20 CA CA A 201 1555 1555 2.44 LINK OD1 ASP A 23 CA CA A 201 1555 1555 2.54 LINK O ASP A 25 CA CA A 201 1555 1555 2.45 LINK OD2 ASP A 27 CA CA A 201 1555 1555 2.54 LINK OD2 ASP A 33 CA CA A 201 1555 1555 2.52 LINK OE2 GLU A 34 CA CA A 201 1555 1555 2.51 LINK O TRP A 63 CA CA A 202 1555 1555 2.73 LINK OD1 ASP A 66 CA CA A 202 1555 1555 2.56 LINK O GLU A 68 CA CA A 202 1555 1555 2.50 LINK OD2 ASP A 70 CA CA A 202 1555 1555 2.59 LINK OD2 ASP A 76 CA CA A 202 1555 1555 2.61 LINK OE2 GLU A 77 CA CA A 202 1555 1555 2.26 LINK O PHE A 102 CA CA A 203 1555 1555 2.54 LINK OD1 ASN A 105 CA CA A 203 1555 1555 2.51 LINK O GLN A 107 CA CA A 203 1555 1555 2.54 LINK OD2 ASP A 109 CA CA A 203 1555 1555 2.28 LINK OD2 ASP A 115 CA CA A 203 1555 1555 2.51 LINK OE2 GLU A 116 CA CA A 203 1555 1555 2.30 SITE 1 AC1 7 TRP A 20 LYS A 21 ASP A 23 ASP A 25 SITE 2 AC1 7 ASP A 27 ASP A 33 GLU A 34 SITE 1 AC2 8 TRP A 63 ARG A 64 CYS A 65 ASP A 66 SITE 2 AC2 8 GLU A 68 ASP A 70 ASP A 76 GLU A 77 SITE 1 AC3 8 PHE A 102 VAL A 103 CYS A 104 ASN A 105 SITE 2 AC3 8 GLN A 107 ASP A 109 ASP A 115 GLU A 116 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