HEADER METAL BINDING PROTEIN 22-MAY-17 5XND TITLE SOLUTION STRUCTURE OF THE MAJOR FISH ALLERGEN PARVALBUMIN SCO J 1 TITLE 2 DERIVED FROM THE PACIFIC MACKEREL COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARVALBUMIN BETA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCOMBER JAPONICUS; SOURCE 3 ORGANISM_COMMON: CHUB MACKEREL; SOURCE 4 ORGANISM_TAXID: 13676; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STRUCTURE FROM CYANA 2.1, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.KUMETA,H.NAKAYAMA,K.OGURA REVDAT 3 15-MAY-24 5XND 1 REMARK REVDAT 2 14-JUN-23 5XND 1 REMARK REVDAT 1 27-DEC-17 5XND 0 JRNL AUTH H.KUMETA,H.NAKAYAMA,K.OGURA JRNL TITL SOLUTION STRUCTURE OF THE MAJOR FISH ALLERGEN PARVALBUMIN JRNL TITL 2 SCO J 1 DERIVED FROM THE PACIFIC MACKEREL JRNL REF SCI REP V. 7 17160 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 29215073 JRNL DOI 10.1038/S41598-017-17281-6 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5XND COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1300003840. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 180 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-13C; U-15N] SCO J 1, 7 REMARK 210 % [U-2H] D2O, 20 MM MES, 150 MM REMARK 210 SODIUM CHLORIDE, 10 MM CACL2, 93% REMARK 210 H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCO; 3D HN(CO)CA; REMARK 210 3D HNCA; 3D CBCA(CO)NH; 3D REMARK 210 HNCACB; 3D C(CO)NH; 3D HBHA(CO) REMARK 210 NH; 3D HN(CA)HA; 3D 1H-15N NOESY; REMARK 210 3D 3D HCCH-TOCSY ALIPHATIC; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 2D REMARK 210 HBCBCGCDHD; 2D HBCBCGCDCEHE; 3D REMARK 210 1H-13C NOESY AROMATIC; 3D HCCH- REMARK 210 TOCSY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD; UNITY REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1C, TOPSPIN 3.2, NMRPIPE REMARK 210 8.2, SPARKY 3.113, TALOS+ 3.80F1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 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 A 1 77.62 -68.69 REMARK 500 1 LYS A 39 -171.57 -54.27 REMARK 500 1 ASP A 52 103.60 -40.38 REMARK 500 1 ILE A 59 76.93 -118.83 REMARK 500 1 GLU A 60 163.24 -47.50 REMARK 500 1 ALA A 73 64.56 -103.09 REMARK 500 1 ALA A 75 139.03 -39.61 REMARK 500 1 ARG A 76 -170.41 -56.74 REMARK 500 1 SER A 79 -176.34 -60.15 REMARK 500 2 ASP A 52 103.63 -44.24 REMARK 500 2 GLU A 60 166.44 -49.45 REMARK 500 3 LYS A 39 -174.72 -69.04 REMARK 500 3 ASP A 52 103.62 -43.26 REMARK 500 3 GLU A 60 175.96 -48.13 REMARK 500 3 LYS A 72 147.03 179.47 REMARK 500 4 MET A 1 78.71 -62.02 REMARK 500 4 LYS A 39 -171.38 -68.38 REMARK 500 4 ILE A 51 -70.54 -66.91 REMARK 500 4 ASP A 52 103.57 -41.02 REMARK 500 4 ILE A 59 83.32 -68.71 REMARK 500 4 LYS A 72 149.59 -175.15 REMARK 500 4 ARG A 76 -170.41 -61.59 REMARK 500 5 LYS A 39 -172.80 -53.84 REMARK 500 5 ASP A 52 103.73 -43.84 REMARK 500 5 LYS A 72 148.36 -179.02 REMARK 500 5 ARG A 76 -177.53 -57.37 REMARK 500 6 MET A 1 98.62 -39.77 REMARK 500 6 LYS A 39 -170.37 -54.77 REMARK 500 6 ASP A 52 103.62 -42.08 REMARK 500 6 GLU A 61 -34.59 -40.00 REMARK 500 6 LYS A 72 149.41 -175.32 REMARK 500 6 ASP A 91 93.65 -57.75 REMARK 500 7 MET A 1 39.35 38.37 REMARK 500 7 ASP A 52 103.56 -40.24 REMARK 500 7 LYS A 55 33.91 72.20 REMARK 500 7 LYS A 72 143.49 -177.88 REMARK 500 8 ASP A 52 103.43 -40.40 REMARK 500 8 ILE A 59 77.48 -119.91 REMARK 500 8 LYS A 72 141.80 -178.04 REMARK 500 8 ASP A 91 89.64 -55.20 REMARK 500 9 SER A 5 -0.62 84.06 REMARK 500 9 LYS A 39 -178.13 -63.15 REMARK 500 9 ASP A 52 103.53 -40.52 REMARK 500 9 GLU A 60 170.51 -45.47 REMARK 500 9 LYS A 72 146.37 -177.37 REMARK 500 9 ALA A 75 144.15 -39.78 REMARK 500 9 ARG A 76 -173.65 -57.67 REMARK 500 9 LEU A 78 158.67 -40.18 REMARK 500 9 ASP A 91 93.88 -65.73 REMARK 500 10 ASP A 52 103.49 -40.45 REMARK 500 REMARK 500 THIS ENTRY HAS 104 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 ASP A 52 OD1 REMARK 620 2 ASP A 54 OD1 140.9 REMARK 620 3 SER A 56 OG 114.0 77.6 REMARK 620 4 PHE A 58 O 85.3 130.2 62.9 REMARK 620 5 GLU A 63 OE1 147.6 69.3 50.3 62.4 REMARK 620 6 GLU A 63 OE2 155.9 47.3 89.2 100.7 46.1 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 ASP A 91 OD1 REMARK 620 2 ASP A 93 OD1 78.2 REMARK 620 3 ASP A 95 OD1 96.6 46.7 REMARK 620 4 LYS A 97 O 49.9 105.1 85.5 REMARK 620 5 GLU A 102 OE1 93.8 109.2 150.1 121.9 REMARK 620 6 GLU A 102 OE2 50.5 83.9 127.9 94.7 46.1 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36086 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE MAJOR FISH ALLERGEN PARVALBUMIN SCO J 1 REMARK 900 DERIVED FROM THE PACIFIC MACKEREL DBREF 5XND A 1 109 UNP P59747 PRVB_SCOJP 1 109 SEQADV 5XND GLY A -4 UNP P59747 EXPRESSION TAG SEQADV 5XND PRO A -3 UNP P59747 EXPRESSION TAG SEQADV 5XND LEU A -2 UNP P59747 EXPRESSION TAG SEQADV 5XND GLY A -1 UNP P59747 EXPRESSION TAG SEQADV 5XND SER A 0 UNP P59747 EXPRESSION TAG SEQRES 1 A 114 GLY PRO LEU GLY SER MET ALA PHE ALA SER VAL LEU LYS SEQRES 2 A 114 ASP ALA GLU VAL THR ALA ALA LEU ASP GLY CYS LYS ALA SEQRES 3 A 114 ALA GLY SER PHE ASP HIS LYS LYS PHE PHE LYS ALA CYS SEQRES 4 A 114 GLY LEU SER GLY LYS SER THR ASP GLU VAL LYS LYS ALA SEQRES 5 A 114 PHE ALA ILE ILE ASP GLN ASP LYS SER GLY PHE ILE GLU SEQRES 6 A 114 GLU GLU GLU LEU LYS LEU PHE LEU GLN ASN PHE LYS ALA SEQRES 7 A 114 GLY ALA ARG ALA LEU SER ASP ALA GLU THR LYS ALA PHE SEQRES 8 A 114 LEU LYS ALA GLY ASP SER ASP GLY ASP GLY LYS ILE GLY SEQRES 9 A 114 ILE ASP GLU PHE ALA ALA MET ILE LYS GLY HET CA A 201 1 HET CA A 202 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) HELIX 1 AA1 ALA A 2 LEU A 7 1 6 HELIX 2 AA2 LYS A 8 GLY A 18 1 11 HELIX 3 AA3 ASP A 26 GLY A 35 1 10 HELIX 4 AA4 SER A 40 ASP A 52 1 13 HELIX 5 AA5 GLU A 61 LYS A 65 1 5 HELIX 6 AA6 ALA A 81 ALA A 89 1 9 HELIX 7 AA7 GLY A 99 ALA A 104 1 6 HELIX 8 AA8 ALA A 104 GLY A 109 1 6 SHEET 1 AA1 2 ILE A 59 GLU A 60 0 SHEET 2 AA1 2 LYS A 97 ILE A 98 -1 O ILE A 98 N ILE A 59 LINK OD1 ASP A 52 CA CA A 201 1555 1555 2.85 LINK OD1 ASP A 54 CA CA A 201 1555 1555 3.19 LINK OG SER A 56 CA CA A 201 1555 1555 2.85 LINK O PHE A 58 CA CA A 201 1555 1555 2.85 LINK OE1 GLU A 63 CA CA A 201 1555 1555 2.85 LINK OE2 GLU A 63 CA CA A 201 1555 1555 2.85 LINK OD1 ASP A 91 CA CA A 202 1555 1555 2.85 LINK OD1 ASP A 93 CA CA A 202 1555 1555 3.20 LINK OD1 ASP A 95 CA CA A 202 1555 1555 2.85 LINK O LYS A 97 CA CA A 202 1555 1555 2.85 LINK OE1 GLU A 102 CA CA A 202 1555 1555 2.85 LINK OE2 GLU A 102 CA CA A 202 1555 1555 2.85 SITE 1 AC1 5 ASP A 52 ASP A 54 SER A 56 PHE A 58 SITE 2 AC1 5 GLU A 63 SITE 1 AC2 5 ASP A 91 ASP A 93 ASP A 95 LYS A 97 SITE 2 AC2 5 GLU A 102 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