HEADER LIPID BINDING PROTEIN 09-OCT-19 6UM9 TITLE GYPSY MOTH PHEROMONE-BINDING PROTEIN 1 (LDISPBP1) NMR STRUCTURE AT PH TITLE 2 4.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHEROMONE BINDING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LYMANTRIA DISPAR; SOURCE 3 ORGANISM_COMMON: GYPSY MOTH; SOURCE 4 ORGANISM_TAXID: 13123; SOURCE 5 GENE: PBP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET 30 XA/LIC KEYWDS LIPID BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.TERRADO,E.PLETTNER REVDAT 3 14-JUN-23 6UM9 1 REMARK REVDAT 2 07-OCT-20 6UM9 1 JRNL REVDAT 1 23-SEP-20 6UM9 0 JRNL AUTH M.TERRADO,M.OKON,L.P.MCINTOSH,E.PLETTNER JRNL TITL LIGAND- AND PH-INDUCED STRUCTURAL TRANSITION OF GYPSY MOTH JRNL TITL 2 LYMANTRIA DISPAR PHEROMONE-BINDING PROTEIN 1 (LDISPBP1). JRNL REF BIOCHEMISTRY V. 59 3411 2020 JRNL REFN ISSN 0006-2960 JRNL PMID 32877603 JRNL DOI 10.1021/ACS.BIOCHEM.0C00592 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRE REMARK 3 AUTHORS : RYU H, LIM GT, SUNG BH, LEE J REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6UM9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1000244636. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.2 M [U-99% 13C; U-99% 15N] REMARK 210 LDISPBP1, 50 MM SODIUM ACETATE, REMARK 210 1 MM EDTA, 0.05 % W/V SODIUM REMARK 210 AZIDE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HNCO; 3D HN(CO)CA; 3D C(CO)NH; REMARK 210 3D HBHA(CO)NH; 3D 1H-13C NOESY; REMARK 210 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, SPARKY REMARK 210 METHOD USED : STAP REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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: 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 LEU A 55 CB - CG - CD2 ANGL. DEV. = 10.2 DEGREES REMARK 500 2 TYR A 41 CB - CG - CD2 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 TYR A 41 CB - CG - CD1 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 HIS A 95 CA - CB - CG ANGL. DEV. = 10.8 DEGREES REMARK 500 3 TYR A 41 CB - CG - CD2 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 TYR A 41 CB - CG - CD1 ANGL. DEV. = -5.1 DEGREES REMARK 500 4 TYR A 41 CB - CG - CD2 ANGL. DEV. = 3.9 DEGREES REMARK 500 4 TYR A 41 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 5 TYR A 41 CB - CG - CD2 ANGL. DEV. = 3.9 DEGREES REMARK 500 5 TYR A 41 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 5 LEU A 55 CB - CG - CD2 ANGL. DEV. = 10.4 DEGREES REMARK 500 5 PHE A 76 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 5 PHE A 76 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 TYR A 41 CB - CG - CD2 ANGL. DEV. = 3.6 DEGREES REMARK 500 6 LEU A 55 CB - CG - CD2 ANGL. DEV. = 10.8 DEGREES REMARK 500 7 TYR A 41 CB - CG - CD2 ANGL. DEV. = 5.2 DEGREES REMARK 500 7 TYR A 41 CB - CG - CD1 ANGL. DEV. = -5.5 DEGREES REMARK 500 7 LEU A 55 CB - CG - CD2 ANGL. DEV. = 10.3 DEGREES REMARK 500 8 TYR A 41 CB - CG - CD2 ANGL. DEV. = 4.4 DEGREES REMARK 500 8 TYR A 41 CB - CG - CD1 ANGL. DEV. = -4.4 DEGREES REMARK 500 9 TYR A 41 CB - CG - CD2 ANGL. DEV. = 4.2 DEGREES REMARK 500 9 TYR A 41 CB - CG - CD1 ANGL. DEV. = -4.1 DEGREES REMARK 500 9 LEU A 55 CB - CG - CD2 ANGL. DEV. = 10.6 DEGREES REMARK 500 10 TYR A 41 CB - CG - CD2 ANGL. DEV. = 4.5 DEGREES REMARK 500 10 TYR A 41 CB - CG - CD1 ANGL. DEV. = -4.7 DEGREES REMARK 500 11 TYR A 41 CB - CG - CD2 ANGL. DEV. = 4.8 DEGREES REMARK 500 11 TYR A 41 CB - CG - CD1 ANGL. DEV. = -5.1 DEGREES REMARK 500 13 TYR A 41 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 13 LEU A 55 CB - CG - CD2 ANGL. DEV. = 10.4 DEGREES REMARK 500 14 LEU A 23 CB - CG - CD2 ANGL. DEV. = 10.6 DEGREES REMARK 500 14 TYR A 41 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 15 LEU A 23 CB - CG - CD2 ANGL. DEV. = 10.4 DEGREES REMARK 500 15 TYR A 41 CB - CG - CD2 ANGL. DEV. = 5.2 DEGREES REMARK 500 15 TYR A 41 CB - CG - CD1 ANGL. DEV. = -5.5 DEGREES REMARK 500 15 LEU A 55 CB - CG - CD2 ANGL. DEV. = 10.5 DEGREES REMARK 500 16 TYR A 41 CB - CG - CD2 ANGL. DEV. = 4.6 DEGREES REMARK 500 16 TYR A 41 CB - CG - CD1 ANGL. DEV. = -4.9 DEGREES REMARK 500 17 LEU A 55 CB - CG - CD2 ANGL. DEV. = 10.5 DEGREES REMARK 500 19 LEU A 55 CB - CG - CD2 ANGL. DEV. = 10.4 DEGREES REMARK 500 20 LEU A 23 CB - CG - CD2 ANGL. DEV. = 10.4 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 LYS A 58 38.48 -93.92 REMARK 500 1 ASP A 142 32.82 -96.70 REMARK 500 2 LYS A 58 49.47 -92.07 REMARK 500 3 LYS A 58 33.58 -98.04 REMARK 500 4 VAL A 4 -60.28 -107.50 REMARK 500 4 LYS A 58 44.50 -90.95 REMARK 500 6 ASP A 142 34.58 -91.91 REMARK 500 7 GLN A 7 -29.40 -148.46 REMARK 500 7 THR A 9 -9.58 75.03 REMARK 500 7 LYS A 58 46.59 -89.96 REMARK 500 8 MET A 5 -40.43 68.85 REMARK 500 8 ASP A 142 32.99 -95.93 REMARK 500 9 LYS A 58 43.95 -92.02 REMARK 500 9 ASP A 142 34.72 -97.03 REMARK 500 10 LYS A 58 48.39 -91.28 REMARK 500 10 ASP A 142 38.29 -98.15 REMARK 500 11 GLU A 3 19.62 59.15 REMARK 500 11 LYS A 58 33.47 -97.68 REMARK 500 12 VAL A 4 -62.34 -108.61 REMARK 500 12 LYS A 58 32.86 -97.57 REMARK 500 13 LYS A 58 45.19 -91.72 REMARK 500 15 GLU A 3 27.00 47.63 REMARK 500 15 ASP A 142 34.62 -96.71 REMARK 500 16 LYS A 58 38.80 -98.21 REMARK 500 18 ILE A 10 110.45 73.19 REMARK 500 19 ASP A 142 33.36 -96.67 REMARK 500 20 LYS A 58 42.68 -89.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 4 MET A 5 1 -148.83 REMARK 500 VAL A 4 MET A 5 2 -146.44 REMARK 500 VAL A 4 MET A 5 3 -147.66 REMARK 500 VAL A 4 MET A 5 7 -147.33 REMARK 500 VAL A 4 MET A 5 9 -148.25 REMARK 500 VAL A 4 MET A 5 11 -146.71 REMARK 500 VAL A 4 MET A 5 13 -148.65 REMARK 500 VAL A 4 MET A 5 15 -146.50 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 4 PHE A 34 0.10 SIDE CHAIN REMARK 500 5 PHE A 34 0.10 SIDE CHAIN REMARK 500 5 HIS A 80 0.08 SIDE CHAIN REMARK 500 6 PHE A 34 0.09 SIDE CHAIN REMARK 500 7 PHE A 34 0.10 SIDE CHAIN REMARK 500 7 HIS A 80 0.08 SIDE CHAIN REMARK 500 8 PHE A 34 0.09 SIDE CHAIN REMARK 500 9 PHE A 34 0.08 SIDE CHAIN REMARK 500 11 PHE A 34 0.09 SIDE CHAIN REMARK 500 13 PHE A 34 0.09 SIDE CHAIN REMARK 500 15 PHE A 34 0.09 SIDE CHAIN REMARK 500 17 PHE A 34 0.09 SIDE CHAIN REMARK 500 18 PHE A 34 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30679 RELATED DB: BMRB REMARK 900 GYPSY MOTH PHEROMONE-BINDING PROTEIN 1 (LDISPBP1) NMR STRUCTURE AT REMARK 900 PH 4.5 DBREF 6UM9 A 1 143 UNP O16105 O16105_LYMDI 20 162 SEQRES 1 A 143 SER LYS GLU VAL MET LYS GLN MET THR ILE ASN PHE ALA SEQRES 2 A 143 LYS PRO MET GLU ALA CYS LYS GLN GLU LEU ASN VAL PRO SEQRES 3 A 143 ASP ALA VAL MET GLN ASP PHE PHE ASN PHE TRP LYS GLU SEQRES 4 A 143 GLY TYR GLN ILE THR ASN ARG GLU ALA GLY CYS VAL ILE SEQRES 5 A 143 LEU CYS LEU ALA LYS LYS LEU GLU LEU LEU ASP GLN ASP SEQRES 6 A 143 MET ASN LEU HIS HIS GLY LYS ALA MET GLU PHE ALA MET SEQRES 7 A 143 LYS HIS GLY ALA ASP GLU ALA MET ALA LYS GLN LEU LEU SEQRES 8 A 143 ASP ILE LYS HIS SER CYS GLU LYS VAL ILE THR ILE VAL SEQRES 9 A 143 ALA ASP ASP PRO CYS GLN THR MET LEU ASN LEU ALA MET SEQRES 10 A 143 CYS PHE LYS ALA GLU ILE HIS LYS LEU ASP TRP ALA PRO SEQRES 11 A 143 THR LEU ASP VAL ALA VAL GLY GLU LEU LEU ALA ASP THR HELIX 1 AA1 SER A 1 MET A 5 5 5 HELIX 2 AA2 PHE A 12 LEU A 23 1 12 HELIX 3 AA3 PRO A 26 TRP A 37 1 12 HELIX 4 AA4 ASN A 45 LYS A 58 1 14 HELIX 5 AA5 ASP A 63 ASN A 67 5 5 HELIX 6 AA6 LYS A 72 HIS A 80 1 9 HELIX 7 AA7 ASP A 83 LYS A 99 1 17 HELIX 8 AA8 ASP A 107 LEU A 126 1 20 HELIX 9 AA9 THR A 131 ASP A 142 1 12 SSBOND 1 CYS A 19 CYS A 54 1555 1555 2.01 SSBOND 2 CYS A 50 CYS A 109 1555 1555 2.04 SSBOND 3 CYS A 97 CYS A 118 1555 1555 2.05 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