10 20 30 40 50 60 70 80 1XFR - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSPORT PROTEIN 15-SEP-04 1XFR
TITLE SOLUTION STRUCTURE OF THE BOMBYX MORI PHEROMONE-BINDING TITLE 2 PROTEIN FRAGMENT BMPBP(1-128) AT PH 6.5
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHEROMONE-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BMPBP(1-128); COMPND 5 SYNONYM: PBP; COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOMBYX MORI; SOURCE 3 ORGANISM_COMMON: DOMESTIC SILKWORM; SOURCE 4 ORGANISM_TAXID: 7091; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET22B
KEYWDS INSECT ODORANT-BINDING PROTEIN, BOMBYX MORI PHEROMONE- KEYWDS 2 BINDING PROTEIN, BMPBPB, ALPHA-HELICAL TRANSPORT PROTEIN, KEYWDS 3 TRUNCATED FRAGMENT BMPBP(1-128)
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR E.MICHEL,F.F.DAMBERGER,W.S.LEAL,K.WUTHRICH
REVDAT 2 24-FEB-09 1XFR 1 VERSN REVDAT 1 27-SEP-05 1XFR 0
JRNL AUTH E.MICHEL,F.F.DAMBERGER,W.S.LEAL,K.WUTHRICH JRNL TITL SOLUTION STRUCTURE OF THE BOMBYX MORI JRNL TITL 2 PHEROMONE-BINDING PROTEIN FRAGMENT BMPBP(1-128) AT JRNL TITL 3 PH 6.5 JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 6.01 REMARK 3 AUTHORS : T.HERRMANN, P.GUNTERT REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON 2368 NOE- REMARK 3 DERIVED DISTANCE CONSTRAINTS, AND 560 DIHEDRAL ANGLE REMARK 3 CONSTRAINTS
REMARK 4 REMARK 4 1XFR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-SEP-04. REMARK 100 THE RCSB ID CODE IS RCSB030312.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 78MM REMARK 210 PRESSURE : 1ATM REMARK 210 SAMPLE CONTENTS : 1.1MM BMPBP(1-128) U-15N,13C; REMARK 210 50MM POTASSIUM PHOSPHATE REMARK 210 BUFFER; 0.2% SODIUM AZIDE; 95% REMARK 210 H2O, 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, 3D_ REMARK 210 13C-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 1.1, DYANA 6.01 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 ENERGY MINIMIZATION 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 : 5 REMARK 210 REMARK 210 REMARK: TWO 13C-RESOLVED NOESY SPECTRA WERE USED FOR THE REMARK 210 ALIPHATIC AND AROMATIC CARBONS RESPECTIVELY.
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 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 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 CYS A 108 CA - CB - SG ANGL. DEV. = 7.1 DEGREES REMARK 500 5 CYS A 108 CA - CB - SG ANGL. DEV. = 8.3 DEGREES REMARK 500 6 CYS A 108 CA - CB - SG ANGL. DEV. = 8.0 DEGREES REMARK 500 8 CYS A 108 CA - CB - SG ANGL. DEV. = 6.9 DEGREES REMARK 500 14 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 14 CYS A 117 CA - CB - SG ANGL. DEV. = 8.0 DEGREES REMARK 500 15 CYS A 108 CA - CB - SG ANGL. DEV. = 6.8 DEGREES REMARK 500 19 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.0 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 1 ALA A 15 14.54 -69.77 REMARK 500 1 THR A 24 77.17 51.71 REMARK 500 1 TRP A 37 47.17 -89.99 REMARK 500 1 LEU A 68 123.34 63.75 REMARK 500 2 ALA A 15 8.56 -68.29 REMARK 500 2 THR A 24 73.85 50.38 REMARK 500 2 ASP A 32 -70.51 -74.65 REMARK 500 2 PRO A 64 4.33 -67.68 REMARK 500 2 LEU A 68 107.38 63.07 REMARK 500 2 HIS A 69 93.09 -66.53 REMARK 500 3 ALA A 15 25.99 -79.73 REMARK 500 3 THR A 24 83.54 50.18 REMARK 500 3 ASP A 106 97.37 -68.57 REMARK 500 4 LYS A 14 -72.98 -66.01 REMARK 500 4 ALA A 15 26.26 -72.90 REMARK 500 4 THR A 24 86.05 51.63 REMARK 500 4 LYS A 38 -168.34 -65.57 REMARK 500 4 PRO A 64 43.59 -82.52 REMARK 500 4 GLU A 65 -35.87 -149.81 REMARK 500 4 ASN A 104 -169.82 -74.02 REMARK 500 5 ALA A 15 22.02 -72.85 REMARK 500 5 THR A 24 75.12 47.00 REMARK 500 5 GLU A 39 32.28 -77.06 REMARK 500 5 TYR A 41 150.57 -46.07 REMARK 500 5 ASN A 60 81.76 42.25 REMARK 500 5 PRO A 64 41.85 -84.35 REMARK 500 5 GLU A 65 -23.92 -147.61 REMARK 500 5 ASP A 106 96.26 -61.95 REMARK 500 5 TRP A 127 42.43 -94.74 REMARK 500 6 THR A 24 87.86 46.76 REMARK 500 6 TRP A 37 45.25 -90.10 REMARK 500 6 GLU A 39 83.76 -49.79 REMARK 500 6 ASN A 60 74.69 75.93 REMARK 500 6 ASN A 67 25.51 -72.33 REMARK 500 6 LEU A 68 125.24 65.15 REMARK 500 6 CYS A 97 -33.15 -132.12 REMARK 500 6 ASP A 106 97.91 -63.52 REMARK 500 6 TRP A 110 -72.97 -50.16 REMARK 500 7 GLU A 22 -71.48 -71.20 REMARK 500 7 THR A 24 68.64 61.19 REMARK 500 7 GLU A 39 40.33 -87.10 REMARK 500 7 PRO A 64 -5.81 -57.95 REMARK 500 7 LEU A 68 113.50 43.56 REMARK 500 7 ASP A 106 96.12 -69.62 REMARK 500 8 SER A 9 1.21 -64.54 REMARK 500 8 THR A 24 83.27 40.17 REMARK 500 8 TRP A 37 44.20 -88.14 REMARK 500 8 ASP A 63 -179.45 -64.31 REMARK 500 8 LEU A 68 156.36 49.57 REMARK 500 8 ASP A 106 97.12 -68.53 REMARK 500 8 ASN A 126 27.58 95.42 REMARK 500 9 THR A 24 72.25 40.89 REMARK 500 9 MET A 61 52.62 -100.03 REMARK 500 9 ASP A 106 96.05 -66.17 REMARK 500 10 GLN A 2 -67.00 55.80 REMARK 500 10 ALA A 15 22.55 -75.65 REMARK 500 10 THR A 24 82.83 46.49 REMARK 500 10 LYS A 38 -174.92 -64.25 REMARK 500 10 GLU A 39 54.27 -117.37 REMARK 500 10 ASN A 60 19.22 59.39 REMARK 500 10 ASP A 63 171.56 -58.83 REMARK 500 10 PRO A 64 42.32 -83.15 REMARK 500 10 GLU A 65 -41.99 -145.53 REMARK 500 10 LYS A 99 -30.14 -131.44 REMARK 500 10 ASP A 105 3.34 -68.23 REMARK 500 10 ASP A 106 94.26 -58.93 REMARK 500 10 TRP A 127 34.79 -77.98 REMARK 500 11 THR A 24 73.02 48.33 REMARK 500 11 LYS A 44 -23.58 -142.17 REMARK 500 11 PRO A 64 43.74 -77.60 REMARK 500 11 GLU A 65 -28.16 -146.94 REMARK 500 11 LEU A 68 145.36 55.90 REMARK 500 11 ASP A 106 93.46 -63.41 REMARK 500 12 ALA A 15 26.42 -72.61 REMARK 500 12 THR A 24 85.33 60.91 REMARK 500 12 PHE A 36 -51.35 -24.72 REMARK 500 12 TRP A 37 26.09 -66.72 REMARK 500 12 GLU A 39 102.93 -57.32 REMARK 500 12 ASP A 106 90.24 -66.82 REMARK 500 13 THR A 24 83.97 43.18 REMARK 500 13 ASP A 32 -72.13 -78.60 REMARK 500 13 GLU A 39 24.46 -77.20 REMARK 500 13 PRO A 64 41.87 -83.62 REMARK 500 13 GLU A 65 -31.93 -150.67 REMARK 500 13 ASP A 105 -9.32 -57.65 REMARK 500 13 ASP A 106 94.98 -62.59 REMARK 500 14 ALA A 15 44.92 -78.61 REMARK 500 14 GLU A 18 -72.34 -54.96 REMARK 500 14 THR A 24 77.66 47.52 REMARK 500 14 ASN A 45 105.15 -59.95 REMARK 500 14 ASP A 63 175.68 -56.62 REMARK 500 14 PRO A 64 43.61 -77.81 REMARK 500 14 GLU A 65 -54.76 -152.35 REMARK 500 14 CYS A 97 -50.07 -130.17 REMARK 500 15 ALA A 15 27.05 -77.49 REMARK 500 15 THR A 24 70.04 49.85 REMARK 500 15 PRO A 64 40.94 -81.05 REMARK 500 15 GLU A 65 -25.57 -146.56 REMARK 500 15 LEU A 68 140.27 60.75 REMARK 500 15 ASP A 106 94.26 -68.04 REMARK 500 16 THR A 24 78.92 42.46 REMARK 500 16 GLU A 39 49.50 -103.23 REMARK 500 16 ASN A 60 100.14 63.94 REMARK 500 16 LEU A 68 112.25 62.98 REMARK 500 16 TRP A 127 31.72 -79.81 REMARK 500 17 GLN A 2 -78.00 22.20 REMARK 500 17 LEU A 10 -51.60 -129.07 REMARK 500 17 ALA A 15 22.36 -69.79 REMARK 500 17 THR A 24 87.92 57.36 REMARK 500 17 ASN A 45 93.46 -63.84 REMARK 500 17 PRO A 64 41.60 -84.98 REMARK 500 17 GLU A 65 -18.38 -147.38 REMARK 500 18 GLN A 2 -87.18 23.48 REMARK 500 18 THR A 24 84.20 44.72 REMARK 500 18 LEU A 68 124.06 24.36 REMARK 500 18 ASP A 106 96.01 -65.82 REMARK 500 19 ALA A 15 25.69 -77.12 REMARK 500 19 THR A 24 81.80 58.97 REMARK 500 19 TRP A 37 38.51 -82.86 REMARK 500 19 PRO A 64 41.75 -75.25 REMARK 500 19 TRP A 127 46.35 -82.65 REMARK 500 20 GLN A 2 -76.40 21.47 REMARK 500 20 ALA A 15 27.48 -76.97 REMARK 500 20 THR A 24 81.63 49.99 REMARK 500 20 LYS A 44 -20.52 -142.02 REMARK 500 20 PRO A 64 6.67 -69.03 REMARK 500 20 HIS A 70 -55.88 67.28 REMARK 500 20 ASP A 106 96.04 -67.15 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 GLY A 66 ASN A 67 2 -147.22 REMARK 500 TRP A 127 ALA A 128 5 -146.61 REMARK 500 MET A 61 LEU A 62 9 147.42 REMARK 500 ALA A 103 ASN A 104 9 148.94 REMARK 500 ALA A 103 ASN A 104 10 149.75 REMARK 500 ASN A 104 ASP A 105 12 147.62 REMARK 500 SER A 1 GLN A 2 17 147.12 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 2 TYR A 41 0.08 SIDE_CHAIN REMARK 500 6 TYR A 41 0.12 SIDE_CHAIN REMARK 500 12 ARG A 46 0.10 SIDE_CHAIN REMARK 500 13 ARG A 46 0.10 SIDE_CHAIN REMARK 500 14 TYR A 34 0.07 SIDE_CHAIN REMARK 500 16 ARG A 46 0.14 SIDE_CHAIN REMARK 500 20 TYR A 41 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6313 RELATED DB: BMRB REMARK 900 1H,13C,AND 15N NMR ASSIGNMENTS OF THE BOMBYX MORI PHEROMONE REMARK 900 -BINDING PROTEIN FRAGMENT BMPBP(1-128) AT PH 6.5 REMARK 900 RELATED ID: 1LS8 RELATED DB: PDB REMARK 900 SOLUTION STRUTURE OF THE UNLIGANDED WILD-TYPE BOMBYX MORI REMARK 900 PHEROMONE-BINDING PROTEIN AT PH 6.5 REMARK 900 RELATED ID: 1DQE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE LIGANDED WILD-TYPE BOMBYX MORI REMARK 900 PHEROMONE-BINDING PROTEIN AT PH 8.2 REMARK 900 RELATED ID: 1GM0 RELATED DB: PDB REMARK 900 SOLUTION STRUTURE OF THE UNLIGANDED WILD-TYPE BOMBYX MORI REMARK 900 PHEROMONE-BINDING PROTEIN AT PH 4.5
DBREF 1XFR A 1 128 UNP P34174 PBP_BOMMO 23 150
SEQRES 1 A 128 SER GLN GLU VAL MET LYS ASN LEU SER LEU ASN PHE GLY SEQRES 2 A 128 LYS ALA LEU ASP GLU CYS LYS LYS GLU MET THR LEU THR SEQRES 3 A 128 ASP ALA ILE ASN GLU ASP PHE TYR ASN PHE TRP LYS GLU SEQRES 4 A 128 GLY TYR GLU ILE LYS ASN ARG GLU THR GLY CYS ALA ILE SEQRES 5 A 128 MET CYS LEU SER THR LYS LEU ASN MET LEU ASP PRO GLU SEQRES 6 A 128 GLY ASN LEU HIS HIS GLY ASN ALA MET GLU PHE ALA LYS SEQRES 7 A 128 LYS HIS GLY ALA ASP GLU THR MET ALA GLN GLN LEU ILE SEQRES 8 A 128 ASP ILE VAL HIS GLY CYS GLU LYS SER THR PRO ALA ASN SEQRES 9 A 128 ASP ASP LYS CYS ILE TRP THR LEU GLY VAL ALA THR CYS SEQRES 10 A 128 PHE LYS ALA GLU ILE HIS LYS LEU ASN TRP ALA
HELIX 1 1 SER A 1 GLY A 13 1 13 HELIX 2 2 ALA A 15 THR A 24 1 10 HELIX 3 3 ASP A 27 PHE A 36 1 10 HELIX 4 4 ASN A 45 LEU A 59 1 15 HELIX 5 5 HIS A 69 HIS A 80 1 12 HELIX 6 6 ASP A 83 LYS A 99 1 17 HELIX 7 7 ASP A 106 LEU A 125 1 20
SSBOND 1 CYS A 19 CYS A 54 1555 1555 2.03 SSBOND 2 CYS A 50 CYS A 108 1555 1555 2.03 SSBOND 3 CYS A 97 CYS A 117 1555 1555 2.03
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