HEADER BIOSYNTHETIC PROTEIN 03-OCT-23 8QPY
TITLE SOLUTION NMR STRUCTURE OF THE PEPTIDYL CARRIER DOMAIN TOMAPCP FROM THE
TITLE 2 TOMAYMYCIN NON-RIBOSOMAL PEPTIDE SYNTHETASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CARRIER PROTEIN TOMAPCP;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: FIRST FOUR RESIDUES (GPMA) IN THE PROTEIN ARE FROM
COMPND 6 CLONING ARTIFACTS. THEREFORE, THE APPROPRIATE RESIDUE NUMBERING HAS
COMPND 7 THE FIRST RESIDUE (G) DESIGNATED AS RESIDUE-NUMBER '-3', SO THAT THE
COMPND 8 FIFTH RESIDUE HAS RESIDUE-NUMBER '1'. A SPECIAL MODIFIED RESIDUE SPP
COMPND 9 IS DESIGNATED FOR THE SERINE RESIDUE COVALENTLY LINKED TO A 4'-
COMPND 10 PHOSPHOPANTETHEINE PROSTHETIC GROUP.
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES REGENSIS;
SOURCE 3 ORGANISM_TAXID: 68263;
SOURCE 4 VARIANT: FH6421;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008
KEYWDS NON-RIBOSOMAL PEPTIDE SYNTHETASE, TOMAYMYCIN, PCP,
KEYWDS 2 PHOSPHOPANTETHEINE, DONOR, BIOSYNTHETIC PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR M.N.KARANTH,J.P.KIRKPATRICK,T.CARLOMAGNO
REVDAT 2 03-JUL-24 8QPY 1 JRNL
REVDAT 1 26-JUN-24 8QPY 0
JRNL AUTH M.N.KARANTH,J.P.KIRKPATRICK,J.KRAUSZE,S.SCHMELZ,A.SCRIMA,
JRNL AUTH 2 T.CARLOMAGNO
JRNL TITL THE SPECIFICITY OF INTERMODULAR RECOGNITION IN A
JRNL TITL 2 PROTOTYPICAL NONRIBOSOMAL PEPTIDE SYNTHETASE DEPENDS ON AN
JRNL TITL 3 ADAPTOR DOMAIN.
JRNL REF SCI ADV V. 10 M9404 2024
JRNL REFN ESSN 2375-2548
JRNL PMID 38896613
JRNL DOI 10.1126/SCIADV.ADM9404
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.21, CNS 1.21, CNS 1.21
REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ
REMARK 3 (CNS), BRUNGER, ADAMS, CLORE, GROS, NILGES AND
REMARK 3 READ (CNS), BRUNGER, ADAMS, CLORE, GROS, NILGES
REMARK 3 AND READ (CNS)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 8QPY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-OCT-23.
REMARK 100 THE DEPOSITION ID IS D_1292133510.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 308
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 265
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 500 UM [U-13C; U-15N] APCP, 50
REMARK 210 MM SODIUM PHOSPHATE, 150 MM
REMARK 210 SODIUM CHLORIDE, 5 MM DTT, 10 V/
REMARK 210 V [U-2H] D2O, 0.02 % W/V SODIUM
REMARK 210 AZIDE, 90% H2O/10% D2O; 500 UM
REMARK 210 [U-13C; U-15N] APCP, 50 MM
REMARK 210 SODIUM PHOSPHATE, 150 MM SODIUM
REMARK 210 CHLORIDE, 5 MM DTT, 0.02 W/V
REMARK 210 SODIUM AZIDE, 100 % V/V [U-2H]
REMARK 210 D2O, 100% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D
REMARK 210 HNCA; 3D CBCA(CO)NH; 3D HNCACB;
REMARK 210 3D H(CCO)NH; 3D C(CO)NH; 3D HCCH-
REMARK 210 TOCSY; 3D HBHA(CO)NH; 3D 1H-15N
REMARK 210 NOESY; 2D 1H-13C HSQC; 2D
REMARK 210 HBCBCGCDHDGP; 2D HBCBCGCDCEHEGP;
REMARK 210 3D 1H-13C NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ; 850 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE III; AVANCE III HD
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : TOPSPIN 3.2, NMRPIPE 10.2,
REMARK 210 CCPNMR ANALYSIS 2.4, ARIA 2.3
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 9
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: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
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 0 -70.66 -86.28
REMARK 500 1 ALA A 2 -82.71 66.93
REMARK 500 1 ASP A 23 35.36 -82.14
REMARK 500 1 LEU A 31 45.16 -58.47
REMARK 500 1 4HH A 37 -143.31 -82.80
REMARK 500 1 LEU A 38 -13.94 -40.81
REMARK 500 2 VAL A 3 99.03 67.26
REMARK 500 2 ASP A 22 -49.69 -149.02
REMARK 500 2 LEU A 31 48.20 -60.50
REMARK 500 2 ASN A 36 -35.80 -131.55
REMARK 500 2 4HH A 37 -142.73 -104.74
REMARK 500 2 LEU A 38 -15.30 -38.72
REMARK 500 2 ARG A 81 88.53 -68.48
REMARK 500 2 ASN A 82 82.14 55.52
REMARK 500 2 ALA A 84 47.98 -152.64
REMARK 500 2 GLN A 86 86.35 55.93
REMARK 500 3 PRO A -2 -71.00 -60.43
REMARK 500 3 MET A -1 -39.87 -151.88
REMARK 500 3 THR A 1 -63.59 75.98
REMARK 500 3 ASP A 23 40.57 -82.77
REMARK 500 3 LEU A 31 47.45 -60.85
REMARK 500 3 4HH A 37 -141.39 -106.56
REMARK 500 3 LEU A 38 -15.43 -40.07
REMARK 500 3 ASN A 82 62.11 -156.10
REMARK 500 3 GLN A 86 -56.47 -157.06
REMARK 500 4 ALA A 2 59.56 -119.06
REMARK 500 4 4HH A 37 -143.51 -110.57
REMARK 500 4 LEU A 38 -17.12 -41.27
REMARK 500 4 ALA A 84 63.07 -151.46
REMARK 500 5 ASP A 22 -54.50 -138.25
REMARK 500 5 ASP A 23 41.39 -81.44
REMARK 500 5 4HH A 37 -143.64 -110.86
REMARK 500 5 LEU A 38 -16.96 -40.05
REMARK 500 6 MET A -1 -83.48 64.83
REMARK 500 6 GLN A 4 -52.86 72.78
REMARK 500 6 ASP A 23 40.38 -81.56
REMARK 500 6 LEU A 31 48.75 -59.35
REMARK 500 6 4HH A 37 -141.22 -110.26
REMARK 500 6 LEU A 38 -16.53 -37.13
REMARK 500 6 THR A 79 -78.14 -103.89
REMARK 500 6 ARG A 81 -156.72 -128.69
REMARK 500 6 ALA A 84 -52.76 -138.09
REMARK 500 7 ASP A 22 -76.07 -113.25
REMARK 500 7 ASP A 23 40.25 -85.94
REMARK 500 7 LEU A 31 49.15 -56.70
REMARK 500 7 4HH A 37 -143.22 -110.04
REMARK 500 7 LEU A 38 -15.73 -40.98
REMARK 500 7 ASN A 82 89.75 55.84
REMARK 500 7 ALA A 84 22.36 -153.86
REMARK 500 7 GLN A 86 85.20 -170.65
REMARK 500
REMARK 500 THIS ENTRY HAS 70 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 34868 RELATED DB: BMRB
REMARK 900 SOLUTION NMR STRUCTURE OF THE PEPTIDYL CARRIER DOMAIN TOMAPCP FROM
REMARK 900 THE TOMAYMYCIN NON-RIBOSOMAL PEPTIDE SYNTHETASE
DBREF 8QPY A -3 88 PDB 8QPY 8QPY -3 88
SEQRES 1 A 92 GLY PRO MET ALA THR ALA VAL GLN ASN PRO LEU GLU THR
SEQRES 2 A 92 VAL VAL LEU GLN ALA TRP LYS ASP ILE SER GLY ALA ASP
SEQRES 3 A 92 ASP PHE THR THR THR ASP SER PHE LEU GLY HIS GLY GLY
SEQRES 4 A 92 ASN 4HH LEU HIS PHE VAL GLN LEU ALA SER ARG LEU GLN
SEQRES 5 A 92 LYS ILE PHE GLY VAL GLU VAL SER THR GLU ASP VAL PHE
SEQRES 6 A 92 ARG HIS GLY THR VAL GLU GLN LEU ALA ARG PHE VAL GLU
SEQRES 7 A 92 GLN SER ARG ASP THR GLY ARG ASN PRO ALA ALA GLN THR
SEQRES 8 A 92 GLN
MODRES 8QPY 4HH A 37 SER MODIFIED RESIDUE
HET 4HH A 37 52
HETNAM 4HH 4'-PHOSPHOPANTHETHEINE-SERINE
HETSYN 4HH O-[(S)-HYDROXY{[(3R)-3-HYDROXY-2,2-DIMETHYL-4-OXO-4-
HETSYN 2 4HH ({3-OXO-3-[(2-SULFANYLETHYL)AMINO]PROPYL}AMINO)
HETSYN 3 4HH BUTYL]OXY}PHOSPHORYL]-L-SERINE
FORMUL 1 4HH C14 H28 N3 O9 P S
HELIX 1 AA1 PRO A 6 SER A 19 1 14
HELIX 2 AA2 LEU A 38 PHE A 51 1 14
HELIX 3 AA3 THR A 57 HIS A 63 1 7
HELIX 4 AA4 VAL A 66 SER A 76 1 11
LINK C ASN A 36 N 4HH A 37 1555 1555 1.31
LINK C 4HH A 37 N LEU A 38 1555 1555 1.33
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