10 20 30 40 50 60 70 80 2KGD - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER BIOSYNTHETIC PROTEIN 08-MAR-09 2KGD
TITLE NMR SOLUTION STRUCTURES OF 3-OXO-BUTYL-ACP, AN INTERMEDIATE TITLE 2 MIMIC FROM THE ACTINORHODIN POLYKETIDE SYNTHASE IN TITLE 3 STREPTOMYCES COELICOLOR
COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACTINORHODIN POLYKETIDE SYNTHASE ACYL CARRIER COMPND 3 PROTEIN; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: ACP, ACTI ORF3; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES COELICOLOR; SOURCE 3 ORGANISM_TAXID: 1902; SOURCE 4 STRAIN: A3(2); SOURCE 5 GENE: SCO5089, SCBAC28G1.15; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: DE3; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET11C
KEYWDS ACP, POLYKETIDE MIMIC, DIKETIDE, ACTINORHODIN, COELICOLOR, KEYWDS 2 ANTIBIOTIC BIOSYNTHESIS, PHOSPHOPANTETHEINE, BIOSYNTHETIC KEYWDS 3 PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR M.P.CRUMP,S.E.EVANS,C.WILLIAMS
REVDAT 2 09-JUN-09 2KGD 1 JRNL REVDAT 1 14-APR-09 2KGD 0
JRNL AUTH S.E.EVANS,C.WILLIAMS,C.J.ARTHUR,E.PLOSKON, JRNL AUTH 2 P.WATTANA-AMORN,R.J.COX,J.CROSBY,C.L.WILLIS, JRNL AUTH 3 T.J.SIMPSON,M.P.CRUMP JRNL TITL PROBING THE INTERACTIONS OF EARLY POLYKETIDE JRNL TITL 2 INTERMEDIATES WITH THE ACTINORHODIN ACP FROM S. JRNL TITL 3 COELICOLOR A3(2). JRNL REF J.MOL.BIOL. V. 389 511 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19361520 JRNL DOI 10.1016/J.JMB.2009.03.072
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 1.2 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 ALL STRUCTURE CALCULATIONS WERE CARRIED OUT USING THE REMARK 3 AMBIGUOUS RESTRAINTS FOR ITERATIVE ASSIGNMENT OF NOES REMARK 3 (ARIA) PROTOCOL VERSION 1.2. THE 20 BEST STRUCTURES REMARK 3 (SORTED ACCORDING TO TOTAL ENERGY) WERE SELECTED FOR REMARK 3 WATER REFINEMENT. WATER REFINED STRUCTURES WERE CALCULATED REMARK 3 USING THE SLIGHTLY MODIFIED REFINEMENT SCRIPT APPLIED TO REMARK 3 THE RECOORD DATABASE. PROCHECK AND WHATCHECK AND QUALITY REMARK 3 INDICATORS WERE COMPARED TO THE AVERAGE VALUES FOR THE REMARK 3 RECOORD DATABASE OF PROTEIN NMR STRUCTURES.
REMARK 4 REMARK 4 2KGD COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-APR-09. REMARK 100 THE RCSB ID CODE IS RCSB101086.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1-2 MM 4 -PHOSPHOPANTETHEINE REMARK 210 CHAIN DERIVATISED WITH A 3-OXO REMARK 210 -BUTYL GROUP-1, 20 MM REMARK 210 POTASSIUM PHOSPHATE-2, 1 MM REMARK 210 SODIUM AZIDE-3, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO) REMARK 210 NH; 3D C(CO)NH; 3D HNCO; 3D REMARK 210 HNCACB; 3D H(CCO)NH; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY; 2D 13C,15N FILTERED REMARK 210 TOCSY; 2D 13C,15N FILTERED REMARK 210 NOESY; 2D 13C F2 FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ANALYSIS_(CCPN) 1.0, ARIA REMARK 210 1.2, NMRPIPE 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 : 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 2 TYR A 40 CE1 TYR A 40 CZ 0.095 REMARK 500 2 TYR A 40 CZ TYR A 40 CE2 -0.090 REMARK 500 7 TYR A 56 CE1 TYR A 56 CZ 0.102 REMARK 500 7 TYR A 56 CZ TYR A 56 CE2 -0.103 REMARK 500 9 TYR A 40 CE1 TYR A 40 CZ 0.096 REMARK 500 9 TYR A 40 CZ TYR A 40 CE2 -0.115 REMARK 500 11 TYR A 40 CE1 TYR A 40 CZ -0.086 REMARK 500 15 TYR A 40 CE1 TYR A 40 CZ 0.091 REMARK 500 15 TYR A 40 CZ TYR A 40 CE2 -0.100 REMARK 500 15 TYR A 56 CE1 TYR A 56 CZ -0.117 REMARK 500 15 TYR A 56 CZ TYR A 56 CE2 0.115 REMARK 500 19 TYR A 40 CE1 TYR A 40 CZ 0.105 REMARK 500 19 TYR A 40 CZ TYR A 40 CE2 -0.096 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 ASP A 29 89.20 66.29 REMARK 500 3 ALA A 2 121.43 -177.26 REMARK 500 3 ALA A 18 -42.36 -130.71 REMARK 500 3 ASP A 22 -60.22 -171.79 REMARK 500 4 THR A 6 -169.26 -103.07 REMARK 500 4 THR A 24 77.27 -115.91 REMARK 500 5 THR A 21 59.82 -116.53 REMARK 500 5 PHE A 30 12.55 -151.28 REMARK 500 5 ARG A 67 -32.55 -167.20 REMARK 500 6 THR A 21 58.11 -117.12 REMARK 500 6 ASP A 25 98.54 -55.42 REMARK 500 6 VAL A 68 105.56 -52.83 REMARK 500 7 SER A 27 -175.43 67.25 REMARK 500 7 GLU A 84 -55.01 -126.93 REMARK 500 8 ASP A 22 -87.09 -66.34 REMARK 500 9 GLU A 20 79.15 -151.89 REMARK 500 9 THR A 21 -94.40 -82.57 REMARK 500 9 PHE A 30 -3.73 -156.42 REMARK 500 9 GLU A 84 68.78 -112.93 REMARK 500 9 ALA A 85 -55.42 -148.34 REMARK 500 10 ARG A 67 -34.75 -153.73 REMARK 500 11 GLU A 20 122.55 68.60 REMARK 500 11 ALA A 85 -6.90 71.05 REMARK 500 12 THR A 21 94.64 -65.10 REMARK 500 13 THR A 21 72.10 -101.17 REMARK 500 13 ASP A 29 53.81 -91.92 REMARK 500 13 ALA A 85 39.17 -84.89 REMARK 500 14 ASP A 22 -53.56 -132.92 REMARK 500 14 THR A 24 73.16 -118.30 REMARK 500 15 THR A 6 -169.16 -116.33 REMARK 500 15 THR A 21 55.18 -143.35 REMARK 500 16 THR A 6 -169.26 -109.11 REMARK 500 16 LEU A 26 -52.99 -136.20 REMARK 500 16 SER A 27 -162.96 60.31 REMARK 500 16 ASP A 29 96.68 65.67 REMARK 500 16 PHE A 30 26.41 -142.31 REMARK 500 17 ASP A 25 95.26 -66.13 REMARK 500 17 PHE A 30 23.15 -145.90 REMARK 500 18 THR A 21 64.84 -109.48 REMARK 500 18 THR A 24 87.37 -150.78 REMARK 500 18 SER A 27 -175.37 67.10 REMARK 500 18 PHE A 30 22.77 -145.93 REMARK 500 19 GLU A 20 19.10 -144.55 REMARK 500 19 ASP A 22 -57.23 -177.82 REMARK 500 19 LEU A 26 75.67 52.20 REMARK 500 19 PHE A 30 15.95 -154.42 REMARK 500 19 ALA A 85 106.83 -54.55 REMARK 500 20 ALA A 2 110.71 -161.78 REMARK 500 20 THR A 21 67.01 -106.02 REMARK 500 20 ASP A 41 -71.32 -94.38 REMARK 500 20 SER A 42 -50.39 -168.09 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 3 ARG A 67 0.09 SIDE_CHAIN REMARK 500 5 ARG A 34 0.08 SIDE_CHAIN REMARK 500 5 ARG A 67 0.07 SIDE_CHAIN REMARK 500 6 ARG A 72 0.09 SIDE_CHAIN REMARK 500 7 ARG A 55 0.07 SIDE_CHAIN REMARK 500 10 ARG A 72 0.07 SIDE_CHAIN REMARK 500 11 ARG A 55 0.08 SIDE_CHAIN REMARK 500 13 ARG A 55 0.09 SIDE_CHAIN REMARK 500 16 ARG A 67 0.10 SIDE_CHAIN REMARK 500 20 ARG A 12 0.09 SIDE_CHAIN REMARK 500 20 TYR A 56 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SXV A 87
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K0X RELATED DB: PDB REMARK 900 NMR SOLUTIONS STRUCTURE OF HOLO ACP FROM THE ACTINORHODIN REMARK 900 PATHWAY OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 2K0Y RELATED DB: PDB REMARK 900 NMR SOLUTIONS STRUCTURE OF APO ACP FROM THE ACTINORHODIN REMARK 900 PATHWAY OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 2KG6 RELATED DB: PDB REMARK 900 NMR SOLUTIONS STRUCTURE OF ACETYL ACP FROM THE ACTINORHODIN REMARK 900 PATHWAY OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 2KG8 RELATED DB: PDB REMARK 900 NMR SOLUTIONS STRUCTURE OF MALONYL ACP FROM THE REMARK 900 ACTINORHODIN PATHWAY OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 2KG9 RELATED DB: PDB REMARK 900 NMR SOLUTIONS STRUCTURE OF BUTYRYL ACP FROM THE REMARK 900 ACTINORHODIN PATHWAY OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 2KGA RELATED DB: PDB REMARK 900 NMR SOLUTIONS STRUCTURE OF HEXANOYL ACP FROM THE REMARK 900 ACTINORHODIN PATHWAY OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 2KGC RELATED DB: PDB REMARK 900 NMR SOLUTIONS STRUCTURE OF OCTANOYL ACP FROM THE REMARK 900 ACTINORHODIN PATHWAY OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 2KGE RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURES OF 3,5-DIOXOHEXYL ACP (A TRIKETIDE REMARK 900 MIMIC) FROM THE ACTINORHODIN POLYKETIDE SYNTHASE IN REMARK 900 STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 15658 RELATED DB: BMRB REMARK 900 1H, 13C AND 15N NMR ASSIGNMENTS FOR HOLO ACP FROM THE REMARK 900 ACTINORHODIN POLYKETIDE SYNTHASE OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 15659 RELATED DB: BMRB REMARK 900 1H, 13C AND 15N NMR ASSIGNMENTS FOR APO ACP FROM THE REMARK 900 ACTINORHODIN POLYKETIDE SYNTHASE OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 16196 RELATED DB: BMRB REMARK 900 1H, 13C AND 15N NMR ASSIGNMENTS FOR ACETYL ACP FROM THE REMARK 900 ACTINORHODIN POLYKETIDE SYNTHASE OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 16197 RELATED DB: BMRB REMARK 900 1H, 13C AND 15N NMR ASSIGNMENTS FOR MALONYL ACP FROM THE REMARK 900 ACTINORHODIN POLYKETIDE SYNTHASE OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 16199 RELATED DB: BMRB REMARK 900 1H, 13C AND 15N NMR ASSIGNMENTS FOR BUTYRYL ACP FROM THE REMARK 900 ACTINORHODIN POLYKETIDE SYNTHASE OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 16200 RELATED DB: BMRB REMARK 900 1H, 13C AND 15N NMR ASSIGNMENTS FOR HEXANOYL ACP FROM THE REMARK 900 ACTINORHODIN POLYKETIDE SYNTHASE OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 16201 RELATED DB: BMRB REMARK 900 1H, 13C AND 15N NMR ASSIGNMENTS FOR OCTANOYL ACP FROM THE REMARK 900 ACTINORHODIN POLYKETIDE SYNTHASE OF STREPTOMYCES COELICOLOR
DBREF 2KGD A 1 86 UNP Q02054 ACPX_STRCO 1 86
SEQADV 2KGD SER A 17 UNP Q02054 CYS 17 ENGINEERED
SEQRES 1 A 86 MET ALA THR LEU LEU THR THR ASP ASP LEU ARG ARG ALA SEQRES 2 A 86 LEU VAL GLU SER ALA GLY GLU THR ASP GLY THR ASP LEU SEQRES 3 A 86 SER GLY ASP PHE LEU ASP LEU ARG PHE GLU ASP ILE GLY SEQRES 4 A 86 TYR ASP SER LEU ALA LEU MET GLU THR ALA ALA ARG LEU SEQRES 5 A 86 GLU SER ARG TYR GLY VAL SER ILE PRO ASP ASP VAL ALA SEQRES 6 A 86 GLY ARG VAL ASP THR PRO ARG GLU LEU LEU ASP LEU ILE SEQRES 7 A 86 ASN GLY ALA LEU ALA GLU ALA ALA
HET SXV A 87 53
HETNAM SXV N~3~-[(2S)-2-HYDROXY-3,3-DIMETHYL-4-(PHOSPHONOOXY) HETNAM 2 SXV BUTANOYL]-N-{2-[(3-OXOBUTYL)SULFANYL]ETHYL}-BETA- HETNAM 3 SXV ALANINAMIDE
FORMUL 2 SXV C15 H29 N2 O8 P S
HELIX 1 1 THR A 6 SER A 17 1 12 HELIX 2 2 ASP A 41 GLY A 57 1 17 HELIX 3 3 PRO A 61 GLY A 66 1 6 HELIX 4 4 THR A 70 GLU A 84 1 15
LINK OG SER A 42 P24 SXV A 87 1555 1555 1.53
SITE 1 AC1 5 SER A 42 LEU A 43 MET A 46 ASP A 63 SITE 2 AC1 5 GLY A 66
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