PDB Short entry for 2KGE HEADER BIOSYNTHETIC PROTEIN 08-MAR-09 2KGE TITLE NMR SOLUTION STRUCTURES OF 3,5-DIOXOHEXYL ACP (A TRIKETIDE MIMIC) FROM TITLE 2 THE ACTINORHODIN POLYKETIDE SYNTHASE IN STREPTOMYCES COELICOLOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACTINORHODIN POLYKETIDE SYNTHASE ACYL CARRIER PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ACP, ACTI ORF3; COMPND 5 ENGINEERED: YES; COMPND 6 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, TRIKETIDE, POLYKETIDE, ACTINORHODIN, ANTIBIOTIC BIOSYNTHESIS, KEYWDS 2 PHOSPHOPANTETHEINE, BIOSYNTHETIC PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.P.CRUMP,S.E.EVANS,C.WILLIAMS REVDAT 3 20-OCT-21 2KGE 1 REMARK SEQADV LINK REVDAT 2 09-JUN-09 2KGE 1 JRNL REVDAT 1 14-APR-09 2KGE 0 JRNL AUTH S.E.EVANS,C.WILLIAMS,C.J.ARTHUR,E.PLOSKON,P.WATTANA-AMORN, JRNL AUTH 2 R.J.COX,J.CROSBY,C.L.WILLIS,T.J.SIMPSON,M.P.CRUMP JRNL TITL PROBING THE INTERACTIONS OF EARLY POLYKETIDE INTERMEDIATES JRNL TITL 2 WITH THE ACTINORHODIN ACP FROM S. 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ANALYSIS_(CCPN) 1.0, ARIA 1.2 REMARK 3 AUTHORS : RASMUS H. FOGH, WIM F. VRANKEN, WAYNE BOUCHER, TIM REMARK 3 J. STEVENS AND ERNEST D. LAUE (ANALYSIS_(CCPN)), REMARK 3 LINGE, O'DONOGHUE AND NILGES (ARIA) 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 2KGE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000101087. 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 DERIVIATISED WITH A 3,5- REMARK 210 DIOXOHEXYL GROUP. 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D H(CCO)NH; 3D REMARK 210 C(CO)NH; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY; 3D REMARK 210 HNCO; 2D 13C,15N FILTERED NOESY; REMARK 210 2D 13C F2 FILTERED NOESY; 2D 13C, REMARK 210 15N FILTERED TOCSY 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 1.2 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 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: 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 11 TYR A 56 CE1 TYR A 56 CZ 0.089 REMARK 500 15 TYR A 40 CE1 TYR A 40 CZ 0.119 REMARK 500 15 TYR A 40 CZ TYR A 40 CE2 -0.132 REMARK 500 17 TYR A 40 CE1 TYR A 40 CZ 0.110 REMARK 500 17 TYR A 40 CZ TYR A 40 CE2 -0.104 REMARK 500 20 TYR A 40 CE1 TYR A 40 CZ 0.082 REMARK 500 20 TYR A 40 CZ TYR A 40 CE2 -0.090 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 2 176.24 69.38 REMARK 500 1 GLU A 20 92.97 -165.26 REMARK 500 1 ASP A 22 34.50 -80.43 REMARK 500 2 GLU A 20 73.33 63.44 REMARK 500 2 THR A 21 82.82 55.18 REMARK 500 3 THR A 24 43.10 -80.32 REMARK 500 4 ASP A 22 30.12 -98.54 REMARK 500 4 ARG A 67 14.64 -141.27 REMARK 500 5 THR A 21 82.73 65.23 REMARK 500 5 ALA A 85 -55.62 76.70 REMARK 500 7 GLU A 20 15.89 -153.67 REMARK 500 7 THR A 24 77.28 -176.79 REMARK 500 7 PHE A 30 13.97 -171.50 REMARK 500 7 ASP A 69 -66.90 -126.42 REMARK 500 7 ALA A 85 -104.36 53.14 REMARK 500 8 ALA A 2 -164.85 61.92 REMARK 500 8 THR A 24 -165.50 64.73 REMARK 500 9 THR A 21 -169.55 -160.43 REMARK 500 9 THR A 24 -168.06 -124.94 REMARK 500 10 GLU A 20 100.57 -53.49 REMARK 500 10 THR A 21 73.28 57.47 REMARK 500 10 ASP A 25 47.17 -87.62 REMARK 500 10 ASP A 69 -57.42 -129.37 REMARK 500 10 GLU A 84 -64.85 -97.18 REMARK 500 10 ALA A 85 74.33 52.31 REMARK 500 11 THR A 21 44.08 71.60 REMARK 500 12 GLU A 20 57.03 -142.47 REMARK 500 12 THR A 24 40.15 -80.03 REMARK 500 12 ASP A 25 70.67 46.59 REMARK 500 12 ASP A 32 34.65 -93.27 REMARK 500 13 ALA A 2 75.96 64.00 REMARK 500 13 ASP A 29 104.25 76.17 REMARK 500 14 THR A 21 36.40 -140.22 REMARK 500 14 LEU A 26 59.27 -108.91 REMARK 500 14 ASP A 29 83.30 60.13 REMARK 500 15 ALA A 18 -77.01 -113.77 REMARK 500 15 SER A 27 34.09 -77.01 REMARK 500 16 ASP A 22 -92.31 64.37 REMARK 500 16 ASP A 25 79.18 62.47 REMARK 500 16 ASP A 29 110.65 63.87 REMARK 500 16 ARG A 67 -27.75 -157.79 REMARK 500 17 ALA A 2 -171.33 69.62 REMARK 500 17 THR A 24 -169.00 -177.41 REMARK 500 17 PHE A 30 25.53 -156.99 REMARK 500 18 ALA A 2 -155.90 -157.76 REMARK 500 18 THR A 21 68.51 70.12 REMARK 500 18 PHE A 30 10.93 -145.51 REMARK 500 18 ASP A 69 -58.54 -125.90 REMARK 500 19 ALA A 18 -63.06 -95.44 REMARK 500 19 PHE A 30 30.53 -143.42 REMARK 500 REMARK 500 THIS ENTRY HAS 52 RAMACHANDRAN OUTLIERS. 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 8 ARG A 55 0.10 SIDE CHAIN REMARK 500 8 ARG A 67 0.09 SIDE CHAIN REMARK 500 10 TYR A 56 0.10 SIDE CHAIN REMARK 500 11 TYR A 56 0.06 SIDE CHAIN REMARK 500 12 TYR A 40 0.05 SIDE CHAIN REMARK 500 14 ARG A 34 0.10 SIDE CHAIN REMARK 500 14 ARG A 55 0.09 SIDE CHAIN REMARK 500 18 TYR A 40 0.05 SIDE CHAIN REMARK 500 20 TYR A 56 0.06 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 SXD 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 PATHWAY REMARK 900 OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 2K0Y RELATED DB: PDB REMARK 900 NMR SOLUTIONS STRUCTURE OF APO ACP FROM THE ACTINORHODIN PATHWAY OF REMARK 900 STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 2KG6 RELATED DB: PDB REMARK 900 NMR SOLUTIONS STRUCTURE OF ACETYL ACP FROM THE ACTINORHODIN PATHWAY REMARK 900 OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 2KG8 RELATED DB: PDB REMARK 900 NMR SOLUTIONS STRUCTURE OF MALONYL ACP FROM THE ACTINORHODIN REMARK 900 PATHWAY OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 2KG9 RELATED DB: PDB REMARK 900 NMR SOLUTIONS STRUCTURE OF BUTYRYL ACP FROM THE ACTINORHODIN REMARK 900 PATHWAY OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 2KGA RELATED DB: PDB REMARK 900 NMR SOLUTIONS STRUCTURE OF HEXANOYL ACP FROM THE ACTINORHODIN REMARK 900 PATHWAY OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 2KGC RELATED DB: PDB REMARK 900 NMR SOLUTIONS STRUCTURE OF OCTANOYL ACP FROM THE ACTINORHODIN REMARK 900 PATHWAY OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 2KGD RELATED DB: PDB REMARK 900 NMR SOLUTIONS STRUCTURE OF 3-OXOBUTYL ACP FROM THE ACTINORHODIN REMARK 900 PATHWAY OF STREPTOMYCES COELICOLOR REMARK 900 RELATED ID: 15658 RELATED DB: BMRB REMARK 900 1H, 13C AND 15N NMR ASSIGNMENTS FOR HOLO ACP FROM THE ACTINORHODIN REMARK 900 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 ACTINORHODIN REMARK 900 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 REMARK 900 RELATED ID: 16202 RELATED DB: BMRB REMARK 900 1H, 13C AND 15N NMR ASSIGNMENTS FOR 3-XOXBUTYL ACP FROM THE REMARK 900 ACTINORHODIN POLYKETIDE SYNTHASE OF STREPTOMYCES COELICOLOR DBREF 2KGE A 1 86 UNP Q02054 ACPX_STRCO 1 86 SEQADV 2KGE SER A 17 UNP Q02054 CYS 17 ENGINEERED MUTATION 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 SXD A 87 58 HETNAM SXD N-{2-[(3,5-DIOXOHEXYL)SULFANYL]ETHYL}-N~3~-[(2S)-2- HETNAM 2 SXD HYDROXY-3,3-DIMETHYL-4-(PHOSPHONOOXY)BUTANOYL]-BETA- HETNAM 3 SXD ALANINAMIDE FORMUL 2 SXD C17 H31 N2 O9 P S HELIX 1 1 THR A 6 GLY A 19 1 14 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 SXD A 87 1555 1555 1.52 SITE 1 AC1 1 SER A 42 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