PDB Short entry for 2K0X HEADER TRANSPORT PROTEIN 15-FEB-08 2K0X TITLE THE ACTINORHODIN HOLO ACYL CARRIER PROTEIN FROM S. 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 STRAIN: A3(2); SOURCE 4 GENE: ACTI; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET11C; SOURCE 9 OTHER_DETAILS: ACTINORHODIN ACYL CARRIER PROTEIN (ACT ACP) FROM S. SOURCE 10 COELICOLOR WAS HETEROLOGOUSLY OVEREXPRESSED IN ITS APO FORM IN E. SOURCE 11 COLI BL21 (DE3) CELLS. THESE CELLS CONTAINED THE PLASMID PET11C C17S SOURCE 12 ACT ACP (COURTESY OF DR. TOM NICHOLSON). THIS IPTG INDUCIBLE VECTOR SOURCE 13 IS BOTH EASIER TO USE AND MORE RELIABLE THAN THE HEAT INDUCIBLE PT7- SOURCE 14 7 VERSION ORIGINALLY CONSTRUCTED. THE PROTEIN WAS MODIFIED TO THE SOURCE 15 HOLO FORM USING S. COELICOLOR ACPS AND ENZYME COA. KEYWDS ACYL CARRIER PROTEIN, POLYKETIDE, HOLO, PHOSPHOPANTETHEINE, KEYWDS 2 ANTIBIOTIC BIOSYNTHESIS, TRANSPORT PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.P.CRUMP,S.E.EVANS,C.WILLIAMS REVDAT 5 20-OCT-21 2K0X 1 REMARK SEQADV LINK REVDAT 4 27-MAR-13 2K0X 1 REMARK VERSN REVDAT 3 24-FEB-09 2K0X 1 VERSN REVDAT 2 14-OCT-08 2K0X 1 JRNL REVDAT 1 16-SEP-08 2K0X 0 JRNL AUTH S.E.EVANS,C.WILLIAMS,C.J.ARTHUR,S.G.BURSTON,T.J.SIMPSON, JRNL AUTH 2 J.CROSBY,M.P.CRUMP JRNL TITL AN ACP STRUCTURAL SWITCH: CONFORMATIONAL DIFFERENCES BETWEEN JRNL TITL 2 THE APO AND HOLO FORMS OF THE ACTINORHODIN POLYKETIDE JRNL TITL 3 SYNTHASE ACYL CARRIER PROTEIN. JRNL REF CHEMBIOCHEM V. 9 2424 2008 JRNL REFN ISSN 1439-4227 JRNL PMID 18770515 JRNL DOI 10.1002/CBIC.200800180 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 1.2, ARIA 1.2 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), LINGE, REMARK 3 O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ALL STRUCTURE CALCULATIONS WERE CARRIED REMARK 3 OUT USING THE AMBIGUOUS RESTRAINTS FOR ITERATIVE ASSIGNMENT OF REMARK 3 NOES (ARIA) PROTOCOL VERSION 1.2, WHICH INCLUDES AN ALGORITHM REMARK 3 THAT ATTEMPTS TO CORRECT FOR THE EFFECTS OF SPIN DIFFUSION, WAS REMARK 3 USE. TORSION ANGLE LIKELIHOOD OBTAINED FROM SHIFT AND SEQUENCE REMARK 3 SIMILARITY (TALOS) AND WAS USED TO PREDICT φ AND ψ REMARK 3 DIHEDRAL ANGLE RESTRAINTS. INITIALLY, STRUCTURE CALCULATION RUNS REMARK 3 CONTAINED 8 ITERATIONS OF 20 STRUCTURES EACH, WITH THE BEST 7 REMARK 3 STRUCTURES IN EACH ITERATION (SORTED ACCORDING TO TOTAL ENERGY) REMARK 3 BEING USED FOR ANALYSIS AND ASSIGNMENT. THE NUMBER OF DYNAMICS REMARK 3 STEPS WAS INCREASED OVER DEFAULT VALUES TO 20000 AND 16000 FOR REMARK 3 THE FIRST AND SECOND COOLING STAGES RESPECTIVELY. AFTER EACH RUN, REMARK 3 VIOLATED RESTRAINTS WERE CHECKED, AND THOSE ARISING FROM NOISE REMARK 3 PEAKS OR INCORRECT ASSIGNMENTS WERE REMOVED/REASSIGNED. FINAL REMARK 3 ENSEMBLES OF 100 STRUCTURES WERE CALCULATED FROM CALIBRATED REMARK 3 RESTRAINT TABLES. THE 20 BEST STRUCTURES (SORTED ACCORDING TO REMARK 3 TOTAL ENERGY) WERE SELECTED FOR WATER REFINEMENT. WATER REFINED REMARK 3 STRUCTURES WERE CALCULATED USING THE SLIGHTLY MODIFIED REMARK 3 REFINEMENT SCRIPT APPLIED TO THE RECOORD DATABASE. PROCHECK AND REMARK 3 WHATCHECK AND QUALITY INDICATORS WERE COMPARED TO THE AVERAGE REMARK 3 VALUES FOR THE RECOORD DATABASE OF PROTEIN NMR STRUCTURES. REMARK 4 REMARK 4 2K0X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000100536. 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 [U-98% 13C; U-98% 15N] REMARK 210 ACT HOLO-ACP, 1-2 MM REMARK 210 PHOSPHOPANTETHEINE SIDE CHAIN, REMARK 210 95 % H2O, 5 % D2O, 20 MM REMARK 210 POTASSIUM PHOSPHATE, 5 MM TCEP, REMARK 210 1 MM SODIUM AZIDE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-13C NOESY; REMARK 210 3D 1H-15N NOESY; 3D CBCA(CO)NH; REMARK 210 3D HNCACB; 3D HCCH-TOCSY; 3D REMARK 210 HNCO; F1,F2 DOUBLE FILTERED REMARK 210 NOESY; F1,F2 DOUBLE FILTERED REMARK 210 TOCSY; 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 : ARIA 1.2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 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 1 TYR A 40 CZ TYR A 40 CE2 -0.084 REMARK 500 4 TYR A 40 CE1 TYR A 40 CZ 0.080 REMARK 500 4 TYR A 40 CZ TYR A 40 CE2 -0.078 REMARK 500 5 TYR A 40 CE1 TYR A 40 CZ 0.099 REMARK 500 5 TYR A 40 CZ TYR A 40 CE2 -0.112 REMARK 500 13 TYR A 40 CE1 TYR A 40 CZ 0.093 REMARK 500 13 TYR A 40 CZ TYR A 40 CE2 -0.092 REMARK 500 14 TYR A 40 CE1 TYR A 40 CZ 0.100 REMARK 500 14 TYR A 40 CZ TYR A 40 CE2 -0.098 REMARK 500 14 TYR A 56 CE1 TYR A 56 CZ 0.093 REMARK 500 17 TYR A 56 CE1 TYR A 56 CZ 0.096 REMARK 500 18 TYR A 40 CE1 TYR A 40 CZ 0.081 REMARK 500 18 TYR A 40 CZ TYR A 40 CE2 -0.093 REMARK 500 19 TYR A 40 CE1 TYR A 40 CZ 0.110 REMARK 500 19 TYR A 40 CZ TYR A 40 CE2 -0.094 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 82.02 -157.42 REMARK 500 2 ASP A 25 67.01 67.28 REMARK 500 2 PHE A 30 14.59 -145.80 REMARK 500 3 THR A 21 61.09 63.33 REMARK 500 3 ASP A 22 -36.40 72.58 REMARK 500 3 LEU A 26 39.35 -140.93 REMARK 500 4 THR A 24 -147.31 54.60 REMARK 500 4 PHE A 30 19.45 -147.25 REMARK 500 5 THR A 21 107.59 73.06 REMARK 500 5 ASP A 22 -164.38 68.28 REMARK 500 5 THR A 24 -170.61 162.22 REMARK 500 5 ASP A 29 91.05 49.84 REMARK 500 5 GLU A 84 -57.00 -124.56 REMARK 500 6 GLU A 20 106.97 -161.46 REMARK 500 6 THR A 21 61.96 61.89 REMARK 500 6 ASP A 22 -58.28 73.30 REMARK 500 6 LEU A 26 15.03 58.50 REMARK 500 6 ARG A 67 17.13 -145.53 REMARK 500 6 ALA A 85 79.60 59.35 REMARK 500 7 ASP A 22 -21.66 72.07 REMARK 500 7 THR A 24 -174.28 53.69 REMARK 500 7 GLU A 84 -46.36 -132.77 REMARK 500 8 THR A 6 -169.33 -101.89 REMARK 500 8 THR A 21 -140.29 -123.36 REMARK 500 8 ASP A 25 -66.07 68.53 REMARK 500 9 THR A 24 77.17 -43.10 REMARK 500 9 LEU A 26 25.73 -79.84 REMARK 500 10 GLU A 20 -177.71 63.92 REMARK 500 10 ASP A 22 41.42 -140.90 REMARK 500 10 THR A 24 -171.05 -170.03 REMARK 500 11 THR A 21 70.12 46.08 REMARK 500 11 ASP A 22 -48.99 -148.03 REMARK 500 11 ASP A 29 138.17 67.99 REMARK 500 11 PHE A 30 18.48 -147.98 REMARK 500 12 GLU A 20 -145.94 -102.14 REMARK 500 12 ASP A 22 -64.74 -147.95 REMARK 500 12 ALA A 85 -64.79 -168.26 REMARK 500 13 ARG A 67 -36.80 -153.28 REMARK 500 14 ASP A 22 108.43 63.31 REMARK 500 14 THR A 24 159.56 71.54 REMARK 500 15 THR A 6 -168.62 -113.42 REMARK 500 15 ALA A 18 -65.68 -93.26 REMARK 500 15 ALA A 85 -63.35 170.07 REMARK 500 16 THR A 21 -145.89 -143.89 REMARK 500 16 THR A 24 -156.53 178.08 REMARK 500 16 PHE A 30 8.49 -156.83 REMARK 500 17 LEU A 26 32.88 -82.10 REMARK 500 17 ALA A 85 88.34 69.64 REMARK 500 18 GLU A 20 99.14 -55.73 REMARK 500 18 THR A 24 -169.14 -169.01 REMARK 500 REMARK 500 THIS ENTRY HAS 57 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 1 ARG A 67 0.07 SIDE CHAIN REMARK 500 2 ARG A 11 0.08 SIDE CHAIN REMARK 500 3 ARG A 12 0.07 SIDE CHAIN REMARK 500 4 ARG A 72 0.10 SIDE CHAIN REMARK 500 5 ARG A 51 0.10 SIDE CHAIN REMARK 500 6 ARG A 34 0.08 SIDE CHAIN REMARK 500 8 ARG A 34 0.09 SIDE CHAIN REMARK 500 11 ARG A 51 0.07 SIDE CHAIN REMARK 500 11 TYR A 56 0.07 SIDE CHAIN REMARK 500 14 TYR A 56 0.06 SIDE CHAIN REMARK 500 17 TYR A 56 0.08 SIDE CHAIN REMARK 500 20 TYR A 40 0.07 SIDE CHAIN REMARK 500 20 TYR A 56 0.09 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 PNS A 87 DBREF 2K0X A 1 86 UNP Q02054 ACPX_STRCO 1 86 SEQADV 2K0X 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 PNS A 87 42 HETNAM PNS 4'-PHOSPHOPANTETHEINE FORMUL 2 PNS C11 H23 N2 O7 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 ALA A 85 1 16 LINK OG SER A 42 P24 PNS A 87 1555 1555 1.53 SITE 1 AC1 7 PHE A 35 GLU A 36 TYR A 40 ASP A 41 SITE 2 AC1 7 SER A 42 LEU A 43 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