HEADER BIOSYNTHETIC PROTEIN 24-MAY-22 8CZC TITLE AT FROM FIRST MODULE OF THE PIKROMYCIN SYNTHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NARBONOLIDE/10-DEOXYMETHYNOLIDE SYNTHASE PIKA1, MODULES 1 COMPND 3 AND 2; COMPND 4 CHAIN: B; COMPND 5 SYNONYM: NARBONOLIDE/10-DEOXYMETHYNOLIDE SYNTHASE PIKAI,PIKROMYCIN COMPND 6 POLYKETIDE SYNTHASE COMPONENT PIKAI,PIKROMYCIN PKS COMPONENT PIKAI, COMPND 7 TYPE I MODULAR POLYKETIDE SYNTHASE PIKAI,PKS; COMPND 8 EC: 2.3.1.239,2.3.1.240; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: FIRST AT DOMAIN OF PIKROMYCIN SYNTHASE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES VENEZUELAE; SOURCE 3 ORGANISM_TAXID: 54571; SOURCE 4 ATCC: 15439; SOURCE 5 GENE: PIKAI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: K207-3 KEYWDS ACYLTRANSFERASE, METHYLMALONYL-SPECIFIC, POLYKETIDE SYNTHASE, KEYWDS 2 BIOSYNTHETIC PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR A.T.KEATINGE-CLAY,M.S.DICKINSON,T.MIYAZAWA,R.S.MCCOOL REVDAT 3 14-SEP-22 8CZC 1 JRNL REVDAT 2 06-JUL-22 8CZC 1 JRNL REVDAT 1 08-JUN-22 8CZC 0 JRNL AUTH M.S.DICKINSON,T.MIYAZAWA,R.S.MCCOOL,A.T.KEATINGE-CLAY JRNL TITL PRIMING ENZYMES FROM THE PIKROMYCIN SYNTHASE REVEAL HOW JRNL TITL 2 ASSEMBLY-LINE KETOSYNTHASES CATALYZE CARBON-CARBON JRNL TITL 3 CHEMISTRY. JRNL REF STRUCTURE V. 30 1331 2022 JRNL REFN ISSN 0969-2126 JRNL PMID 35738283 JRNL DOI 10.1016/J.STR.2022.05.021 REMARK 2 REMARK 2 RESOLUTION. 2.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SERIALEM, CRYOSPARC, UCSF CHIMERAX, REMARK 3 PHENIX, COOT, PHENIX, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 2QO3 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : PHENIX REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 2.860 REMARK 3 NUMBER OF PARTICLES : 184737 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: MAPS WERE DENSITY MODIFIED USING PHENIX TO A REMARK 3 CALCULATED RESOLUTION OF 2.77 ANGSTROMS. REMARK 4 REMARK 4 8CZC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000265738. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : PIK127 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.50 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOTTED FOR 3 SECONDS WITH A REMARK 245 FORCE OF "1" BEFORE PLUNGING. REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : POLYKETIDE SYNTHASE ENGINEERED REMARK 245 FROM THE FIRST, SECOND, AND SEVENTH MODULES OF THE PIKROMYCIN REMARK 245 SYNTHASE AS DESCRIBED IN MIYAZAWA ET AL., 2021, CHEM. COMMUN. 57: REMARK 245 8762-8765 REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 7196 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 7000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : 61728 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : COLLECTED 4284 MOVIES AT 0 REMARK 245 DEGREES TILT AND 2912 MOVIES AT -30 DEGREES TILT REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: B 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: 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 PRO B 670 13.15 -67.89 REMARK 500 TYR B 671 -35.07 -139.49 REMARK 500 ASP B 673 -33.45 71.34 REMARK 500 LEU B 689 11.23 55.93 REMARK 500 SER B 724 -124.01 57.28 REMARK 500 HIS B 756 -38.51 -140.47 REMARK 500 PRO B 791 24.72 -72.97 REMARK 500 THR B 792 -22.45 -140.11 REMARK 500 PRO B 821 75.57 -69.88 REMARK 500 PRO B 866 63.54 -69.39 REMARK 500 LEU B 868 52.10 -110.29 REMARK 500 ASP B 893 -76.18 -85.99 REMARK 500 MET B 910 41.34 -80.75 REMARK 500 ALA B 911 -11.25 -154.53 REMARK 500 THR B 921 -78.59 -114.74 REMARK 500 ASP B 925 -13.85 64.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-26839 RELATED DB: EMDB REMARK 900 PIK(KSQ+AT1) REMARK 900 RELATED ID: EMD-27094 RELATED DB: EMDB REMARK 900 AT FROM FIRST MODULE OF THE PIKROMYCIN SYNTHASE DBREF 8CZC B 628 942 UNP Q9ZGI5 PIKA1_STRVZ 628 942 SEQRES 1 B 315 GLY VAL GLY ARG VAL ALA PHE VAL PHE PRO GLY GLN GLY SEQRES 2 B 315 THR GLN TRP ALA GLY MET GLY ALA GLU LEU LEU ASP SER SEQRES 3 B 315 SER ALA VAL PHE ALA ALA ALA MET ALA GLU CYS GLU ALA SEQRES 4 B 315 ALA LEU SER PRO TYR VAL ASP TRP SER LEU GLU ALA VAL SEQRES 5 B 315 VAL ARG GLN ALA PRO GLY ALA PRO THR LEU GLU ARG VAL SEQRES 6 B 315 ASP VAL VAL GLN PRO VAL THR PHE ALA VAL MET VAL SER SEQRES 7 B 315 LEU ALA ARG VAL TRP GLN HIS HIS GLY VAL THR PRO GLN SEQRES 8 B 315 ALA VAL VAL GLY HIS SER GLN GLY GLU ILE ALA ALA ALA SEQRES 9 B 315 TYR VAL ALA GLY ALA LEU SER LEU ASP ASP ALA ALA ARG SEQRES 10 B 315 VAL VAL THR LEU ARG SER LYS SER ILE ALA ALA HIS LEU SEQRES 11 B 315 ALA GLY LYS GLY GLY MET LEU SER LEU ALA LEU SER GLU SEQRES 12 B 315 ASP ALA VAL LEU GLU ARG LEU ALA GLY PHE ASP GLY LEU SEQRES 13 B 315 SER VAL ALA ALA VAL ASN GLY PRO THR ALA THR VAL VAL SEQRES 14 B 315 SER GLY ASP PRO VAL GLN ILE GLU GLU LEU ALA ARG ALA SEQRES 15 B 315 CYS GLU ALA ASP GLY VAL ARG ALA ARG VAL ILE PRO VAL SEQRES 16 B 315 ASP TYR ALA SER HIS SER ARG GLN VAL GLU ILE ILE GLU SEQRES 17 B 315 SER GLU LEU ALA GLU VAL LEU ALA GLY LEU SER PRO GLN SEQRES 18 B 315 ALA PRO ARG VAL PRO PHE PHE SER THR LEU GLU GLY ALA SEQRES 19 B 315 TRP ILE THR GLU PRO VAL LEU ASP GLY GLY TYR TRP TYR SEQRES 20 B 315 ARG ASN LEU ARG HIS ARG VAL GLY PHE ALA PRO ALA VAL SEQRES 21 B 315 GLU THR LEU ALA THR ASP GLU GLY PHE THR HIS PHE VAL SEQRES 22 B 315 GLU VAL SER ALA HIS PRO VAL LEU THR MET ALA LEU PRO SEQRES 23 B 315 GLY THR VAL THR GLY LEU ALA THR LEU ARG ARG ASP ASN SEQRES 24 B 315 GLY GLY GLN ASP ARG LEU VAL ALA SER LEU ALA GLU ALA SEQRES 25 B 315 TRP ALA ASN HELIX 1 AA1 GLY B 647 SER B 654 1 8 HELIX 2 AA2 SER B 654 ASP B 673 1 20 HELIX 3 AA3 SER B 675 ARG B 681 1 7 HELIX 4 AA4 ARG B 691 HIS B 713 1 23 HELIX 5 AA5 GLN B 725 ALA B 734 1 10 HELIX 6 AA6 SER B 738 LEU B 757 1 20 HELIX 7 AA7 SER B 769 LEU B 777 1 9 HELIX 8 AA8 ASP B 799 ASP B 813 1 15 HELIX 9 AA9 ARG B 829 ILE B 833 5 5 HELIX 10 AB1 ILE B 834 LEU B 842 1 9 HELIX 11 AB2 ASP B 869 HIS B 879 1 11 HELIX 12 AB3 GLY B 882 ASP B 893 1 12 HELIX 13 AB4 LEU B 908 LEU B 912 5 5 HELIX 14 AB5 GLY B 928 ALA B 941 1 14 SHEET 1 AA1 6 ALA B 861 ILE B 863 0 SHEET 2 AA1 6 PHE B 854 SER B 856 -1 N SER B 856 O ALA B 861 SHEET 3 AA1 6 ALA B 719 GLY B 722 1 N VAL B 720 O PHE B 855 SHEET 4 AA1 6 ARG B 631 PHE B 636 1 N PHE B 634 O VAL B 721 SHEET 5 AA1 6 PHE B 896 GLU B 901 1 O VAL B 900 N ALA B 633 SHEET 6 AA1 6 THR B 917 LEU B 919 1 O THR B 917 N THR B 897 SHEET 1 AA2 4 LEU B 783 GLY B 790 0 SHEET 2 AA2 4 ALA B 793 GLY B 798 -1 O VAL B 795 N ALA B 786 SHEET 3 AA2 4 GLY B 762 LEU B 766 -1 N LEU B 764 O VAL B 796 SHEET 4 AA2 4 ALA B 817 ILE B 820 -1 O ARG B 818 N SER B 765 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