HEADER BIOSYNTHETIC PROTEIN 02-JUL-18 6DYO TITLE C-TERMINAL CONDENSATION DOMAIN OF EBONY IN COMPLEX WITH L-DOPAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: EBONY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS NRPS, CONDENSATION DOMAIN, PEPTIDE-BOND FORMATION, BIOSYNTHETIC KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.IZORE,J.TAILHADES,M.H.HANSEN,J.A.KACZMARSKI,C.J.JACKSON,M.J.CRYLE REVDAT 5 11-OCT-23 6DYO 1 REMARK REVDAT 4 08-JAN-20 6DYO 1 REMARK REVDAT 3 06-MAR-19 6DYO 1 JRNL REVDAT 2 13-FEB-19 6DYO 1 JRNL REVDAT 1 30-JAN-19 6DYO 0 JRNL AUTH T.IZORE,J.TAILHADES,M.H.HANSEN,J.A.KACZMARSKI,C.J.JACKSON, JRNL AUTH 2 M.J.CRYLE JRNL TITL DROSOPHILA MELANOGASTERNONRIBOSOMAL PEPTIDE SYNTHETASE EBONY JRNL TITL 2 ENCODES AN ATYPICAL CONDENSATION DOMAIN. JRNL REF PROC. NATL. ACAD. SCI. V. 116 2913 2019 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 30705105 JRNL DOI 10.1073/PNAS.1811194116 REMARK 2 REMARK 2 RESOLUTION. 2.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 5580 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 280 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 46.0800 - 3.5800 1.00 2679 158 0.1911 0.2333 REMARK 3 2 3.5800 - 2.8400 0.98 2621 122 0.2181 0.3190 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.423 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.222 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 1799 REMARK 3 ANGLE : 0.448 2439 REMARK 3 CHIRALITY : 0.040 268 REMARK 3 PLANARITY : 0.003 317 REMARK 3 DIHEDRAL : 6.076 1077 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6DYO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1000235444. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5590 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.840 REMARK 200 RESOLUTION RANGE LOW (A) : 46.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.99 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 6DYM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400, HEPES, CACL2, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 28.59750 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 878 REMARK 465 LYS A 879 REMARK 465 GLY A 880 REMARK 465 SER A 881 REMARK 465 HIS A 882 REMARK 465 HIS A 883 REMARK 465 HIS A 884 REMARK 465 HIS A 885 REMARK 465 HIS A 886 REMARK 465 HIS A 887 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 ASN A 691 7.38 57.68 REMARK 500 ASN A 747 31.22 -150.36 REMARK 500 TYR A 775 -32.59 -135.21 REMARK 500 LYS A 794 30.09 -91.30 REMARK 500 HIS A 840 37.92 71.28 REMARK 500 ASN A 846 68.97 -119.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 903 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 741 O REMARK 620 2 ASN A 742 OD1 63.9 REMARK 620 3 SER A 786 OG 113.6 90.5 REMARK 620 4 MET A 788 O 70.5 131.0 124.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 902 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 744 OD1 REMARK 620 2 GLY A 779 O 129.7 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LDP A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 903 DBREF 6DYO A 666 879 UNP A4GK78 A4GK78_DROME 666 879 SEQADV 6DYO MET A 665 UNP A4GK78 INITIATING METHIONINE SEQADV 6DYO GLY A 880 UNP A4GK78 EXPRESSION TAG SEQADV 6DYO SER A 881 UNP A4GK78 EXPRESSION TAG SEQADV 6DYO HIS A 882 UNP A4GK78 EXPRESSION TAG SEQADV 6DYO HIS A 883 UNP A4GK78 EXPRESSION TAG SEQADV 6DYO HIS A 884 UNP A4GK78 EXPRESSION TAG SEQADV 6DYO HIS A 885 UNP A4GK78 EXPRESSION TAG SEQADV 6DYO HIS A 886 UNP A4GK78 EXPRESSION TAG SEQADV 6DYO HIS A 887 UNP A4GK78 EXPRESSION TAG SEQRES 1 A 223 MET LEU LYS MET GLU ALA VAL PRO LEU ARG LEU GLU HIS SEQRES 2 A 223 ARG GLN GLU VAL ILE ASP ILE ILE VAL ALA SER PHE TYR SEQRES 3 A 223 ASN LYS ALA ASP LEU GLU GLN TRP LEU LYS PRO GLY VAL SEQRES 4 A 223 LEU ARG THR ASP TYR SER ASP ILE LEU ASN ASP ILE TRP SEQRES 5 A 223 ASN VAL LEU VAL GLU ARG ASP LEU SER PHE VAL VAL TYR SEQRES 6 A 223 ASP THR ASN THR ASP ARG ILE ILE GLY THR ALA LEU ASN SEQRES 7 A 223 PHE ASP ALA ARG ASN GLU PRO GLU VAL ASP ILE LYS SER SEQRES 8 A 223 LYS LEU LEU ILE VAL PHE GLU PHE LEU GLU PHE CYS GLU SEQRES 9 A 223 GLY PRO ILE ARG ASP ASN TYR LEU PRO LYS GLY LEU ASN SEQRES 10 A 223 GLN ILE LEU HIS SER PHE MET MET GLY THR ALA GLU LYS SEQRES 11 A 223 LEU ASN PRO ARG GLU ASN ILE ALA CYS MET HIS PHE MET SEQRES 12 A 223 GLU HIS GLU VAL LEU ARG VAL ALA ARG GLU LYS GLN PHE SEQRES 13 A 223 ALA GLY ILE PHE THR THR ASN THR SER PRO LEU THR GLN SEQRES 14 A 223 GLN LEU ALA ASP VAL TYR HIS TYR LYS THR LEU LEU ASN SEQRES 15 A 223 PHE GLN VAL ASN GLU TYR VAL HIS SER ASP GLY SER ARG SEQRES 16 A 223 PRO PHE GLY ASP ALA PRO ASP GLU GLN ARG ALA ILE VAL SEQRES 17 A 223 HIS TRP LYS GLU VAL GLY LYS GLY SER HIS HIS HIS HIS SEQRES 18 A 223 HIS HIS HET LDP A 901 11 HET CA A 902 1 HET CA A 903 1 HETNAM LDP L-DOPAMINE HETNAM CA CALCIUM ION HETSYN LDP DOPAMINE FORMUL 2 LDP C8 H11 N O2 FORMUL 3 CA 2(CA 2+) HELIX 1 AA1 ARG A 674 GLU A 676 5 3 HELIX 2 AA2 HIS A 677 TYR A 690 1 14 HELIX 3 AA3 LEU A 695 LYS A 700 5 6 HELIX 4 AA4 ARG A 705 ARG A 722 1 18 HELIX 5 AA5 LYS A 756 ASP A 773 1 18 HELIX 6 AA6 ASN A 796 LYS A 818 1 23 HELIX 7 AA7 SER A 829 TYR A 839 1 11 HELIX 8 AA8 ASN A 850 TYR A 852 5 3 SHEET 1 AA1 7 MET A 668 PRO A 672 0 SHEET 2 AA1 7 PHE A 726 ASP A 730 -1 O VAL A 727 N VAL A 671 SHEET 3 AA1 7 ARG A 735 ASP A 744 -1 O GLY A 738 N VAL A 728 SHEET 4 AA1 7 ILE A 783 THR A 791 -1 O HIS A 785 N PHE A 743 SHEET 5 AA1 7 GLY A 822 ASN A 827 1 O GLY A 822 N LEU A 784 SHEET 6 AA1 7 ARG A 869 GLU A 876 -1 O ILE A 871 N ASN A 827 SHEET 7 AA1 7 LYS A 842 GLN A 848 -1 N LEU A 844 O VAL A 872 LINK O LEU A 741 CA CA A 903 1555 1555 3.12 LINK OD1 ASN A 742 CA CA A 903 1555 1555 2.81 LINK OD1 ASP A 744 CA CA A 902 1555 1555 2.74 LINK O GLY A 779 CA CA A 902 1555 1555 3.14 LINK OG SER A 786 CA CA A 903 1555 1555 2.82 LINK O MET A 788 CA CA A 903 1555 1555 2.70 CISPEP 1 LYS A 700 PRO A 701 0 -2.98 SITE 1 AC1 4 GLU A 696 VAL A 760 PHE A 787 THR A 826 SITE 1 AC2 7 ASP A 744 ARG A 746 GLY A 779 LEU A 780 SITE 2 AC2 7 ASN A 781 GLN A 782 ILE A 783 SITE 1 AC3 5 LEU A 741 ASN A 742 SER A 786 MET A 788 SITE 2 AC3 5 MET A 789 CRYST1 44.967 57.195 50.427 90.00 114.00 90.00 P 1 21 1 2 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 0.022239 0.000000 0.009899 0.00000 SCALE2 0.000000 0.017484 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021707 0.00000