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- PDB-6dyn: C-terminal condensation domain of Ebony in complex with Histamine -

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Basic information

Entry
Database: PDB / ID: 6dyn
TitleC-terminal condensation domain of Ebony in complex with Histamine
ComponentsEbony
KeywordsBIOSYNTHETIC PROTEIN / NRPS / Condensation domain / Peptide-bond formation
Function / homology
Function and homology information


ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsIzore, T. / Tailhades, J. / Hansen, M.H. / Kaczmarski, J.A. / Jackson, C.J. / Cryle, M.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1140619 Australia
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Drosophila melanogasternonribosomal peptide synthetase Ebony encodes an atypical condensation domain.
Authors: Izore, T. / Tailhades, J. / Hansen, M.H. / Kaczmarski, J.A. / Jackson, C.J. / Cryle, M.J.
History
DepositionJul 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 6, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ebony
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1433
Polymers25,9921
Non-polymers1512
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.580, 57.470, 50.130
Angle α, β, γ (deg.)90.00, 113.23, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Ebony


Mass: 25991.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4GK78
#2: Chemical ChemComp-HSM / HISTAMINE


Mass: 111.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9N3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.24 % / Description: Long thin needles
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, PEG 400, CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→40.97 Å / Num. obs: 13655 / % possible obs: 99.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 27.6 Å2 / Rpim(I) all: 0.05 / Net I/av σ(I): 11.9 / Net I/σ(I): 11.9
Reflection shellResolution: 2.1→2.16 Å / Mean I/σ(I) obs: 2 / CC1/2: 0.63 / Rpim(I) all: 0.4

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Processing

Software
NameVersionClassification
PHENIX1.13_2998:000refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DYM

6dym


Resolution: 2.102→40.97 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.25 -5 %
Rwork0.18 --
obs-13655 99.73 %
Refinement stepCycle: LAST / Resolution: 2.102→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 9 146 1903

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