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- PDB-8oom: Structural and functional studies of geldanamycin amide synthase ... -

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Basic information

Entry
Database: PDB / ID: 8oom
TitleStructural and functional studies of geldanamycin amide synthase ShGdmF
ComponentsGdmF
KeywordsBIOSYNTHETIC PROTEIN / amide synthase / geldanamycin / amidase / alpha-beta
Function / homology: / Arylamine N-acetyltransferase / N-acetyltransferase / arylamine N-acetyltransferase activity / Papain-like cysteine peptidase superfamily / ACETATE ION / Chem-PNY / GdmF
Function and homology information
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsEwert, W. / Zeilinger, C. / Kirschning, A. / Preller, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Structure and function of the geldanamycin amide synthase from Streptomyces hygroscopicus.
Authors: Ewert, W. / Bartens, C. / Ongouta, J. / Holmes, M. / Heutling, A. / Kishore, A. / Urbansky, T. / Zeilinger, C. / Preller, M. / Kirschning, A.
History
DepositionApr 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Apr 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GdmF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3135
Polymers29,8571
Non-polymers4564
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-1 kcal/mol
Surface area11640 Å2
Unit cell
Length a, b, c (Å)72.874, 96.184, 86.754
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

21A-481-

HOH

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Components

#1: Protein GdmF


Mass: 29857.455 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces hygroscopicus (bacteria) / Gene: gdmF / Production host: Escherichia coli (E. coli) / References: UniProt: Q84G21
#2: Chemical ChemComp-PNY / (2R)-2,4-dihydroxy-3,3-dimethyl-N-{3-oxo-3-[(2-sulfanylethyl)amino]propyl}butanamide / pantetheine / (R)-2,4-Dihydroxy-N-(3-((2-mercaptoethyl)amino)-3-oxopropyl)-3,3-dimethylbutanamide


Mass: 278.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H22N2O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 100 mM HEPES, pH: 7.5, 25% PEG4000, 150 mM sodium acide, 200 mM lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.82→48.27 Å / Num. obs: 27488 / % possible obs: 99.29 % / Redundancy: 13.04 % / Biso Wilson estimate: 22.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08638 / Net I/σ(I): 13.04
Reflection shellResolution: 1.82→1.885 Å / Rmerge(I) obs: 0.7653 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 2723 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.17.1_3660refinement
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→48.27 Å / SU ML: 0.201 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.4941
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1959 1411 5.13 %
Rwork0.1702 26073 -
obs0.1716 27484 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.42 Å2
Refinement stepCycle: LAST / Resolution: 1.82→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 30 90 2065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152085
X-RAY DIFFRACTIONf_angle_d1.3232846
X-RAY DIFFRACTIONf_chiral_restr0.0869308
X-RAY DIFFRACTIONf_plane_restr0.0102381
X-RAY DIFFRACTIONf_dihedral_angle_d27.5972300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.890.27261340.25442589X-RAY DIFFRACTION99.49
1.89-1.960.28441350.23222573X-RAY DIFFRACTION99.56
1.96-2.050.22111360.19932573X-RAY DIFFRACTION99.19
2.05-2.160.21631380.17192588X-RAY DIFFRACTION98.98
2.16-2.290.18811360.1582571X-RAY DIFFRACTION99.01
2.29-2.470.18521400.16192573X-RAY DIFFRACTION99.23
2.47-2.720.20461270.16392630X-RAY DIFFRACTION99.32
2.72-3.110.19281620.16682595X-RAY DIFFRACTION99.49
3.11-3.920.16261450.15682648X-RAY DIFFRACTION99.43
3.92-48.270.19441580.16392733X-RAY DIFFRACTION99.24

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