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

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Basic information

Entry
Database: PDB / ID: 8osz
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 / 3-aminophenol / DI(HYDROXYETHYL)ETHER / GdmF
Function and homology information
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: GdmF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1644
Polymers29,8891
Non-polymers2743
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint0 kcal/mol
Surface area11850 Å2
Unit cell
Length a, b, c (Å)74.328, 95.374, 86.479
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-436-

HOH

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Components

#1: Protein GdmF


Mass: 29889.455 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-K5V / 3-aminophenol


Mass: 109.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 100 mM HEPES, pH 7.5, 25 % PEG4000, 150 mM sodium acetate, 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: 1.26→43.24 Å / Num. obs: 82845 / % possible obs: 99.92 % / Redundancy: 13.3 % / Biso Wilson estimate: 16.32 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04587 / Net I/σ(I): 24.42
Reflection shellResolution: 1.26→1.305 Å / Rmerge(I) obs: 0.9903 / Num. unique obs: 8191 / CC1/2: 0.878 / Rrim(I) all: 2.08 / % possible all: 99.83

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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: 1.26→43.24 Å / SU ML: 0.1131 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7699
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1912 4151 5.01 %
Rwork0.1695 78694 -
obs0.1706 82845 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.16 Å2
Refinement stepCycle: LAST / Resolution: 1.26→43.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 19 191 2159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01622137
X-RAY DIFFRACTIONf_angle_d1.50922922
X-RAY DIFFRACTIONf_chiral_restr0.1104314
X-RAY DIFFRACTIONf_plane_restr0.0112391
X-RAY DIFFRACTIONf_dihedral_angle_d36.2969320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.270.27151640.26092542X-RAY DIFFRACTION99.96
1.27-1.290.27591160.25022664X-RAY DIFFRACTION99.82
1.29-1.310.27481390.24732552X-RAY DIFFRACTION99.7
1.31-1.320.25371440.23672585X-RAY DIFFRACTION99.78
1.32-1.340.25181250.23042621X-RAY DIFFRACTION99.93
1.34-1.360.24321410.23712587X-RAY DIFFRACTION99.93
1.36-1.380.28811250.22982621X-RAY DIFFRACTION99.93
1.38-1.40.21151430.22422564X-RAY DIFFRACTION99.85
1.4-1.420.23621500.20472588X-RAY DIFFRACTION99.89
1.42-1.440.22151270.20172647X-RAY DIFFRACTION99.89
1.44-1.470.22791620.19222565X-RAY DIFFRACTION99.96
1.47-1.490.20431420.18772592X-RAY DIFFRACTION99.89
1.49-1.520.21911280.18032624X-RAY DIFFRACTION99.96
1.52-1.550.17281450.18122620X-RAY DIFFRACTION99.89
1.55-1.590.21461210.17982607X-RAY DIFFRACTION100
1.59-1.620.21451420.16882616X-RAY DIFFRACTION99.96
1.62-1.670.18481330.16622608X-RAY DIFFRACTION99.93
1.67-1.710.16271200.16952632X-RAY DIFFRACTION99.89
1.71-1.760.18861500.17062608X-RAY DIFFRACTION99.93
1.76-1.820.16861490.17412605X-RAY DIFFRACTION100
1.82-1.880.21191240.16912657X-RAY DIFFRACTION100
1.88-1.960.17751430.16152625X-RAY DIFFRACTION100
1.96-2.050.17991430.1572594X-RAY DIFFRACTION100
2.05-2.150.16791320.15772674X-RAY DIFFRACTION100
2.15-2.290.17061250.15812640X-RAY DIFFRACTION99.96
2.29-2.470.18591400.15942638X-RAY DIFFRACTION100
2.47-2.710.20291180.16632684X-RAY DIFFRACTION99.93
2.71-3.110.17461530.17292658X-RAY DIFFRACTION99.89
3.11-3.910.19821440.15772698X-RAY DIFFRACTION100
3.91-43.240.18251630.16032778X-RAY DIFFRACTION99.93

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