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

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Basic information

Entry
Database: PDB / ID: 8osv
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 / DI(HYDROXYETHYL)ETHER / : / GdmF
Function and homology information
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 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 1.1Nov 20, 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)30,2045
Polymers29,8571
Non-polymers3464
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint3 kcal/mol
Surface area11920 Å2
Unit cell
Length a, b, c (Å)74.304, 95.288, 86.591
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-430-

HOH

21A-565-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 209 molecules

#2: Chemical ChemComp-W0K / ~{N}-(2-sulfanylethyl)ethanamide


Mass: 119.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NOS / 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.28→43.3 Å / Num. obs: 79149 / % possible obs: 99.96 % / Redundancy: 13.4 % / Biso Wilson estimate: 17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05978 / Net I/σ(I): 19.7
Reflection shellResolution: 1.28→1.326 Å / Mean I/σ(I) obs: 1.89 / Num. unique obs: 7826 / CC1/2: 0.825

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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: 1.28→43.3 Å / SU ML: 0.1221 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.6463
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1803 3891 4.92 %
Rwork0.1653 75238 -
obs0.1661 79129 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.5 Å2
Refinement stepCycle: LAST / Resolution: 1.28→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 22 205 2189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162147
X-RAY DIFFRACTIONf_angle_d1.4242932
X-RAY DIFFRACTIONf_chiral_restr0.1039318
X-RAY DIFFRACTIONf_plane_restr0.0094392
X-RAY DIFFRACTIONf_dihedral_angle_d30.1795318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.30.25151240.25612688X-RAY DIFFRACTION99.96
1.3-1.310.24061370.24862660X-RAY DIFFRACTION99.93
1.31-1.330.27031580.24132642X-RAY DIFFRACTION99.89
1.33-1.350.23341430.24492649X-RAY DIFFRACTION99.96
1.35-1.370.26991290.24142667X-RAY DIFFRACTION99.96
1.37-1.390.24871410.22772639X-RAY DIFFRACTION100
1.39-1.410.23311350.2142683X-RAY DIFFRACTION99.96
1.41-1.430.2251540.20522659X-RAY DIFFRACTION99.96
1.43-1.460.21491320.19952658X-RAY DIFFRACTION99.96
1.46-1.480.20851230.1922682X-RAY DIFFRACTION100
1.48-1.510.20391260.17922699X-RAY DIFFRACTION99.96
1.51-1.540.19831400.17842654X-RAY DIFFRACTION99.96
1.54-1.580.2041370.17922666X-RAY DIFFRACTION99.93
1.58-1.610.18261300.17422670X-RAY DIFFRACTION99.96
1.61-1.650.191330.16772697X-RAY DIFFRACTION99.93
1.65-1.70.17731260.1692682X-RAY DIFFRACTION99.89
1.7-1.750.1751390.17242663X-RAY DIFFRACTION99.93
1.75-1.80.1781190.16952693X-RAY DIFFRACTION99.96
1.8-1.870.1811290.17032697X-RAY DIFFRACTION100
1.87-1.940.17611550.15952681X-RAY DIFFRACTION100
1.94-2.030.1711550.15292685X-RAY DIFFRACTION100
2.03-2.140.18261440.15522676X-RAY DIFFRACTION100
2.14-2.270.15311560.15542687X-RAY DIFFRACTION100
2.27-2.450.18231330.1492705X-RAY DIFFRACTION99.93
2.45-2.690.15641490.15972714X-RAY DIFFRACTION100
2.69-3.080.16141450.15922734X-RAY DIFFRACTION100
3.08-3.880.16591390.15452750X-RAY DIFFRACTION100
3.89-43.30.19211600.16022858X-RAY DIFFRACTION99.87

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