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

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Basic information

Entry
Database: PDB / ID: 8btm
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 / GdmF
Function and homology information
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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
DepositionNov 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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)30,1775
Polymers29,9321
Non-polymers2454
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.250, 95.859, 86.444
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-429-

HOH

21A-543-

HOH

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Components

#1: Protein GdmF


Mass: 29931.533 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.53 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / 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: Sep 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→48.28 Å / Num. obs: 60070 / % possible obs: 99.94 % / Redundancy: 13.3 % / Biso Wilson estimate: 17.47 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0546 / Net I/σ(I): 25.56
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 1.139 / Mean I/σ(I) obs: 2 / Num. unique obs: 5911 / CC1/2: 0.825 / % possible all: 99.88

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.17.1_3660refinement
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→48.28 Å / SU ML: 0.1292 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.8076
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1842 2950 4.91 %
Rwork0.1727 57093 -
obs0.1732 60043 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.94 Å2
Refinement stepCycle: LAST / Resolution: 1.4→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 16 159 2122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01012166
X-RAY DIFFRACTIONf_angle_d1.18712964
X-RAY DIFFRACTIONf_chiral_restr0.0831318
X-RAY DIFFRACTIONf_plane_restr0.0072399
X-RAY DIFFRACTIONf_dihedral_angle_d32.8403333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.24641290.26482695X-RAY DIFFRACTION99.82
1.42-1.450.26231230.25212699X-RAY DIFFRACTION99.93
1.45-1.470.26341540.23322679X-RAY DIFFRACTION99.96
1.47-1.50.24781430.22472688X-RAY DIFFRACTION99.86
1.5-1.530.21421480.21052668X-RAY DIFFRACTION99.93
1.53-1.570.20291470.20712677X-RAY DIFFRACTION99.82
1.57-1.60.21141370.19382706X-RAY DIFFRACTION99.86
1.6-1.640.2011350.1972703X-RAY DIFFRACTION99.93
1.64-1.690.21881470.18572691X-RAY DIFFRACTION99.93
1.69-1.740.21741460.18732690X-RAY DIFFRACTION99.89
1.74-1.790.18291220.18432720X-RAY DIFFRACTION99.96
1.79-1.860.21621590.18122687X-RAY DIFFRACTION100
1.86-1.930.20351390.1782717X-RAY DIFFRACTION99.96
1.93-2.020.18891410.16462726X-RAY DIFFRACTION99.97
2.02-2.130.19531600.16882678X-RAY DIFFRACTION100
2.13-2.260.17671320.16232735X-RAY DIFFRACTION100
2.26-2.430.16761310.16542740X-RAY DIFFRACTION100
2.43-2.680.19751360.16732739X-RAY DIFFRACTION100
2.68-3.070.15581390.16782772X-RAY DIFFRACTION100
3.07-3.860.17721420.1582774X-RAY DIFFRACTION99.97
3.86-48.280.16091400.16372909X-RAY DIFFRACTION99.93

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