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- PDB-9jhq: Crystal structure of GodF, a post-translational modification enzy... -

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Basic information

Entry
Database: PDB / ID: 9jhq
TitleCrystal structure of GodF, a post-translational modification enzyme involved in the biosynthesis of goadsporin
ComponentsGoadsporin biosynthetic protein
KeywordsTRANSFERASE / tRNA-dependent glutamylation / biosynthetic protein / goadsporin
Function / homologyACETATE ION / Goadsporin biosynthetic protein
Function and homology information
Biological speciesStreptomyces sp. TP-A0584 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsShimizu-Ibuka, A. / Kato, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural analysis of GodF, a post-translational modification enzyme involved in the biosynthesis of goadsporin
Authors: Kato, Y. / Shimizu-Ibuka, A.
History
DepositionSep 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Goadsporin biosynthetic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9663
Polymers93,8151
Non-polymers1512
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint0 kcal/mol
Surface area35300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.340, 69.670, 75.450
Angle α, β, γ (deg.)90.000, 105.830, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Goadsporin biosynthetic protein


Mass: 93814.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. TP-A0584 (bacteria) / Gene: godF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3C2F5
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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 interestN
Has protein modificationN

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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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.9 M sodium acetate, 0.1 M sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.34→72.6 Å / Num. obs: 39491 / % possible obs: 99.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 38.51 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.063 / Net I/av σ(I): 8 / Net I/σ(I): 6.9
Reflection shellResolution: 2.34→2.43 Å / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2795 / CC1/2: 0.819

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→72.59 Å / SU ML: 0.2846 / Cross valid method: FREE R-VALUE / Phase error: 24.7385
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.236 2009 5.09 %
Rwork0.1835 37482 -
obs0.1863 39491 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.54 Å2
Refinement stepCycle: LAST / Resolution: 2.34→72.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6203 0 10 159 6372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00786372
X-RAY DIFFRACTIONf_angle_d0.87088678
X-RAY DIFFRACTIONf_chiral_restr0.0488995
X-RAY DIFFRACTIONf_plane_restr0.00911130
X-RAY DIFFRACTIONf_dihedral_angle_d15.83892329
LS refinement shellResolution: 2.34→2.4 Å
RfactorNum. reflection% reflection
Rfree0.3172 127 -
Rwork0.2387 2806 -
obs--99.96 %

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