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- PDB-7xrj: crystal structure of N-acetyltransferase DgcN-25328 -

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Basic information

Entry
Database: PDB / ID: 7xrj
Titlecrystal structure of N-acetyltransferase DgcN-25328
ComponentsPutative NAD-dependent epimerase/dehydratase family protein
KeywordsTRANSFERASE / N-acetyltransferase / D-Glu metabolism / D-Glu / acetyl-CoA
Function / homologyUncharacterised conserved protein UCP026760 / Domain of unknown function DUF1611, P-loop / Domain of unknown function DUF1611-N, Rossmann-like domain / Domain of unknown function (DUF1611_C) P-loop domain / Domain of unknown function (DUF1611_N) Rossmann-like domain / P-loop containing nucleoside triphosphate hydrolase / Putative NAD-dependent epimerase/dehydratase family protein
Function and homology information
Biological speciesTritonibacter scottomollicae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhang, Y.Z. / Yu, Y. / Cao, H.Y. / Chen, X.L. / Wang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)U1706207 China
CitationJournal: Isme J / Year: 2023
Title: Novel D-glutamate catabolic pathway in marine Proteobacteria and halophilic archaea.
Authors: Yu, Y. / Wang, P. / Cao, H.Y. / Teng, Z.J. / Zhu, Y. / Wang, M. / McMinn, A. / Chen, Y. / Xiang, H. / Zhang, Y.Z. / Chen, X.L. / Zhang, Y.Q.
History
DepositionMay 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative NAD-dependent epimerase/dehydratase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9003
Polymers36,7081
Non-polymers1922
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-16 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.490, 130.800, 131.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-783-

HOH

21A-831-

HOH

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Components

#1: Protein Putative NAD-dependent epimerase/dehydratase family protein


Mass: 36707.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tritonibacter scottomollicae (bacteria)
Gene: CLV89_10851 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2T1AE85
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.37 Å3/Da / Density % sol: 63.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M NaCl, 0.1 M Bis-Tris (pH 6.5) and 1.5 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5406 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Oct 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.2→46.36 Å / Num. obs: 25305 / % possible obs: 99 % / Redundancy: 4.9 % / CC1/2: 0.98 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.069 / Rrim(I) all: 0.159 / Net I/σ(I): 11.9
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 2118 / CC1/2: 0.915 / Rpim(I) all: 0.196 / Rrim(I) all: 0.435 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OBN

2obn


Resolution: 2.2→30.91 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 1997 7.9 %
Rwork0.1817 23289 -
obs0.1838 25286 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.43 Å2 / Biso mean: 21.9546 Å2 / Biso min: 1.28 Å2
Refinement stepCycle: final / Resolution: 2.2→30.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 10 339 2829
Biso mean--20.05 28.66 -
Num. residues----331
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.250.22421390.19311605174497
2.26-2.320.25871440.20561636178099
2.32-2.380.23591420.199316661808100
2.38-2.460.23041370.20216351772100
2.46-2.550.24511430.19811670181399
2.55-2.650.25741410.201416551796100
2.65-2.770.22441420.202216751817100
2.77-2.920.241420.21241642178499
2.92-3.10.23071410.20411656179799
3.1-3.340.21721430.18451672181599
3.34-3.670.19541440.16061669181399
3.67-4.210.16221460.15031690183699
4.21-5.290.15951450.14711696184198
5.3-30.910.20131480.1821722187095

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