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- PDB-8hi8: Crystal structure of a holoenzyme TglHI with three Fe ions for Ps... -

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Basic information

Entry
Database: PDB / ID: 8hi8
TitleCrystal structure of a holoenzyme TglHI with three Fe ions for Pseudomonas syringae Peptidyl (S) 2-mercaptoglycine biosynthesis
Components
  • DUF692 family protein
  • RiPP Recognition Protein
KeywordsMETAL BINDING PROTEIN / Biosynthesis / Complex / FE BINDING PROTEIN / PEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


Uncharacterised protein family UPF0276 / RiPP precursor modification enzyme MbnB/TglH/ChrH / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / DUF692 family protein / Uncharacterized protein
Similarity search - Component
Biological speciesPseudomonas syringae pv. maculicola str. ES4326 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsCheng, W. / Zheng, Y.H. / Fu, X.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81930125 China
CitationJournal: Structure / Year: 2023
Title: Structures of the holoenzyme TglHI required for 3-thiaglutamate biosynthesis.
Authors: Zheng, Y. / Xu, X. / Fu, X. / Zhou, X. / Dou, C. / Yu, Y. / Yan, W. / Yang, J. / Xiao, M. / van der Donk, W.A. / Zhu, X. / Cheng, W.
History
DepositionNov 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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: RiPP Recognition Protein
B: DUF692 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9225
Polymers65,7542
Non-polymers1683
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-56 kcal/mol
Surface area26140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.943, 118.943, 87.460
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein RiPP Recognition Protein


Mass: 31180.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. maculicola str. ES4326 (bacteria)
Gene: PMA4326_007960
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A8T8BZN3
#2: Protein DUF692 family protein


Mass: 34574.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. maculicola str. ES4326 (bacteria)
Gene: PMA4326_007955
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A8T8BZJ9
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 200 mM ammonium sulfate, 30% PEG 4000, 15% glycerin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.49→29.74 Å / Num. obs: 9013 / % possible obs: 99.49 % / Redundancy: 19.2 % / Biso Wilson estimate: 90.33 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.95
Reflection shellResolution: 3.494→3.618 Å / Num. unique obs: 899 / CC1/2: 0.958

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2 Prediction

Resolution: 3.49→29.74 Å / SU ML: 0.2933 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0915
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2598 849 4.86 %
Rwork0.2041 16618 -
obs0.2067 9013 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 109.85 Å2
Refinement stepCycle: LAST / Resolution: 3.49→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4556 0 3 58 4617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00194671
X-RAY DIFFRACTIONf_angle_d0.46936349
X-RAY DIFFRACTIONf_chiral_restr0.0357683
X-RAY DIFFRACTIONf_plane_restr0.0036829
X-RAY DIFFRACTIONf_dihedral_angle_d4.3696622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.49-3.710.38181400.24582786X-RAY DIFFRACTION99.9
3.71-40.27331460.21752770X-RAY DIFFRACTION99.73
4-4.40.22221500.18662762X-RAY DIFFRACTION99.83
4.4-5.040.19121030.19342805X-RAY DIFFRACTION100
5.04-6.340.30671700.22932747X-RAY DIFFRACTION99.97
6.34-29.740.24221400.18682748X-RAY DIFFRACTION98.5

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