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- PDB-8hci: Crystal structure of a holoenzyme Fe-free TglHI for Pseudomonas s... -

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Basic information

Entry
Database: PDB / ID: 8hci
TitleCrystal structure of a holoenzyme Fe-free TglHI for Pseudomonas syringae Peptidyl (S) 2-mercaptoglycine biosynthesis
Components
  • DUF692 family protein
  • RiPP Recognition protein
KeywordsBIOSYNTHETIC 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: 3.399 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 1, 2022Deposition site: PDBJ / Processing site: PDBC
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

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Assembly

Deposited unit
C: RiPP Recognition protein
D: DUF692 family protein
A: RiPP Recognition protein
B: DUF692 family protein


Theoretical massNumber of molelcules
Total (without water)131,5094
Polymers131,5094
Non-polymers00
Water84747
1
C: RiPP Recognition protein
D: DUF692 family protein


Theoretical massNumber of molelcules
Total (without water)65,7542
Polymers65,7542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-19 kcal/mol
Surface area25400 Å2
MethodPISA
2
A: RiPP Recognition protein
B: DUF692 family protein


Theoretical massNumber of molelcules
Total (without water)65,7542
Polymers65,7542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-20 kcal/mol
Surface area25490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.952, 86.314, 91.994
Angle α, β, γ (deg.)90.000, 109.660, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 9 or resid 11...
d_2ens_1(chain "C" and (resid 2 through 9 or resid 11...
d_1ens_2(chain "B" and (resid 1 through 26 or resid 28...
d_2ens_2(chain "D" and (resid 1 through 26 or resid 28...

NCS ensembles :
ID
ens_1
ens_2

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Components

#1: Protein RiPP Recognition protein


Mass: 31180.402 Da / Num. of mol.: 2
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.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 20% w/v polyethylene glycol 3350

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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: Jul 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.399→61.15 Å / Num. obs: 15758 / % possible obs: 98.32 % / Redundancy: 3.3 % / Biso Wilson estimate: 65.14 Å2 / CC1/2: 0.958 / Net I/σ(I): 5.58
Reflection shellResolution: 3.399→3.52 Å / Num. unique obs: 1580 / CC1/2: 0.861

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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 Predict

Resolution: 3.399→61.15 Å / SU ML: 0.473 / Cross valid method: FREE R-VALUE / Phase error: 27.923
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2581 --
Rwork0.2265 28392 -
obs-15758 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.54 Å2
Refinement stepCycle: LAST / Resolution: 3.399→61.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9116 0 0 47 9163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00279348
X-RAY DIFFRACTIONf_angle_d0.595812708
X-RAY DIFFRACTIONf_chiral_restr0.04121366
X-RAY DIFFRACTIONf_plane_restr0.00411660
X-RAY DIFFRACTIONf_dihedral_angle_d4.79891244
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CX-RAY DIFFRACTIONTorsion NCS0.879914793413
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.994385836851
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.510.28551450.27112638X-RAY DIFFRACTION98.13
3.51-3.630.33261510.2572636X-RAY DIFFRACTION98.76
3.63-3.780.23221210.26632657X-RAY DIFFRACTION98.23
3.78-3.950.29061440.22972624X-RAY DIFFRACTION97.36
3.95-4.160.27921410.22382563X-RAY DIFFRACTION96.09
4.16-4.420.34181130.22622530X-RAY DIFFRACTION94.53
4.42-4.760.30511310.21712346X-RAY DIFFRACTION87.87
4.76-5.240.24931290.21232611X-RAY DIFFRACTION96.14
5.24-60.26791630.23432659X-RAY DIFFRACTION99.23
6-7.550.26591410.23672636X-RAY DIFFRACTION98.69
7.55-61.150.15221370.18662492X-RAY DIFFRACTION92.86

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