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- PDB-7zgn: Plant/insect N-glycan active PNGase -

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Basic information

Entry
Database: PDB / ID: 7zgn
TitlePlant/insect N-glycan active PNGase
ComponentsGlpgli family protein
KeywordsHYDROLASE / plant N-glycans / PNGase / gut microbiota
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen
Similarity search - Function
N-glycanase peptide, N-terminal domain / Peptide-N-glycosidase F, N-terminal / Peptide-N-glycosidase F, N-terminal domain superfamily / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, C-terminal / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, C terminal / PHM/PNGase F domain superfamily / Copper type II, ascorbate-dependent monooxygenase-like, C-terminal
Similarity search - Domain/homology
Glpgli family protein
Similarity search - Component
Biological speciesPhocaeicola massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBasle, A. / Crouch, L. / Bolam, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M029018/1 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Plant N -glycan breakdown by human gut Bacteroides.
Authors: Crouch, L.I. / Urbanowicz, P.A. / Basle, A. / Cai, Z.P. / Liu, L. / Voglmeir, J. / Melo Diaz, J.M. / Benedict, S.T. / Spencer, D.I.R. / Bolam, D.N.
History
DepositionApr 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: 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
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_alt_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glpgli family protein
B: Glpgli family protein


Theoretical massNumber of molelcules
Total (without water)124,1662
Polymers124,1662
Non-polymers00
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-19 kcal/mol
Surface area43870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.050, 100.550, 180.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LEU / End label comp-ID: LEU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 27 - 569 / Label seq-ID: 8 - 550

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Glpgli family protein / B035DRAFT_03341PNGase


Mass: 62082.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phocaeicola massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223 (bacteria)
Gene: HMPREF1534_02483 / Production host: Escherichia coli (E. coli) / References: UniProt: U6RE59
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10 mM Cobalt chloride hexahydrate, 100 mM Tris pH 8.5 and 10% w/v Polyvinylpyrrolidone K15

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.95→45.09 Å / Num. obs: 79080 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 0.999 / Net I/σ(I): 12.6
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4454 / CC1/2: 0.517 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0326refinement
Cootmodel building
MolProbitymodel building
PHASERphasing
Aimlessdata scaling
pointlessdata scaling
xia2data reduction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4r4z

4r4z


Resolution: 1.95→44.379 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.194 / SU ML: 0.139 / Cross valid method: NONE / ESU R: 0.174 / ESU R Free: 0.162
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2395 3990 5.05 %
Rwork0.1892 75017 -
all0.192 --
obs-79007 99.77 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 45.568 Å2
Baniso -1Baniso -2Baniso -3
1-0.568 Å2-0 Å20 Å2
2---0.597 Å2-0 Å2
3---0.029 Å2
Refinement stepCycle: LAST / Resolution: 1.95→44.379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8305 0 0 336 8641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0118529
X-RAY DIFFRACTIONr_bond_other_d0.0020.0167992
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.63811572
X-RAY DIFFRACTIONr_angle_other_deg0.5771.56818437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.08951060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.29222105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.53510.2221417
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.83710326
X-RAY DIFFRACTIONr_chiral_restr0.0820.21238
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0210018
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022002
X-RAY DIFFRACTIONr_nbd_refined0.2080.21460
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.27571
X-RAY DIFFRACTIONr_nbtor_refined0.1850.24120
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.25022
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2400
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0340.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1510.225
X-RAY DIFFRACTIONr_nbd_other0.1890.2108
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2010.27
X-RAY DIFFRACTIONr_mcbond_it5.6684.4184240
X-RAY DIFFRACTIONr_mcbond_other5.6674.4184240
X-RAY DIFFRACTIONr_mcangle_it7.2136.6055294
X-RAY DIFFRACTIONr_mcangle_other7.2136.6055295
X-RAY DIFFRACTIONr_scbond_it6.3654.944289
X-RAY DIFFRACTIONr_scbond_other6.3654.944289
X-RAY DIFFRACTIONr_scangle_it8.8747.1586276
X-RAY DIFFRACTIONr_scangle_other8.8737.1576277
X-RAY DIFFRACTIONr_lrange_it10.79259.9649334
X-RAY DIFFRACTIONr_lrange_other10.79159.9629335
X-RAY DIFFRACTIONr_ncsr_local_group_10.1050.0516486
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.105310.05008
12AX-RAY DIFFRACTIONLocal ncs0.105310.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.95-2.0010.3242720.30454800.30557790.9260.92999.53280.293
2.001-2.0550.3362860.28153120.28456210.9260.94499.59080.265
2.055-2.1150.3162700.27351980.27554830.9240.94799.72640.254
2.115-2.180.2992630.25450620.25653430.940.95599.66310.231
2.18-2.2510.2912610.23648740.23951460.9440.96499.78620.211
2.251-2.330.32610.23447210.23749950.9430.96599.73970.204
2.33-2.4170.3082450.22945610.23348150.9360.96699.81310.2
2.417-2.5160.3072320.21744160.22146580.940.9799.78530.188
2.516-2.6270.2752230.21242460.21544740.9560.97399.88820.187
2.627-2.7550.3132070.21140740.21542880.9490.97499.83680.186
2.755-2.9030.2662140.20538690.20840830.9590.9751000.185
2.903-3.0790.2741950.20336850.20738800.9540.9741000.185
3.079-3.290.2531720.20434710.20636490.9550.97599.83560.195
3.29-3.5520.2331710.18932290.19234030.9680.9899.91180.185
3.552-3.8890.2291770.17429910.17731750.9690.98399.77950.175
3.889-4.3440.1741500.1426880.14228390.9840.98899.96480.149
4.344-5.0080.171380.12924330.13125730.9840.99199.92230.141
5.008-6.1140.1821210.14420600.14721810.980.9891000.157
6.114-8.5650.197840.14616480.14817360.9760.98899.76960.161
8.565-44.3790.206480.1829990.18310570.9710.97899.05390.201

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