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- PDB-7zgm: Plant N-glycan specific alpha-1,3-mannosidase -

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Basic information

Entry
Database: PDB / ID: 7zgm
TitlePlant N-glycan specific alpha-1,3-mannosidase
ComponentsGlycoside hydrolase family 92 protein
KeywordsHYDROLASE / plant N-glycans / PNGase / gut microbiota
Function / homology
Function and homology information


carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Alpha-1,2-mannosidase, putative / Glycosyl hydrolase family 92 / Glycosyl hydrolase family 92 N-terminal domain / Glycosyl hydrolase family 92 catalytic domain / Glycosyl hydrolase family 92 N-terminal domain / Glycoside hydrolase-type carbohydrate-binding / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
: / Uncharacterized protein
Similarity search - Component
Biological speciesPhocaeicola massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 92 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,64318
Polymers80,1871
Non-polymers45617
Water11,638646
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-132 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.941, 84.335, 132.581
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycoside hydrolase family 92 protein / B035DRAFT_03340GH92 / GH92 family glycosyl hydrolase


Mass: 80187.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phocaeicola massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223 (bacteria)
Gene: HMPREF1534_02484 / Production host: Escherichia coli (E. coli) / References: UniProt: U6RD63
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200 mM Potassium citrate and 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.43→66.29 Å / Num. obs: 135130 / % possible obs: 98.8 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.048 / Rrim(I) all: 0.095 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.83-66.296.30.0341351300.9940.020.039
1.43-1.455.91.19664770.5020.7941.444

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Processing

Software
NameVersionClassification
REFMAC5.8.0326refinement
Cootmodel building
MolProbitymodel building
PHASERphasing
pointlessdata scaling
xia2data reduction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wvx

2wvx


Resolution: 1.43→66.29 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.506 / SU ML: 0.041 / Cross valid method: FREE R-VALUE / ESU R: 0.058 / ESU R Free: 0.056
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1725 6731 4.993 %
Rwork0.1327 128079 -
all0.135 --
obs-134810 98.519 %
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: 18.793 Å2
Baniso -1Baniso -2Baniso -3
1-0.932 Å20 Å2-0 Å2
2---0.799 Å20 Å2
3----0.132 Å2
Refinement stepCycle: LAST / Resolution: 1.43→66.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5591 0 17 646 6254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0125879
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165211
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.6417955
X-RAY DIFFRACTIONr_angle_other_deg0.4441.56412034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6625726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63821.22857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84910.173925
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg7.213102
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.19810256
X-RAY DIFFRACTIONr_chiral_restr0.0650.2838
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026879
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021406
X-RAY DIFFRACTIONr_nbd_refined0.2240.21215
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.24998
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22858
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23092
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2497
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1280.22
X-RAY DIFFRACTIONr_metal_ion_refined0.280.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2560.220
X-RAY DIFFRACTIONr_nbd_other0.2340.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.221
X-RAY DIFFRACTIONr_mcbond_it1.9541.832833
X-RAY DIFFRACTIONr_mcbond_other1.9471.832833
X-RAY DIFFRACTIONr_mcangle_it2.3982.7543543
X-RAY DIFFRACTIONr_mcangle_other2.3982.7563544
X-RAY DIFFRACTIONr_scbond_it2.7212.113046
X-RAY DIFFRACTIONr_scbond_other2.72.113043
X-RAY DIFFRACTIONr_scangle_it3.2133.0554399
X-RAY DIFFRACTIONr_scangle_other3.2133.0564400
X-RAY DIFFRACTIONr_lrange_it3.86228.0977004
X-RAY DIFFRACTIONr_lrange_other3.57225.6276842
X-RAY DIFFRACTIONr_rigid_bond_restr2.162311090
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
1.43-1.4670.2715110.25791610.258100130.940.94396.59440.254
1.467-1.5070.2634970.21389960.21697590.9480.95297.27430.204
1.507-1.5510.234920.18387190.18694650.9630.97497.31640.172
1.551-1.5990.2414380.15986020.16292500.9640.98397.72970.147
1.599-1.6510.2034420.1483450.14389690.9740.98697.97080.128
1.651-1.7090.1814610.12580370.12886350.9810.9998.41340.114
1.709-1.7730.1733940.11378430.11683880.9820.99298.19980.103
1.773-1.8460.1733580.10376130.10680830.9820.99398.61440.094
1.846-1.9280.1783470.1172830.11377240.9810.99298.7830.102
1.928-2.0220.1593770.10669640.10974260.9840.99298.85540.098
2.022-2.1310.1733320.12466570.12670650.9620.9998.92430.117
2.131-2.260.1463370.10863210.1166860.9870.99399.58120.103
2.26-2.4160.1563170.10559690.10763240.9860.99399.39910.101
2.416-2.6090.1552630.10255940.10458790.9870.99499.62580.099
2.609-2.8580.162680.12151520.12354320.9840.99199.77910.12
2.858-3.1950.1612510.14246580.14349160.9830.98899.85760.142
3.195-3.6870.182300.14841780.1544100.9820.98899.95460.15
3.687-4.5130.1381890.12635400.12737290.990.9911000.13
4.513-6.3670.171450.14228020.14429490.9880.99199.93220.147
6.367-66.290.198820.1916440.1917320.9760.97599.65360.208

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