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- PDB-9ep5: GH191 family Alpha-Galactosaminidase from Environmental sample (9... -

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Basic information

Entry
Database: PDB / ID: 9ep5
TitleGH191 family Alpha-Galactosaminidase from Environmental sample (99.2% identity to Myxococcus fulvus enzyme)
ComponentsGlycoside-hydrolase family GH114 TIM-barrel domain-containing protein
KeywordsHYDROLASE / GH114 family / crystal pathology / environmental sample
Biological speciesenvironmental samples (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsRoth, C. / Moroz, O.V. / Miranda, S.A.D. / Jahn, L. / Blagova, E. / Lebedev, A.A. / Segura, D.R. / Stringer, M.A. / Friis, E.P. / Davies, G.J. / Wilson, K.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2025
Title: Structures of alpha-galactosaminidases from the CAZy GH114 family and homologs defining a new GH191 family of glycosidases.
Authors: Roth, C. / Moroz, O.V. / Miranda, S.A.D. / Jahn, L. / Blagova, E.V. / Lebedev, A.A. / Segura, D.R. / Stringer, M.A. / Friis, E.P. / Franco Cairo, J.P.L. / Davies, G.J. / Wilson, K.S.
History
DepositionMar 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein
D: Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7754
Polymers65,5832
Non-polymers1922
Water8,359464
1
A: Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8872
Polymers32,7911
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8872
Polymers32,7911
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.84, 185.324, 128.391
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-610-

HOH

21A-831-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLN / End label comp-ID: GLN / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 197 - 468 / Label seq-ID: 29 - 300

Dom-ID
1
2

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

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Components

#1: Protein Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein


Mass: 32791.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This entry is a periodic representation of an aperiodic partially disordered crystal, in which chain D has occupancy 1/3 and overlaps with its symmetry equivalent. The minimal periodic ...Details: This entry is a periodic representation of an aperiodic partially disordered crystal, in which chain D has occupancy 1/3 and overlaps with its symmetry equivalent. The minimal periodic representation without overlaps has a three times larger unit cell and contains two additional chains B and C related to A by translation. In the latter representation, the chain D has occupancy 1 but the completeness of data is 1/3.
Source: (gene. exp.) environmental samples (Diatom) / Production host: Bacillus subtilis (bacteria)
#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.: 464 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.9 Å3/Da / Density % sol: 35.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.6% Ammonium Sulphate, 3% PEG 1K,10% glycerol, 24 well format Linbro plate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9119 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 1.64→46.33 Å / Num. obs: 61821 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 14.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.067 / Rrim(I) all: 0.175 / Χ2: 1.15 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.98-46.3311.70.05404530.9990.020.0531.1199.5
1.64-1.6713.33.2030.830550.4671.3133.4660.9100

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Processing

Software
NameVersionClassification
xia2data reduction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5.8.0425refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→46.33 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.887 / SU B: 2.71 / SU ML: 0.085 / Cross valid method: FREE R-VALUE / ESU R: 0.113 / ESU R Free: 0.114
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2405 3200 5.18 %
Rwork0.1966 58581 -
all0.199 --
obs-61781 99.989 %
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: 20.374 Å2
Baniso -1Baniso -2Baniso -3
1-1.469 Å20 Å2-0 Å2
2--0.567 Å20 Å2
3----2.035 Å2
Refinement stepCycle: LAST / Resolution: 1.64→46.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4231 0 10 464 4705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124380
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163977
X-RAY DIFFRACTIONr_angle_refined_deg1.451.85996
X-RAY DIFFRACTIONr_angle_other_deg0.5431.7529119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1965548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.37532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16310642
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.86310208
X-RAY DIFFRACTIONr_chiral_restr0.0780.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025396
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021064
X-RAY DIFFRACTIONr_nbd_refined0.210.2467
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.22015
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21130
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21162
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2290
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.218
X-RAY DIFFRACTIONr_nbd_other0.1440.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1480.265
X-RAY DIFFRACTIONr_mcbond_it1.5421.9372189
X-RAY DIFFRACTIONr_mcbond_other1.5411.9372189
X-RAY DIFFRACTIONr_mcangle_it2.1613.4762738
X-RAY DIFFRACTIONr_mcangle_other2.163.4752739
X-RAY DIFFRACTIONr_scbond_it2.0372.0672191
X-RAY DIFFRACTIONr_scbond_other2.0352.0642188
X-RAY DIFFRACTIONr_scangle_it3.0953.7463258
X-RAY DIFFRACTIONr_scangle_other3.0933.743253
X-RAY DIFFRACTIONr_lrange_it4.96321.143817
X-RAY DIFFRACTIONr_lrange_other4.96521.1633811
X-RAY DIFFRACTIONr_ncsr_local_group_10.0770.059216
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.077490.05009
12AX-RAY DIFFRACTIONLocal ncs0.077490.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.6830.4512380.4614291X-RAY DIFFRACTION100
1.683-1.7290.3872380.3954140X-RAY DIFFRACTION100
1.729-1.7790.3381920.3344069X-RAY DIFFRACTION99.9765
1.779-1.8330.3232120.2683962X-RAY DIFFRACTION99.9761
1.833-1.8930.2421990.2263851X-RAY DIFFRACTION100
1.893-1.960.2532080.2123662X-RAY DIFFRACTION99.9742
1.96-2.0340.2181980.1853568X-RAY DIFFRACTION100
2.034-2.1160.2211940.1723457X-RAY DIFFRACTION100
2.116-2.210.1841940.1663315X-RAY DIFFRACTION100
2.21-2.3180.1851650.163185X-RAY DIFFRACTION100
2.318-2.4430.2111460.1443011X-RAY DIFFRACTION100
2.443-2.5910.1821740.1412849X-RAY DIFFRACTION100
2.591-2.7690.1831480.1372688X-RAY DIFFRACTION100
2.769-2.990.1771210.1492575X-RAY DIFFRACTION100
2.99-3.2740.2151270.1782318X-RAY DIFFRACTION100
3.274-3.6580.2331270.1692094X-RAY DIFFRACTION100
3.658-4.220.1751170.151893X-RAY DIFFRACTION100
4.22-5.1570.221790.1591613X-RAY DIFFRACTION100
5.157-7.2490.312710.2541277X-RAY DIFFRACTION100
7.249-46.330.704520.513764X-RAY DIFFRACTION100

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