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- PDB-6ibw: Crh5 transglycosylase in complex with NAG -

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Basic information

Entry
Database: PDB / ID: 6ibw
TitleCrh5 transglycosylase in complex with NAG
ComponentsProbable glycosidase crf1
KeywordsHYDROLASE / cross-link / transglycosylase / GH16 / cell wall assembly
Function / homology
Function and homology information


Hydrolases; Glycosylases / fungal-type cell wall / IgE binding / hydrolase activity, hydrolyzing O-glycosyl compounds / cell wall organization / carbohydrate metabolic process / extracellular region / plasma membrane
Similarity search - Function
Glycoside hydrolase, family 16, CRH1, predicted / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Probable glycosidase crf1
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsFang, W. / Bartual, S.G. / van Aalten, D.M.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)M004139 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Mechanisms of redundancy and specificity of the Aspergillus fumigatus Crh transglycosylases.
Authors: Fang, W. / Sanz, A.B. / Bartual, S.G. / Wang, B. / Ferenbach, A.T. / Farkas, V. / Hurtado-Guerrero, R. / Arroyo, J. / van Aalten, D.M.F.
History
DepositionDec 1, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 27, 2019ID: 5NDL
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.3Oct 16, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable glycosidase crf1
B: Probable glycosidase crf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7056
Polymers53,1942
Non-polymers2,5104
Water82946
1
A: Probable glycosidase crf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8523
Polymers26,5971
Non-polymers1,2552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable glycosidase crf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8523
Polymers26,5971
Non-polymers1,2552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.390, 75.300, 117.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A24 - 266
2010B24 - 266

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Components

#1: Protein Probable glycosidase crf1 / Crh-like protein 1


Mass: 26597.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: crf1, AFUA_1G16190
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8J0P4, Hydrolases; Glycosylases
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium acetate trihydrate pH 4.0, 1,6M ammonium sulphate, 21mM ZnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 2.8→46.3 Å / Num. obs: 12543 / % possible obs: 98.93 % / Redundancy: 4 % / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.079 / Rrim(I) all: 0.133 / Net I/σ(I): 14.26
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.362 / Rpim(I) all: 0.27 / Rrim(I) all: 0.454

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 2.8→46.34 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.892 / SU B: 15.507 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24013 623 5 %RANDOM
Rwork0.18873 ---
obs0.19129 11876 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.111 Å2
Baniso -1Baniso -2Baniso -3
1--1.6 Å20 Å20 Å2
2--2.02 Å20 Å2
3----0.41 Å2
Refinement stepCycle: 1 / Resolution: 2.8→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3674 0 172 46 3892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133964
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183387
X-RAY DIFFRACTIONr_angle_refined_deg1.7971.7225441
X-RAY DIFFRACTIONr_angle_other_deg1.431.6377910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2845481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33223.898177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.09715529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.5931512
X-RAY DIFFRACTIONr_chiral_restr0.080.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024409
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02819
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8412.8031933
X-RAY DIFFRACTIONr_mcbond_other1.8412.8021932
X-RAY DIFFRACTIONr_mcangle_it3.1284.1942411
X-RAY DIFFRACTIONr_mcangle_other3.1274.1952412
X-RAY DIFFRACTIONr_scbond_it2.2883.1392031
X-RAY DIFFRACTIONr_scbond_other2.2883.1422032
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6824.6253031
X-RAY DIFFRACTIONr_long_range_B_refined7.06654.08416791
X-RAY DIFFRACTIONr_long_range_B_other7.06554.09516785
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 7179 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 49 -
Rwork0.261 840 -
obs--99.22 %

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