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- PDB-6nwz: Crystal structure of Agd3 a novel carbohydrate deacetylase -

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Basic information

Entry
Database: PDB / ID: 6nwz
TitleCrystal structure of Agd3 a novel carbohydrate deacetylase
ComponentsCarbohydrate deacetylase Agd3
KeywordsHYDROLASE / carbohydrate esterase / glycosylated / galactosaminogalactan de-N-acetylase
Function / homology: / metal ion binding / alpha-D-mannopyranose / Extracellular serine-rich protein, putative
Function and homology information
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsBamford, N.C. / Howell, P.L.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)627443 Canada
Canadian Institutes of Health Research (CIHR)FDN154327 Canada
CitationJournal: Nat Commun / Year: 2020
Title: Structural and biochemical characterization of the exopolysaccharide deacetylase Agd3 required for Aspergillus fumigatus biofilm formation.
Authors: Bamford, N.C. / Le Mauff, F. / Van Loon, J.C. / Ostapska, H. / Snarr, B.D. / Zhang, Y. / Kitova, E.N. / Klassen, J.S. / Codee, J.D.C. / Sheppard, D.C. / Howell, P.L.
History
DepositionFeb 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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_struct_conn_angle / pdbx_struct_special_symmetry / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 26, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbohydrate deacetylase Agd3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,21314
Polymers74,4641
Non-polymers1,74913
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Agd3 elutes at a mass equivalent to a monomer using size exclusion chromatrography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.970, 77.970, 640.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-912-

ZN

21A-1115-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carbohydrate deacetylase Agd3


Mass: 74464.203 Da / Num. of mol.: 1
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: AFUA_3G07870 / Production host: Komagataella pastoris (fungus) / Strain (production host): PichiaPink Strain 4 / References: UniProt: Q4WX15

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Sugars , 3 types, 4 molecules

#2: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 129 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
13.8868.29half hexagonal prisms
23.8868.29From the same drop as Crystal one and same morphology
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop7.51.7 % (w/v) PEG 400, 15 % (v/v) glycerol, 1.7 M ammonium sulfate, 0.25 % (w/v) PEG3350, 85 mM HEPES pH 7.5
2932vapor diffusion, hanging drop7.51.7 % (w/v) PEG 400, 15 % (v/v) glycerol, 1.7 M ammonium sulfate, 0.25 % (w/v) PEG3350, 85 mM HEPES pH 7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21002N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS-II 17-ID-111.28308
SYNCHROTRONNSLS-II 17-ID-121.28308
Detector
TypeIDDetectorDate
DECTRIS EIGER X 16M1PIXELJul 11, 2017
DECTRIS EIGER X 16M2PIXELJul 11, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.283081
21
Reflection

Entry-ID: 6NWZ

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
2.59-29.873731486.1320.9990.024670.024670.03489117.91
2.7-29.212201599.6116.9229.24
Reflection shellResolution: 2.59→2.694 Å / Rmerge(I) obs: 0.364 / Num. unique obs: 487 / CC1/2: 0.968 / Rpim(I) all: 0.257 / Rrim(I) all: 0.364 / % possible all: 13.57

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimless0.5.21data scaling
SHELXphasing
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.6→29.865 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2423 1690 5.25 %Random
Rwork0.1895 30501 --
obs0.1923 32191 86.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.14 Å2 / Biso mean: 47.4631 Å2 / Biso min: 18.17 Å2
Refinement stepCycle: final / Resolution: 2.6→29.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5095 0 90 120 5305
Biso mean--91.71 41.07 -
Num. residues----665
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5999-2.67640.3497180.232532033811
2.6764-2.76270.3055540.2609999105335
2.7627-2.86140.32361390.26692345248482
2.8614-2.97580.32881660.271928593025100
2.9758-3.11110.32361530.24829073060100
3.1111-3.2750.27911560.223929083064100
3.275-3.47990.2691420.206929073049100
3.4799-3.74810.24481810.172229303111100
3.7481-4.12440.20541520.158729783130100
4.1244-4.71920.17631710.140529573128100
4.7192-5.9380.22641740.163730813255100
5.938-29.86670.22251840.190533103494100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.19440.2980.41982.14810.86943.28590.1745-0.17090.23540.2101-0.1933-0.0345-0.374-0.2093-0.01560.2932-0.05880.07090.254-0.01460.268865.274421.82916.5637
21.00160.12170.41650.66270.05252.31490.04470.28070.2303-0.3518-0.0574-0.02-0.4395-0.21130.00510.42640.15340.060.34690.06770.289458.646119.2011-30.2665
30.803-0.16470.42920.9360.50732.98110.12940.0110.2616-0.1471-0.15410.0595-0.4295-0.4885-0.01870.26240.11120.01880.31580.00520.327957.283119.5069-9.1126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 142 through 358 )A142 - 358
2X-RAY DIFFRACTION2chain 'A' and (resid 360 through 562 )A360 - 562
3X-RAY DIFFRACTION3chain 'A' and (resid 563 through 806 )A563 - 806

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