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- PDB-5d6t: Crystal Structure of Aspergillus clavatus Sph3 in complex with GalNAc -

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Basic information

Entry
Database: PDB / ID: 5d6t
TitleCrystal Structure of Aspergillus clavatus Sph3 in complex with GalNAc
ComponentsSPHERULIN-4
KeywordsHYDROLASE / spherulin / (beta/alpha) barrel / glycoside hydrolase / GalNAc complex
Function / homologySpherulation-specific family 4 / Spherulation-specific family 4 / 2-acetamido-2-deoxy-beta-D-galactopyranose / Cell surface spherulin 4-like protein
Function and homology information
Biological speciesAspergillus clavatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å
AuthorsBamford, N.C. / Little, D.J. / Howell, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)81361 Canada
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Sph3 Is a Glycoside Hydrolase Required for the Biosynthesis of Galactosaminogalactan in Aspergillus fumigatus.
Authors: Bamford, N.C. / Snarr, B.D. / Gravelat, F.N. / Little, D.J. / Lee, M.J. / Zacharias, C.A. / Chabot, J.C. / Geller, A.M. / Baptista, S.D. / Baker, P. / Robinson, H. / Howell, P.L. / Sheppard, D.C.
History
DepositionAug 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPHERULIN-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4134
Polymers30,0601
Non-polymers3533
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.740, 58.880, 96.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SPHERULIN-4


Mass: 30060.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1) (mold)
Strain: ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1
Gene: ACLA_035820 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A1CJQ5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.0 M ammonium sulfate, 0.1 M HEPES:NaOH pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97859 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97859 Å / Relative weight: 1
ReflectionResolution: 1.93→37.39 Å / Num. obs: 19185 / % possible obs: 96.55 % / Redundancy: 5 % / Rmerge(I) obs: 0.06221 / Net I/σ(I): 21.36
Reflection shellResolution: 1.93→1.99 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.4024 / % possible all: 98.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXdev_1760refinement
XSCALEdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C5G

5c5g


Resolution: 1.93→37.387 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.217 960 5 %Random selection
Rwork0.1695 ---
obs0.1719 19185 96.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→37.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 21 203 2197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072047
X-RAY DIFFRACTIONf_angle_d1.0022803
X-RAY DIFFRACTIONf_dihedral_angle_d12.56731
X-RAY DIFFRACTIONf_chiral_restr0.042311
X-RAY DIFFRACTIONf_plane_restr0.006368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-2.03180.25791370.22012607X-RAY DIFFRACTION98
2.0318-2.1590.23451360.19532580X-RAY DIFFRACTION98
2.159-2.32570.26311370.18772598X-RAY DIFFRACTION98
2.3257-2.55970.24631360.18612585X-RAY DIFFRACTION97
2.5597-2.930.24881370.18732598X-RAY DIFFRACTION97
2.93-3.6910.23251370.16452611X-RAY DIFFRACTION96
3.691-37.3940.15531400.13432646X-RAY DIFFRACTION93
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)
12.91770.51790.64682.1976-0.52373.62710.02760.1426-0.26920.1962-0.10450.1340.08350.17360.03430.12390.01380.01840.1086-0.00690.1887-8.8839-0.8217-11.7197
21.46720.92650.40954.07650.50390.67760.1493-0.0312-0.23660.4383-0.0528-0.14590.11970.042-0.11290.22960.0073-0.01550.23160.00810.1644-1.15353.2791-6.4148
34.573-2.31622.85113.2341-2.03793.2512-0.00190.0320.13950.2543-0.0137-0.0529-0.18370.06370.0310.1907-0.02290.04380.1901-0.01760.1387-1.636418.3454-10.689
44.4611-1.49222.54292.0738-1.47522.40410.0170.39470.1986-0.01-0.1656-0.1374-0.14210.33040.14730.1724-0.01420.01170.1889-0.00160.1489-2.867618.2496-19.5863
51.99711.8615-0.42174.0799-1.48841.73690.00690.19790.2290.10480.0770.328-0.1042-0.1152-0.01010.13810.0094-0.00770.1907-0.03850.1494-17.113110.94-21.0221
61.92181.8336-0.16344.0053-1.83022.1728-0.12190.34270.0896-0.30940.06740.06460.1013-0.1032-0.00060.18510.02710.00450.1887-0.01790.1744-17.78177.5615-25.7346
72.32231.7102-0.2654.122-1.37141.65950.02340.1421-0.3107-0.00270.0377-0.02780.242-0.1781-0.0250.1587-0.0324-0.00290.168-0.06410.1932-21.8199-6.1563-18.0046
82.1552-0.6308-0.09643.4858-0.01544.9770.0134-0.1013-0.25020.1723-0.0560.13380.14180.03340.04270.1269-0.0403-0.01460.1609-0.02820.1795-15.2059-1.9727-12.4597
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 73 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 128 )
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 173 )
4X-RAY DIFFRACTION4chain 'A' and (resid 174 through 208 )
5X-RAY DIFFRACTION5chain 'A' and (resid 209 through 230 )
6X-RAY DIFFRACTION6chain 'A' and (resid 231 through 253 )
7X-RAY DIFFRACTION7chain 'A' and (resid 254 through 272 )
8X-RAY DIFFRACTION8chain 'A' and (resid 273 through 304 )

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