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- PDB-5c5g: Crystal Structure of Aspergillus clavatus Sph3 -

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Basic information

Entry
Database: PDB / ID: 5c5g
TitleCrystal Structure of Aspergillus clavatus Sph3
Componentsspherulin-4
KeywordsHYDROLASE / spherulin / (beta/alpha) barrel / glycoside hydrolase
Function / homologySpherulation-specific family 4 / Spherulation-specific family 4 / Cell surface spherulin 4-like protein
Function and homology information
Biological speciesAspergillus clavatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.248 Å
AuthorsBamford, N.C. / Little, D.J. / Howell, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)43998 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
DepositionJun 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: spherulin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3793
Polymers28,2551
Non-polymers1242
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.748, 60.205, 98.595
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 spherulin-4 / cell surface Spherulin-4 like protein / SPH3


Mass: 28254.932 Da / Num. of mol.: 1 / Fragment: spherulin-4 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus clavatus (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(DE3) / References: UniProt: A1CJQ5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.09 M HEPES:NaOH pH 7.5, 1.26 M sodium citrate, and 10% (v/v) glycerol

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A10.9792
SYNCHROTRONNSLS X29A21.075
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDAug 30, 2014
ADSC QUANTUM 315r2CCDAug 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
21.0751
ReflectionResolution: 1.248→50 Å / Num. obs: 141016 / % possible obs: 99.1 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 52.5
Reflection shellResolution: 1.248→1.29 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 5.2 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.248→40.748 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1663 10419 7.39 %
Rwork0.1481 130597 -
obs0.1495 141016 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.04 Å2 / Biso mean: 17.2382 Å2 / Biso min: 7.22 Å2
Refinement stepCycle: final / Resolution: 1.248→40.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 20 227 2228
Biso mean--22.82 26.75 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082042
X-RAY DIFFRACTIONf_angle_d1.2172790
X-RAY DIFFRACTIONf_chiral_restr0.069307
X-RAY DIFFRACTIONf_plane_restr0.007368
X-RAY DIFFRACTIONf_dihedral_angle_d11.165729
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2476-1.26170.25953120.25793892420489
1.2617-1.27660.28733440.24664267461196
1.2766-1.29210.25683440.23824333467798
1.2921-1.30850.25063370.23524227456497
1.3085-1.32570.2513480.21594294464298
1.3257-1.34390.22243450.21354365471097
1.3439-1.36310.24453500.20464331468197
1.3631-1.38340.19293450.18754300464598
1.3834-1.4050.17713440.18134347469197
1.405-1.42810.19763500.18344351470199
1.4281-1.45270.19173400.16334283462398
1.4527-1.47910.16253590.15684378473799
1.4791-1.50760.16733460.15434354470098
1.5076-1.53840.1723500.14474383473398
1.5384-1.57180.16683480.14264359470799
1.5718-1.60840.15483520.14094365471799
1.6084-1.64860.15833530.13394377473099
1.6486-1.69320.16673460.13624389473599
1.6932-1.7430.15373520.14074410476299
1.743-1.79920.14993410.13754400474199
1.7992-1.86360.15533520.143344294781100
1.8636-1.93820.1413510.133144084759100
1.9382-2.02640.15413430.131744214764100
2.0264-2.13320.13673510.131844304781100
2.1332-2.26680.16093520.130544024754100
2.2668-2.44180.14823520.131643954747100
2.4418-2.68750.1643520.141144424794100
2.6875-3.07630.16093450.149544174762100
3.0763-3.87540.16663610.141644294790100
3.8754-40.76940.163540.140544194773100
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)
11.17-0.55961.30931.4351-2.24816.61910.03140.0059-0.1486-0.1788-0.1369-0.04840.32010.02140.02780.1107-0.00220.02690.0931-0.01160.135531.366229.321262.8118
22.25450.778-0.42613.9095-0.69545.17240.0340.0069-0.2238-0.07390.00430.11650.4827-0.1592-0.02150.0985-0.0124-0.02320.08960.00730.113626.02726.433961.0555
31.49970.22110.70592.6498-0.28011.7470.02410.0682-0.036-0.252-0.00210.01780.01080.0098-0.02960.08890.00890.0080.0954-0.00010.071823.789241.499854.9569
43.58441.18412.39751.7660.44412.8387-0.0351-0.03470.0521-0.09960.01850.0478-0.0816-0.12590.01480.07880.01460.01730.08250.00850.063922.505448.053859.9413
53.90424.13372.90874.82712.69713.3029-0.1324-0.22220.44030.1028-0.02320.1999-0.1433-0.07370.17280.1250.0203-0.00790.1057-0.0260.158424.70254.986969.9252
64.02230.45331.30450.96650.08031.23430.0766-0.01280.00310.0312-0.0386-0.002-0.0082-0.0938-0.03080.0918-0.00010.00060.10320.01040.089426.139944.950667.9805
71.2826-0.5789-0.05591.2689-0.0641.38770.054-0.06110.1293-0.0063-0.0832-0.1412-0.02690.08840.02390.0744-0.0185-0.00870.09910.01550.106939.560142.091270.5325
81.3881-0.6761-0.64571.31881.40242.93890.0149-0.09530.06780.0511-0.0036-0.1221-0.03560.1417-0.00290.1083-0.01630.00190.08890.02210.115940.181438.907775.2984
92.508-1.2614-0.24783.7960.07991.57630.08030.0524-0.0684-0.0448-0.0827-0.12060.18340.13120.05350.07450.0241-0.00450.08290.02220.0943.967124.760368.0895
101.0987-0.0558-0.26861.9302-0.21953.41540.02640.0355-0.0472-0.1205-0.0753-0.04010.22290.1160.060.07920.0236-0.00060.0850.01510.08937.38628.892162.5383
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 73 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 92 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 135 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 136 through 173 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 174 through 189 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 190 through 208 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 209 through 230 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 231 through 253 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 254 through 272 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 273 through 304 )A0

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