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- PDB-4k3a: The structure of a glycoside hydrolase family 81 endo-[beta]-1,3-... -

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Basic information

Entry
Database: PDB / ID: 4k3a
TitleThe structure of a glycoside hydrolase family 81 endo-[beta]-1,3-glucanase
Componentsglycoside hydrolase family 81 endo-beta-1,3-glucanase
KeywordsHYDROLASE / glucoside hydrolases family 81 / endo-beta-1 / 3-glucanase / Rhzmucor miehei / (alpha/alpha)6-barrel / supersandwich / beta-1 / extracellular
Function / homology
Function and homology information


: / endo-1,3(4)-beta-glucanase activity / glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / polysaccharide catabolic process / cell wall organization / extracellular region
Similarity search - Function
glycoside hydrolase family 81 endo-[beta] glucanase / Glycosyl hydrolase family 81, N-terminal / Glycosyl hydrolase family 81 N-terminal domain / Glycosyl hydrolases family 81 (GH81) domain profile. / Endo-1,3(4)-beta-glucanase / Glycosyl hydrolase family 81, C-terminal domain / Glycosyl hydrolase family 81 C-terminal domain / Golgi alpha-mannosidase II; domain 4 / Immunoglobulin FC, subunit C / Beta-galactosidase; Chain A, domain 5 ...glycoside hydrolase family 81 endo-[beta] glucanase / Glycosyl hydrolase family 81, N-terminal / Glycosyl hydrolase family 81 N-terminal domain / Glycosyl hydrolases family 81 (GH81) domain profile. / Endo-1,3(4)-beta-glucanase / Glycosyl hydrolase family 81, C-terminal domain / Glycosyl hydrolase family 81 C-terminal domain / Golgi alpha-mannosidase II; domain 4 / Immunoglobulin FC, subunit C / Beta-galactosidase; Chain A, domain 5 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Distorted Sandwich / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Glucan endo-1,3-beta-D-glucosidase 1
Similarity search - Component
Biological speciesRhizomucor miehei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJiang, Z.Q. / Zhou, P. / Chen, Z.Z. / Yan, Q.J. / Yang, S.Q. / Hilgenfeld, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The structure of a glycoside hydrolase family 81 endo-[beta]-1,3-glucanase
Authors: Zhou, P. / Chen, Z.Z. / Yan, Q.J. / Yang, S.Q. / Hilgenfeld, R. / Jiang, Z.Q.
History
DepositionApr 10, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glycoside hydrolase family 81 endo-beta-1,3-glucanase
B: glycoside hydrolase family 81 endo-beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,0604
Polymers173,8682
Non-polymers1922
Water12,556697
1
A: glycoside hydrolase family 81 endo-beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0302
Polymers86,9341
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: glycoside hydrolase family 81 endo-beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0302
Polymers86,9341
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.875, 91.758, 92.819
Angle α, β, γ (deg.)90.00, 98.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein glycoside hydrolase family 81 endo-beta-1,3-glucanase


Mass: 86933.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizomucor miehei (fungus) / Strain: Rhizomucor miehei CAU432 / Gene: RmLam81A / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: U5HK45*PLUS, glucan endo-1,3-beta-D-glucosidase
#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.: 697 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.06 Å3/Da / Density % sol: 40.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG4000, Tris, MPD, lithium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9794 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 64600 / Num. obs: 61059 / % possible obs: 95.3 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4K35

4k35


Resolution: 2.3→31.399 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 21.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1988 2928 4.9 %
Rwork0.1499 --
obs0.1523 59793 95.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→31.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11366 0 10 697 12073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911711
X-RAY DIFFRACTIONf_angle_d1.19515997
X-RAY DIFFRACTIONf_dihedral_angle_d13.184229
X-RAY DIFFRACTIONf_chiral_restr0.0491741
X-RAY DIFFRACTIONf_plane_restr0.0062077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33770.22821100.18562408X-RAY DIFFRACTION85
2.3377-2.3780.25841360.17732470X-RAY DIFFRACTION88
2.378-2.42120.24111250.18292570X-RAY DIFFRACTION90
2.4212-2.46780.22061390.18052591X-RAY DIFFRACTION92
2.4678-2.51810.25211250.1872566X-RAY DIFFRACTION92
2.5181-2.57290.26271350.17852670X-RAY DIFFRACTION93
2.5729-2.63270.27041520.18152611X-RAY DIFFRACTION94
2.6327-2.69850.23181390.17522672X-RAY DIFFRACTION95
2.6985-2.77140.25841450.17712751X-RAY DIFFRACTION97
2.7714-2.85290.21351520.16812745X-RAY DIFFRACTION98
2.8529-2.94490.22681430.16282758X-RAY DIFFRACTION98
2.9449-3.05010.21691470.16222814X-RAY DIFFRACTION99
3.0501-3.17210.20091370.16172782X-RAY DIFFRACTION98
3.1721-3.31630.20811520.1562797X-RAY DIFFRACTION99
3.3163-3.49090.19081470.15252777X-RAY DIFFRACTION99
3.4909-3.70930.18181400.13842804X-RAY DIFFRACTION98
3.7093-3.99520.18131420.12732784X-RAY DIFFRACTION98
3.9952-4.39630.1621390.11312802X-RAY DIFFRACTION98
4.3963-5.03020.14221370.11222810X-RAY DIFFRACTION98
5.0302-6.3290.17151320.14012825X-RAY DIFFRACTION98
6.329-31.40170.15731540.14222858X-RAY DIFFRACTION98

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