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- PDB-4k35: The structure of a glycoside hydrolase family 81 endo-[beta]-1,3-... -

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Entry
Database: PDB / ID: 4k35
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 / supersandwich / beta-1 / extracellular
Function / homology
Function and homology information


glucan endo-1,4-beta-glucanase activity, C-3 substituted reducing group / glucan endo-1,3-beta-glucanase activity, C-3 substituted reducing group / 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 / SAD / Resolution: 2.003 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

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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)175,6947
Polymers175,0872
Non-polymers6075
Water24,5361362
1
A: glycoside hydrolase family 81 endo-beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7883
Polymers87,5441
Non-polymers2442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: glycoside hydrolase family 81 endo-beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9064
Polymers87,5441
Non-polymers3623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-7 kcal/mol
Surface area49420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.042, 118.802, 139.422
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 glycoside hydrolase family 81 endo-beta-1,3-glucanase


Mass: 87543.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizomucor miehei (fungus) / Strain: CAU432 / Gene: Rhizomucor miehei / 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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1362 / 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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG4000, Tris, MPD, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 106500 / Num. obs: 106346 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2→2.03 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 9.75 / % possible all: 98.3

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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: SAD / Resolution: 2.003→44.122 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 17.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1768 2000 1.88 %
Rwork0.1429 --
obs0.1436 106200 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.003→44.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11405 0 40 1362 12807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811916
X-RAY DIFFRACTIONf_angle_d1.10616304
X-RAY DIFFRACTIONf_dihedral_angle_d13.5954371
X-RAY DIFFRACTIONf_chiral_restr0.0461766
X-RAY DIFFRACTIONf_plane_restr0.0052122
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.003-2.05290.22571370.16347120X-RAY DIFFRACTION96
2.0529-2.10840.19691420.15637366X-RAY DIFFRACTION100
2.1084-2.17040.22041400.14897372X-RAY DIFFRACTION100
2.1704-2.24050.19491430.14377403X-RAY DIFFRACTION100
2.2405-2.32050.17971420.14197396X-RAY DIFFRACTION100
2.3205-2.41340.19131420.14297399X-RAY DIFFRACTION100
2.4134-2.52330.2111420.14367410X-RAY DIFFRACTION100
2.5233-2.65630.18011420.14367423X-RAY DIFFRACTION100
2.6563-2.82270.18191430.14257439X-RAY DIFFRACTION100
2.8227-3.04060.17871430.14527472X-RAY DIFFRACTION100
3.0406-3.34650.17481440.14157481X-RAY DIFFRACTION100
3.3465-3.83050.1631450.13617536X-RAY DIFFRACTION100
3.8305-4.8250.13331460.12667575X-RAY DIFFRACTION100
4.825-44.13280.16981490.15487808X-RAY DIFFRACTION100

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