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- PDB-4x0v: Structure of a GH5 family lichenase from Caldicellulosiruptor sp. F32 -

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Basic information

Entry
Database: PDB / ID: 4x0v
TitleStructure of a GH5 family lichenase from Caldicellulosiruptor sp. F32
ComponentsBeta-1,3-1,4-glucanaseEndo-1,3(4)-b-glucanase
KeywordsHYDROLASE / GLYCOSIDASE / LICHENASE
Function / homology
Function and homology information


organic substance metabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Beta-1,3-1,4-glucanase
Similarity search - Component
Biological speciesCaldicellulosiruptor sp. F32 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.798 Å
AuthorsMeng, D. / Liu, X. / Wang, X. / Li, F. / Feng, Y.
CitationJournal: Biochem. J. / Year: 2017
Title: Structural Insights into the Substrate Specificity of a Glycoside Hydrolase Family 5 Lichenase from Caldicellulosiruptor sp. F32
Authors: Meng, D.D. / Liu, X. / Dong, S. / Wang, Y.F. / Ma, X.Q. / Zhou, H. / Wang, X. / Yao, L.S. / Feng, Y. / Li, F.L.
History
DepositionNov 24, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-1,3-1,4-glucanase
B: Beta-1,3-1,4-glucanase
C: Beta-1,3-1,4-glucanase
D: Beta-1,3-1,4-glucanase
E: Beta-1,3-1,4-glucanase
F: Beta-1,3-1,4-glucanase
G: Beta-1,3-1,4-glucanase
H: Beta-1,3-1,4-glucanase


Theoretical massNumber of molelcules
Total (without water)367,0648
Polymers367,0648
Non-polymers00
Water4,197233
1
A: Beta-1,3-1,4-glucanase


Theoretical massNumber of molelcules
Total (without water)45,8831
Polymers45,8831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-1,3-1,4-glucanase


Theoretical massNumber of molelcules
Total (without water)45,8831
Polymers45,8831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-1,3-1,4-glucanase


Theoretical massNumber of molelcules
Total (without water)45,8831
Polymers45,8831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-1,3-1,4-glucanase


Theoretical massNumber of molelcules
Total (without water)45,8831
Polymers45,8831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Beta-1,3-1,4-glucanase


Theoretical massNumber of molelcules
Total (without water)45,8831
Polymers45,8831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Beta-1,3-1,4-glucanase


Theoretical massNumber of molelcules
Total (without water)45,8831
Polymers45,8831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Beta-1,3-1,4-glucanase


Theoretical massNumber of molelcules
Total (without water)45,8831
Polymers45,8831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Beta-1,3-1,4-glucanase


Theoretical massNumber of molelcules
Total (without water)45,8831
Polymers45,8831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.659, 157.780, 120.803
Angle α, β, γ (deg.)90.00, 109.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-1,3-1,4-glucanase / Endo-1,3(4)-b-glucanase / lichenase F32EG5


Mass: 45883.039 Da / Num. of mol.: 8 / Fragment: UNP residues 24-401
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor sp. F32 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: R9RX81, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Li citrate tribasic, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: RIGAKU / Detector: CCD / Date: Oct 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.798→50 Å / Num. obs: 78399 / % possible obs: 99.8 % / Redundancy: 3.7 % / Net I/σ(I): 11.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EDG

1edg


Resolution: 2.798→46.65 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2379 1842 2.35 %
Rwork0.183 --
obs0.1843 78399 92.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.798→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24476 0 0 233 24709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00925132
X-RAY DIFFRACTIONf_angle_d1.23134067
X-RAY DIFFRACTIONf_dihedral_angle_d14.089205
X-RAY DIFFRACTIONf_chiral_restr0.0673563
X-RAY DIFFRACTIONf_plane_restr0.0064372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7979-2.87350.35531190.2594927X-RAY DIFFRACTION78
2.8735-2.95810.28641280.25415394X-RAY DIFFRACTION85
2.9581-3.05350.35351360.25255441X-RAY DIFFRACTION86
3.0535-3.16260.35421300.25115598X-RAY DIFFRACTION88
3.1626-3.28920.30951320.24355746X-RAY DIFFRACTION90
3.2892-3.43890.30661480.22855912X-RAY DIFFRACTION92
3.4389-3.62010.28381480.20286056X-RAY DIFFRACTION95
3.6201-3.84680.24411440.18156128X-RAY DIFFRACTION96
3.8468-4.14370.2311430.16266174X-RAY DIFFRACTION97
4.1437-4.56040.1831590.14756168X-RAY DIFFRACTION97
4.5604-5.21950.17231520.13946219X-RAY DIFFRACTION97
5.2195-6.57310.19931500.16146339X-RAY DIFFRACTION99
6.5731-46.65670.18691530.14926455X-RAY DIFFRACTION99

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