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- PDB-4wtp: Crystal structure of glycoside hydrolase family 17 beta-1,3-gluca... -

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Basic information

Entry
Database: PDB / ID: 4wtp
TitleCrystal structure of glycoside hydrolase family 17 beta-1,3-glucanosyltransferase from Rhizomucor miehei
Componentsbeta-1,3-glucanosyltransferase
KeywordsTRANSFERASE / beta-1 / 3-glucanosyltransferase / glycoside hydrolases family 17 / Rhizomucor miehei / Transglycosylation
Function / homology
Function and homology information


glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / fungal-type cell wall / cell wall organization / carbohydrate metabolic process / cell surface / extracellular region
Similarity search - Function
: / Glycoside hydrolase family 17 / Glycosyl hydrolases family 17 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
glucan endo-1,3-beta-D-glucosidase
Similarity search - Component
Biological speciesRhizomucor miehei CAU432 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsQin, Z. / Yan, Q. / Lei, J. / Yang, S. / Jiang, Z.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: The first crystal structure of a glycoside hydrolase family 17 beta-1,3-glucanosyltransferase displays a unique catalytic cleft.
Authors: Qin, Z. / Yan, Q. / Lei, J. / Yang, S. / Jiang, Z. / Wu, S.
History
DepositionOct 30, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: beta-1,3-glucanosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8643
Polymers32,7401
Non-polymers1242
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint5 kcal/mol
Surface area11000 Å2
Unit cell
Length a, b, c (Å)45.887, 50.366, 98.405
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 beta-1,3-glucanosyltransferase


Mass: 32739.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizomucor miehei CAU432 (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0M3KKZ6*PLUS, Transferases; Glycosyltransferases; Hexosyltransferases
#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
Has protein modificationY
Sequence detailsSequence has been submitted to GenBank under accession number KP121406. N-terminal 34 residues are ...Sequence has been submitted to GenBank under accession number KP121406. N-terminal 34 residues are expression tags.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.74 Å3/Da / Density % sol: 29.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 25% (w/v) PEG 8000, 0.2M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.299→27.927 Å / Num. obs: 52655 / % possible obs: 92.39 % / Redundancy: 8.5 % / Net I/σ(I): 71.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.3→27.49 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.587 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1864 2640 5 %RANDOM
Rwork0.17806 ---
obs0.17849 50015 92.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.379 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.3→27.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 8 227 2285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022213
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9563028
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7415290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17925.25399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01415356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.96158
X-RAY DIFFRACTIONr_chiral_restr0.0910.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211731
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.52332213
X-RAY DIFFRACTIONr_sphericity_free18.402531
X-RAY DIFFRACTIONr_sphericity_bonded9.85152352
LS refinement shellResolution: 1.299→1.333 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 124 -
Rwork0.295 2450 -
obs--63.48 %

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