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- PDB-3gd9: Crystal structure of laminaripentaose-producing beta-1,3-glucanas... -

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Basic information

Entry
Database: PDB / ID: 3gd9
TitleCrystal structure of laminaripentaose-producing beta-1,3-glucanase in complex with laminaritetraose
ComponentsLaminaripentaose-producing beta-1,3-guluase (LPHase)
KeywordsHYDROLASE / Glycoside hydrolases / Laminaripentaose-producing beta-1 / 3-glucnase (LPHase) / Multi-wavelength anomalous dispersion (MAD)
Function / homology
Function and homology information


Beta-1,3-glucanase, C-terminal domain / Beta-1,3-glucanase, N-terminal, subdomain 2 / Beta-1,3-glucanase, N-terminal / Glucan endo-1,3-beta-glucosidase / Beta-1,3-glucanase / Glycosyl hydrolases family 64 (GH64) domain profile. / Metal Transport, Frataxin; Chain A / Thaumatin / Thaumatin / Osmotin/thaumatin-like superfamily ...Beta-1,3-glucanase, C-terminal domain / Beta-1,3-glucanase, N-terminal, subdomain 2 / Beta-1,3-glucanase, N-terminal / Glucan endo-1,3-beta-glucosidase / Beta-1,3-glucanase / Glycosyl hydrolases family 64 (GH64) domain profile. / Metal Transport, Frataxin; Chain A / Thaumatin / Thaumatin / Osmotin/thaumatin-like superfamily / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Laminaripentaose-producing beta-1,3-guluase (LPHase)
Similarity search - Component
Biological speciesStreptomyces matensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWu, H.M. / Hsu, M.T. / Liu, S.W. / Lai, C.C. / Li, Y.K. / Wang, W.C.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure, mechanistic action, and essential residues of a GH-64 enzyme, laminaripentaose-producing beta-1,3-glucanase.
Authors: Wu, H.M. / Liu, S.W. / Hsu, M.T. / Hung, C.L. / Lai, C.C. / Cheng, W.C. / Wang, H.J. / Li, Y.K. / Wang, W.C.
History
DepositionFeb 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.label_asym_id ..._atom_site.auth_asym_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Laminaripentaose-producing beta-1,3-guluase (LPHase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2592
Polymers39,5931
Non-polymers6671
Water11,746652
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.981, 60.352, 149.118
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 Laminaripentaose-producing beta-1,3-guluase (LPHase)


Mass: 39592.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces matensis (bacteria) / Strain: DIC-108 / Gene: LPHase / Plasmid: pREST_A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9Z4I2, glucan endo-1,3-beta-D-glucosidase
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2-2/a3-b1_b3-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.61 Å3/Da / Density % sol: 52.93 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 6.5
Details: 0.05M ammonium sulfate, 20% PEG8000, 0.1M sodium cacodylate (pH6.5), 20mM laminaripentaose, LIQUID DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2006
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 39457 / Num. obs: 38270 / % possible obs: 97 % / Observed criterion σ(F): 325.5 / Observed criterion σ(I): 103.9 / Redundancy: 8.3 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.038 / Net I/σ(I): 41.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 19.5 / Num. unique all: 3462 / Rsym value: 0.104 / % possible all: 89.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GD0

3gd0


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.911 / SU B: 2.171 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1919 5 %RANDOM
Rwork0.166 ---
obs0.172 36280 97.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.709 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.61 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 45 652 3454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212883
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9633942
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8565360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.58622.636129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31115397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8451525
X-RAY DIFFRACTIONr_chiral_restr0.1040.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022257
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.21468
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.21961
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2489
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.59721824
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.47332890
X-RAY DIFFRACTIONr_scbond_it2.00421186
X-RAY DIFFRACTIONr_scangle_it2.97131052
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 121 -
Rwork0.166 2434 -
obs--88.87 %

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