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- PDB-3gd0: Crystal structure of laminaripentaose-producing beta-1,3-glucanase -

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Basic information

Entry
Database: PDB / ID: 3gd0
TitleCrystal structure of laminaripentaose-producing beta-1,3-glucanase
ComponentsLaminaripentaose-producing beta-1,3-guluase (LPHase)
KeywordsHYDROLASE / Glycoside hydrolase / Laminaripentaose-producing beta-1 / 3-glucnase / Multi-wavelength anomalous dispersion (MAD) method
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 / MAD / Resolution: 1.62 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 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Laminaripentaose-producing beta-1,3-guluase (LPHase)


Theoretical massNumber of molelcules
Total (without water)39,5931
Polymers39,5931
Non-polymers00
Water13,151730
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.164, 60.683, 149.395
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 730 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6453.45
2
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 6.5
Details: 0.15M ammonium sulfate, 30% PEG MME5000, 0.1M MES (pH6.5), LIQUID DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
2772
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL13C110.9762
SYNCHROTRONSPring-8 BL12B220.9794, 0.9796, 0.9642
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJun 8, 2006
ADSC QUANTUM 42CCDJun 8, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Horizontally Focusing Single Crystal MonochromatorSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97621
20.97941
30.97961
40.96421
ReflectionResolution: 1.62→29.7 Å / Num. all: 54287 / Num. obs: 54285 / % possible obs: 100 % / Observed criterion σ(F): 28.5 / Observed criterion σ(I): 16.8 / Redundancy: 14 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.047 / Net I/σ(I): 43.9
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 8.4 / Num. unique all: 5354 / Rsym value: 0.3 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.4.0077refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.62→29.7 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 1.477 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21768 2760 5.1 %RANDOM
Rwork0.1794 ---
obs0.18135 51526 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.074 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.51 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.62→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 0 730 3487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212835
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9443871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0635360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.64722.636129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94315397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6861525
X-RAY DIFFRACTIONr_chiral_restr0.0880.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0222253
X-RAY DIFFRACTIONr_mcbond_it1.07921795
X-RAY DIFFRACTIONr_mcangle_it1.86432890
X-RAY DIFFRACTIONr_scbond_it1.51621040
X-RAY DIFFRACTIONr_scangle_it2.3083981
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 227 -
Rwork0.219 3714 -
obs--99.82 %

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