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- PDB-7wwc: Crystal structure of beta-1,3(4)-glucanase with Laminaritriose -

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Basic information

Entry
Database: PDB / ID: 7wwc
TitleCrystal structure of beta-1,3(4)-glucanase with Laminaritriose
Componentsbeta-1,3(4)-glucanase
KeywordsHYDROLASE / beta-1 / 3(4)-glucanase / GH16 / Laminaritriose
Function / homologyPhosphatidylinositol (PI) phosphodiesterase / Jelly Rolls - #200 / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Function and homology information
Biological speciesPedobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.20216257162 Å
AuthorsJiang, Z.Q. / Ma, J.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of beta-1,3(4)-glucanase with Laminaritriose
Authors: Jiang, Z.Q. / Ma, J.W.
History
DepositionFeb 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-1,3(4)-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7083
Polymers54,8611
Non-polymers8472
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint17 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.648, 120.648, 69.966
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-702-

HOH

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Components

#1: Protein beta-1,3(4)-glucanase


Mass: 54861.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pedobacter sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris pH8.5, 1.2M Potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 90-100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Jan 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→41.867 Å / Num. obs: 29797 / % possible obs: 95 % / Redundancy: 18.9 % / Biso Wilson estimate: 29.8317359248 Å2 / Rrim(I) all: 0.153 / Net I/σ(I): 1.5
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 2786 / CC1/2: 0.915

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Processing

Software
NameVersionClassification
PHENIXdev_2474refinement
HKL-3000data collection
HKL-3000data scaling
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7MM4

7mm4


Resolution: 2.20216257162→41.8603347621 Å / SU ML: 0.284664353773 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.1882568192
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.24223560979 1925 6.73665791776 %
Rwork0.191381445398 26650 -
obs0.194771287542 28575 95.2150878011 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.0041551515 Å2
Refinement stepCycle: LAST / Resolution: 2.20216257162→41.8603347621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3819 0 57 225 4101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009425892285873996
X-RAY DIFFRACTIONf_angle_d0.9957779797185432
X-RAY DIFFRACTIONf_chiral_restr0.784081599923600
X-RAY DIFFRACTIONf_plane_restr0.00609540432843678
X-RAY DIFFRACTIONf_dihedral_angle_d19.78858323271387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2022-2.25720.3646685713361200.2604198995611615X-RAY DIFFRACTION81.4171750352
2.2572-2.31830.3276111408031240.2573051473051740X-RAY DIFFRACTION88.2158069096
2.3183-2.38650.3067755659891280.2391328907141812X-RAY DIFFRACTION92.2053231939
2.3865-2.46350.2891709516041380.2344263913751832X-RAY DIFFRACTION92.7932171455
2.4635-2.55150.3348097097421330.222988992311840X-RAY DIFFRACTION93.5071090047
2.5515-2.65370.3026495712991340.2371219242381902X-RAY DIFFRACTION95.3183520599
2.6537-2.77440.3095291276361360.2223813512131887X-RAY DIFFRACTION95.4245283019
2.7744-2.92070.3079085117751370.2106347754931976X-RAY DIFFRACTION97.8240740741
2.9207-3.10360.2191783036311410.1980524274991955X-RAY DIFFRACTION98.5425481899
3.1036-3.34310.222578154091420.1795941842541976X-RAY DIFFRACTION99.064546305
3.3431-3.67940.2132560088741470.1581310814052001X-RAY DIFFRACTION99.721448468
3.6794-4.21140.1969386105341400.1474166134972005X-RAY DIFFRACTION99.9068467629
4.2114-5.30420.1743318713291480.1486763204052033X-RAY DIFFRACTION99.9083829592
5.3042-41.860.2465546908931570.2191378880612076X-RAY DIFFRACTION98.6743261158

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