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- PDB-7ww4: Crystal structure of multidomain beta-1,3(4)-glucanase -

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Basic information

Entry
Database: PDB / ID: 7ww4
TitleCrystal structure of multidomain beta-1,3(4)-glucanase
Componentsbeta-1,3(4)-glucanase
KeywordsHYDROLASE / multidomain / beta-1 / 3(4)-glucanase / GH16
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 / SAD / Resolution: 2.23006079201 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 multidomain beta-1,3(4)-glucanase
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 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,2555
Polymers54,9901
Non-polymers2644
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-11 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.940, 120.940, 70.050
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-645-

HOH

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Components

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


Mass: 54990.270 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.056M sodium phosphate monobasic monohydrate, 1.344M potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Feb 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.23→24.53 Å / Num. obs: 28796 / % possible obs: 98 % / Redundancy: 7.2 % / Biso Wilson estimate: 38.9554112006 Å2 / Rrim(I) all: 0.136 / Net I/σ(I): 17.7
Reflection shellResolution: 2.2301→2.3097 Å / Num. unique obs: 2685 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data scaling
PHENIXmodel building
PHENIXdev_2474refinement
RefinementMethod to determine structure: SAD / Resolution: 2.23006079201→24.5268135995 Å / SU ML: 0.488665500209 / Cross valid method: FREE R-VALUE / σ(F): 1.34350846829 / Phase error: 39.4748984111
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.285211551395 1466 5.12336618439 %
Rwork0.248011840949 27148 -
obs0.249873564816 28796 98.4787995595 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.1760093071 Å2
Refinement stepCycle: LAST / Resolution: 2.23006079201→24.5268135995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3737 0 14 67 3818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002099526931473851
X-RAY DIFFRACTIONf_angle_d0.4660203044515224
X-RAY DIFFRACTIONf_chiral_restr0.043499970555550
X-RAY DIFFRACTIONf_plane_restr0.0029798293295663
X-RAY DIFFRACTIONf_dihedral_angle_d2.496933619972221
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2301-2.30970.5623163010991160.5560634032642453256990.1403508772
2.3097-2.40210.4168079915321570.37638013846270599.2715920916
2.4021-2.51130.394430358151450.32789705622269899.2667597765
2.5113-2.64360.4019432392731730.334487976131270699.4816862474
2.6436-2.8090.35773462151360.332256115743272399.2363762582
2.809-3.02550.3301705932491390.282651244026275299.5523415978
3.0255-3.32930.2904128742141450.255426951349273999.3797381116
3.3293-3.80950.2768145133941550.231238662494273199.3801652893
3.8095-4.79370.2350460007611690.193563339236276099.863620866
4.7937-24.520.211088003221310.187376226717288199.209486166

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