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- PDB-9vp9: GH64 family beta-1,3-glucanase from Massilia violaceinigra in com... -

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Basic information

Entry
Database: PDB / ID: 9vp9
TitleGH64 family beta-1,3-glucanase from Massilia violaceinigra in complex with a glucose disaccharide
ComponentsGH64 domain-containing protein
KeywordsHYDROLASE / beta-1 / 3-glucanase
Function / homology
Function and homology information


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. / Osmotin/thaumatin-like superfamily
Similarity search - Domain/homology
beta-laminaribiose / ACETATE ION / TRIETHYLENE GLYCOL / GH64 domain-containing protein
Similarity search - Component
Biological speciesMassilia violaceinigra (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsZhang, X.J. / Li, T. / Yin, H.
Funding support1items
OrganizationGrant numberCountry
Other government2023YFC2812200
CitationJournal: To Be Published
Title: GH64 family beta-1,3-glucanase from Massilia violaceinigra
Authors: Zhang, X.J. / Li, T. / Yin, H.
History
DepositionJul 2, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GH64 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,65121
Polymers42,2831
Non-polymers1,36920
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.670, 126.670, 71.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein GH64 domain-containing protein


Mass: 42282.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Massilia violaceinigra (bacteria) / Gene: CR152_26670 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2D2DVX9
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-laminaribiose
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

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Non-polymers , 8 types, 274 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.9 Å3/Da / Density % sol: 68.42 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7 / Details: 2.8M NaAc / PH range: 6.9-7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979145 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 27, 2024
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979145 Å / Relative weight: 1
ReflectionResolution: 1.99→41.46 Å / Num. obs: 44713 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.996 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.081 / Rrim(I) all: 0.359 / Net I/σ(I): 20.1
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 15 % / Rmerge(I) obs: 1.788 / Num. unique obs: 3303 / CC1/2: 0.736 / Rpim(I) all: 0.401 / Rrim(I) all: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia23.6.1data scaling
MOLREP11.9.02phasing
PDB_EXTRACTv1.0data extraction
Coot0.9.8.93model building
autoPROC1.0.5data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→41.46 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.095 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20499 2330 5.2 %RANDOM
Rwork0.17213 ---
obs0.17383 42356 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.094 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å2-0 Å2
2---0.26 Å20 Å2
3---0.83 Å2
Refinement stepCycle: 1 / Resolution: 1.99→41.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2910 0 84 255 3249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123108
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162790
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.7814240
X-RAY DIFFRACTIONr_angle_other_deg0.5941.7296413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0355390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.88511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51110433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023732
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02770
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_it2.6962.7191518
X-RAY DIFFRACTIONr_mcbond_other2.6672.7151515
X-RAY DIFFRACTIONr_mcangle_it3.6864.8641896
X-RAY DIFFRACTIONr_mcangle_other3.6864.8631897
X-RAY DIFFRACTIONr_scbond_it3.7933.0541590
X-RAY DIFFRACTIONr_scbond_other3.7933.0561591
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5935.4272337
X-RAY DIFFRACTIONr_long_range_B_refined7.12528.53527
X-RAY DIFFRACTIONr_long_range_B_other7.03328.323458
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.99→2.042 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 186 -
Rwork0.263 3108 -
obs--100 %

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