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- PDB-9vpa: GH64 family beta-1,3-glucanase from Massilia violaceinigra -

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Basic information

Entry
Database: PDB / ID: 9vpa
TitleGH64 family beta-1,3-glucanase from Massilia violaceinigra
ComponentsGH64 domain-containing protein
KeywordsHYDROLASE / beta-1 / 3-glucanase
Function / homologyBeta-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 / ACETATE ION / DI(HYDROXYETHYL)ETHER / GH64 domain-containing protein
Function and homology information
Biological speciesMassilia violaceinigra (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 3, 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)42,5305
Polymers42,2831
Non-polymers2474
Water3,585199
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)126.260, 126.260, 71.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 68.44 %
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: Dec 21, 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: 2.3→50 Å / Num. obs: 55571 / % possible obs: 98 % / Redundancy: 10.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.048 / Rrim(I) all: 0.157 / Net I/σ(I): 17 / Num. measured all: 569708
Reflection shellResolution: 2.3→2.42 Å / % possible obs: 98.9 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.701 / Num. measured all: 86359 / Num. unique obs: 8198 / CC1/2: 0.942 / Rpim(I) all: 0.223 / Rrim(I) all: 0.736 / Net I/σ(I) obs: 7.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
SCALA8.0.019data scaling
iMOSFLM7.4.0data reduction
MOLREP11.9.02phasing
PDB_EXTRACTv1.0data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.36 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.805 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17962 1425 5 %RANDOM
Rwork0.1637 ---
obs0.16451 27053 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.583 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0.15 Å2-0 Å2
2---0.3 Å20 Å2
3---0.99 Å2
Refinement stepCycle: 1 / Resolution: 2.3→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2910 0 16 199 3125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0123017
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162700
X-RAY DIFFRACTIONr_angle_refined_deg2.091.7774117
X-RAY DIFFRACTIONr_angle_other_deg0.7481.7336187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4275376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.448511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43810422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1130.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023671
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02763
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_it3.6212.7651503
X-RAY DIFFRACTIONr_mcbond_other3.5722.7621501
X-RAY DIFFRACTIONr_mcangle_it4.8314.9571875
X-RAY DIFFRACTIONr_mcangle_other4.834.9571876
X-RAY DIFFRACTIONr_scbond_it4.5973.0831514
X-RAY DIFFRACTIONr_scbond_other4.5963.0841515
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5175.452242
X-RAY DIFFRACTIONr_long_range_B_refined7.59127.573310
X-RAY DIFFRACTIONr_long_range_B_other7.60526.713271
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 107 -
Rwork0.211 1975 -
obs--99.38 %

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