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- PDB-2hyk: The crystal structure of an endo-beta-1,3-glucanase from alkaliph... -

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Basic information

Entry
Database: PDB / ID: 2hyk
TitleThe crystal structure of an endo-beta-1,3-glucanase from alkaliphilic Nocardiopsis sp.strain F96
ComponentsBeta-1,3-glucanase
KeywordsHYDROLASE / family 16 / beta-jelly roll / bacterial endo-beta-1 / 3-glucanase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ETHANOL / Beta-1,3-glucanase
Similarity search - Component
Biological speciesNocardiopsis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsFibriansah, G. / Nakamura, S. / Kumasaka, T.
Citation
Journal: Proteins / Year: 2007
Title: The 1.3 A crystal structure of a novel endo-beta-1,3-glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96.
Authors: Fibriansah, G. / Masuda, S. / Koizumi, N. / Nakamura, S. / Kumasaka, T.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and preliminary crystallographic analysis of endo-beta-1,3-beta-glucanase from alkaliphilic Nocardiopsis sp. strain F96
Authors: Fibriansah, G. / Masuda, S. / Hirose, R. / Hamada, K. / Tanaka, N. / Nakamura, S. / Kumasaka, T.
History
DepositionAug 7, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6328
Polymers27,1271
Non-polymers5057
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.589, 71.843, 39.666
Angle α, β, γ (deg.)90.00, 90.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-1,3-glucanase / endo-beta-1,3-glucanase


Mass: 27127.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardiopsis sp. (bacteria) / Strain: F96 / Plasmid: pET-21b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q2V0H0, glucan endo-1,3-beta-D-glucosidase

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Non-polymers , 5 types, 224 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 31.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl pH 8.0, 1.3-1.4M Ammonium sulfate, 1% Ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2004 / Details: rhodium-coated mirror
RadiationMonochromator: rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionRedundancy: 6.4 % / Av σ(I) over netI: 11.1 / Number: 166200 / Rmerge(I) obs: 0.09 / Χ2: 1.78 / D res high: 1.6 Å / D res low: 50 Å / Num. obs: 25958 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.455099.610.0645.4526.6
2.743.4599.910.0713.1846.9
2.392.7410010.0872.0617
2.172.3910010.0961.5576.9
2.022.1710010.1011.2336.9
1.92.0210010.1250.9417.3
1.81.910010.1670.6936.5
1.721.810010.2040.6056.6
1.661.7299.810.2340.5735.5
1.61.6695.410.2340.4873.6
ReflectionResolution: 1.3→50 Å / Num. obs: 47558 / % possible obs: 99.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.064 / Χ2: 1.766 / Net I/σ(I): 14.2
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.35 / Num. unique all: 4574 / Χ2: 1.157 / % possible all: 95.7

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se9.1160.6240.9950.2570.642
2Se14.7180.540.820.3641.027
3Se11.5260.540.9690.150.777
4Se5.4080.6070.2580.30.58
5Se9.6890.5390.7940.2150.658
6Se36.0390.0580.1090.4220.423
Phasing dmFOM : 0.71 / FOM acentric: 0.71 / FOM centric: 0.69 / Reflection: 24080 / Reflection acentric: 23426 / Reflection centric: 654
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
4.6-35.2440.940.950.831148105098
2.9-4.60.930.940.8834443295149
2.3-2.90.840.850.7142954166129
2-2.30.770.770.6642764171105
1.7-20.590.60.4971326997135
1.6-1.70.410.410.363785374738

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.08phasing
RESOLVE2.08phasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 1.3→39.65 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.352 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.162 2405 5.1 %RANDOM
Rwork0.143 ---
all0.144 ---
obs0.144 47531 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.249 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.27 Å2
2---0.55 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.3→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1859 0 30 217 2106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211984
X-RAY DIFFRACTIONr_angle_refined_deg1.251.9122712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0845236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86724.167108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.32715261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2691512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021617
X-RAY DIFFRACTIONr_nbd_refined0.1840.2912
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21326
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0860.2181
X-RAY DIFFRACTIONr_metal_ion_refined0.0720.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.229
X-RAY DIFFRACTIONr_mcbond_it0.6271.51212
X-RAY DIFFRACTIONr_mcangle_it0.92121910
X-RAY DIFFRACTIONr_scbond_it1.3373919
X-RAY DIFFRACTIONr_scangle_it1.8044.5802
X-RAY DIFFRACTIONr_rigid_bond_restr0.75932131
X-RAY DIFFRACTIONr_sphericity_free2.9093226
X-RAY DIFFRACTIONr_sphericity_bonded1.15431922
LS refinement shellResolution: 1.297→1.331 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 178 -
Rwork0.184 3105 -
obs-3283 91.58 %

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