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Basic information

Entry
Database: PDB / ID: 8c10
TitleBiochemical and structural characterisation of an alkaline family GH5 cellulase from a shipworm symbiont
ComponentsGH5 Cellulase
KeywordsHYDROLASE / GH family 5 / shipworm / symbiont / enzymatic hydrolysis.
Function / homology:
Function and homology information
Biological speciesTeredinibacter waterburyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsLeiros, I. / Vaaje-Kolstad, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biotechnol Biofuels Bioprod / Year: 2023
Title: Biochemical and structural characterisation of a family GH5 cellulase from endosymbiont of shipworm P. megotara.
Authors: Junghare, M. / Manavalan, T. / Fredriksen, L. / Leiros, I. / Altermark, B. / Eijsink, V.G.H. / Vaaje-Kolstad, G.
History
DepositionDec 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GH5 Cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6137
Polymers35,2791
Non-polymers3346
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-3 kcal/mol
Surface area10500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.041, 68.426, 87.188
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GH5 Cellulase


Mass: 35278.766 Da / Num. of mol.: 1 / Mutation: A25M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Teredinibacter waterburyi (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 357 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.9 Å3/Da / Density % sol: 35.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M MgCl2, 0.1 M Tris-HCl, pH 8.5 25 % w/v PEG 3350
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91842 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91842 Å / Relative weight: 1
ReflectionResolution: 1→45.04 Å / Num. obs: 143241 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 6.32 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.5
Reflection shellResolution: 1→1.02 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5490 / % possible all: 77.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→53.83 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.547 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13342 2221 1.6 %RANDOM
Rwork0.11242 ---
obs0.11275 140934 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.485 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0 Å20 Å2
2--0.08 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1→53.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 0 19 351 2695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0192519
X-RAY DIFFRACTIONr_bond_other_d0.0040.022179
X-RAY DIFFRACTIONr_angle_refined_deg2.2561.9073454
X-RAY DIFFRACTIONr_angle_other_deg1.14235074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0525329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5324.846130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13315387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2481512
X-RAY DIFFRACTIONr_chiral_restr0.1430.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022929
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02551
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_it1.2370.8661234
X-RAY DIFFRACTIONr_mcbond_other1.20.8621232
X-RAY DIFFRACTIONr_mcangle_it1.3531.3061553
X-RAY DIFFRACTIONr_mcangle_other1.361.3091554
X-RAY DIFFRACTIONr_scbond_it2.3711.0151285
X-RAY DIFFRACTIONr_scbond_other2.3311.0161285
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4241.4671889
X-RAY DIFFRACTIONr_long_range_B_refined2.88811.9763159
X-RAY DIFFRACTIONr_long_range_B_other2.61611.2953062
X-RAY DIFFRACTIONr_rigid_bond_restr6.91234698
X-RAY DIFFRACTIONr_sphericity_free21.8885213
X-RAY DIFFRACTIONr_sphericity_bonded7.47854765
LS refinement shellResolution: 1→1.025 Å
RfactorNum. reflection% reflection
Rfree0.232 115 -
Rwork0.264 8449 -
obs--79.7 %

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