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- PDB-5y6t: Crystal structure of endo-1,4-beta-mannanase from Eisenia fetida -

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Basic information

Entry
Database: PDB / ID: 5y6t
TitleCrystal structure of endo-1,4-beta-mannanase from Eisenia fetida
Componentsendo-1,4-beta-mannanase
KeywordsCARBOHYDRATE / cold adaptation / GH5 family
Function / homologyCellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / ISOPROPYL ALCOHOL / Endo-1,4-beta-mannanase
Function and homology information
Biological speciesEisenia fetida (common brandling worm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHirano, Y. / Ueda, M. / Tamada, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
The Tojuro Iijima Memorial Foundation for Food Science and Technology Japan
Japan Society for the Promotion of Science Japan
CitationJournal: Enzyme.Microb.Technol. / Year: 2018
Title: Gene cloning, expression, and X-ray crystallographic analysis of a beta-mannanase from Eisenia fetida.
Authors: Ueda, M. / Hirano, Y. / Fukuhara, H. / Naka, Y. / Nakazawa, M. / Sakamoto, T. / Ogata, Y. / Tamada, T.
History
DepositionAug 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: endo-1,4-beta-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8103
Polymers42,6281
Non-polymers1822
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint8 kcal/mol
Surface area12390 Å2
Unit cell
Length a, b, c (Å)50.130, 69.461, 86.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein endo-1,4-beta-mannanase


Mass: 42627.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eisenia fetida (common brandling worm) / Production host: Komagataella pastoris GS115 (fungus) / References: UniProt: A0A3B6UEQ6*PLUS
#2: 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 / Comment: pH buffer*YM
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.91 Å3/Da / Density % sol: 30.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1 M ammonium citrate, 15%(v/v) iso-propanol, 0.1 M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 5, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→55 Å / Num. obs: 33115 / % possible obs: 98.4 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rrim(I) all: 0.088 / Net I/σ(I): 13.1
Reflection shellResolution: 1.7→1.81 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 10039 / CC1/2: 0.825 / Rrim(I) all: 0.554 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C0H

2c0h


Resolution: 1.7→54.2 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.956 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.093
RfactorNum. reflection% reflectionSelection details
Rfree0.16927 1711 5.1 %RANDOM
Rwork0.13036 ---
obs0.13238 31789 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.891 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0 Å2
2---0.79 Å20 Å2
3---0.76 Å2
Refinement stepCycle: 1 / Resolution: 1.7→54.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 12 236 3032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022995
X-RAY DIFFRACTIONr_bond_other_d0.0020.022685
X-RAY DIFFRACTIONr_angle_refined_deg1.9031.9224101
X-RAY DIFFRACTIONr_angle_other_deg1.00836167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5145397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40625.215163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79715459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8521517
X-RAY DIFFRACTIONr_chiral_restr0.1410.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023642
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02765
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_it1.7242.2541491
X-RAY DIFFRACTIONr_mcbond_other1.7242.2521489
X-RAY DIFFRACTIONr_mcangle_it2.3233.3741871
X-RAY DIFFRACTIONr_mcangle_other2.3233.3771872
X-RAY DIFFRACTIONr_scbond_it2.3492.4371504
X-RAY DIFFRACTIONr_scbond_other2.3482.4371505
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3513.5832212
X-RAY DIFFRACTIONr_long_range_B_refined4.60219.1323755
X-RAY DIFFRACTIONr_long_range_B_other4.46418.8513676
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.703→1.747 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 118 -
Rwork0.189 2275 -
obs--97.2 %

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