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- PDB-3wdq: Crystal structure of beta-mannanase from a symbiotic protist of t... -

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Basic information

Entry
Database: PDB / ID: 3wdq
TitleCrystal structure of beta-mannanase from a symbiotic protist of the termite Reticulitermes speratus
ComponentsBeta-mannanase
KeywordsHYDROLASE / Tim Barrel / Carbohydrate Binding
Function / homology
Function and homology information


substituted mannan metabolic process / mannan endo-1,4-beta-mannosidase activity
Similarity search - Function
Glycoside hydrolase family 26 / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesSymbiotic protist of Reticulitermes speratus (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsTsukagoshi, H. / Ishida, T. / Touhara, K.K. / Igarashi, K. / Samejima, M. / Fushinobu, S. / Kitamoto, K. / Arioka, M.
Citation
Journal: J.Biol.Chem. / Year: 2014
Title: Structural and Biochemical Analyses of Glycoside Hydrolase Family 26 beta-Mannanase from a Symbiotic Protist of the Termite Reticulitermes speratus
Authors: Tsukagoshi, H. / Nakamura, A. / Ishida, T. / Touhara, K.K. / Otagiri, M. / Moriya, S. / Samejima, M. / Igarashi, K. / Fushinobu, S. / Kitamoto, K. / Arioka, M.
#1: Journal: FEMS Microbiol.Ecol. / Year: 2007
Title: Environmental cDNA analysis of the genes involved in lignocellulose digestion in the symbiotic protist community of Reticulitermes speratus.
Authors: Todaka, N. / Moriya, S. / Saita, K. / Hondo, T. / Kiuchi, I. / Takasu, H. / Piero, C. / Hayashizaki, Y. / Kudo, T.
History
DepositionJun 20, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Apr 30, 2014Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5736
Polymers40,2571
Non-polymers3165
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.503, 61.405, 57.806
Angle α, β, γ (deg.)90.00, 92.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-mannanase


Mass: 40256.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Symbiotic protist of Reticulitermes speratus (eukaryote)
Gene: RsMan26C, RsManC / Plasmid: pPICZalpha / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H
References: UniProt: H7CGE2, mannan endo-1,4-beta-mannosidase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2 Å3/Da / Density % sol: 38.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG3350, 0.2M magnesium chloride, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 25, 2012
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 77823 / Num. obs: 77766 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rsym value: 0.068 / Net I/σ(I): 34.6
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 3846 / Rsym value: 0.48 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CBW

3cbw


Resolution: 1.3→28.87 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.653 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16364 3908 5 %RANDOM
Rwork0.1439 ---
obs0.14489 73833 99.82 %-
all-77766 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.538 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.045 Å0.043 Å
Refinement stepCycle: LAST / Resolution: 1.3→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2631 0 18 406 3055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022823
X-RAY DIFFRACTIONr_bond_other_d0.0010.022534
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9293862
X-RAY DIFFRACTIONr_angle_other_deg0.81735865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8915355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73925.362138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.14515447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.513157
X-RAY DIFFRACTIONr_chiral_restr0.0940.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213299
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02684
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 296 -
Rwork0.265 5339 -
obs--98.27 %

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