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- PDB-4jho: Structural analysis and insights into glycon specificity of the r... -

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Basic information

Entry
Database: PDB / ID: 4jho
TitleStructural analysis and insights into glycon specificity of the rice GH1 Os7BGlu26 beta-D-mannosidase
ComponentsBeta-mannosidase/beta-glucosidase
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE FAMILY 1 / BETA-D-MANNOSIDASE / ORYZA SATIVA / TIM BARREL / Glycoside Hydrolase
Function / homology
Function and homology information


beta-D-fucosidase activity / beta-mannosidase activity / beta-glucosidase / beta-galactosidase activity / beta-glucosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-glucosidase / beta-glucosidase
Similarity search - Component
Biological speciesOryza sativa Indica Group (long-grained rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsTankrathok, A. / Luang, S. / Robinson, R.C. / Kimura, A. / Hrmova, M. / Ketudat Cairns, J.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural analysis and insights into the glycon specificity of the rice GH1 Os7BGlu26 beta-D-mannosidase
Authors: Tankrathok, A. / Iglesias-Fernandez, J. / Luang, S. / Robinson, R.C. / Kimura, A. / Rovira, C. / Hrmova, M. / Ketudat Cairns, J.R.
History
DepositionMar 5, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-mannosidase/beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5678
Polymers57,7761
Non-polymers7917
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.084, 71.685, 136.675
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 Beta-mannosidase/beta-glucosidase


Mass: 57775.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Indica Group (long-grained rice)
Production host: Escherichia coli (E. coli)
References: UniProt: B5ABY0, UniProt: A2YPH1*PLUS, beta-mannosidase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 0.8M K,Na tartrate, 0.1M Na HEPES, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.21→25.49 Å / Num. obs: 34370 / % possible obs: 99.6 % / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.2-2.28199.9
2.28-2.37199.9
2.37-2.48199.9
2.48-2.61199.9
2.61-2.77199.9
2.77-2.99199.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RGL

2rgl


Resolution: 2.21→25.49 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.82 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21921 1733 5.1 %RANDOM
Rwork0.17626 ---
obs0.17841 32558 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.883 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.21→25.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 51 304 4289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224189
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.9395692
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7195494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17723.023215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45315628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.221529
X-RAY DIFFRACTIONr_chiral_restr0.0840.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023314
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.22016
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22877
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2320
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8581.52505
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.95723921
X-RAY DIFFRACTIONr_scbond_it1.70931999
X-RAY DIFFRACTIONr_scangle_it2.4024.51771
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.205→2.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 126 -
Rwork0.259 2248 -
obs--95.88 %

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