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- PDB-5d8z: Structrue of a lucidum protein -

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Basic information

Entry
Database: PDB / ID: 5d8z
TitleStructrue of a lucidum protein
ComponentsendoglucanaseCellulase
KeywordsHYDROLASE / GH5 family / Ganoderma lucidum / endoglucanase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-cellobiose / Endoglucanase
Similarity search - Component
Biological speciesGanoderma lucidum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGuo, R. / Li, Q. / Shang, N. / Liu, G. / Ko, T.P. / Chen, C.C. / Liu, W.
CitationJournal: Enzyme.Microb.Technol. / Year: 2016
Title: Functional and structural analyses of a 1,4-beta-endoglucanase from Ganoderma lucidum.
Authors: Liu, G. / Li, Q. / Shang, N. / Huang, J.W. / Ko, T.P. / Liu, W. / Zheng, Y. / Han, X. / Chen, Y. / Chen, C.C. / Jin, J. / Guo, R.T.
History
DepositionAug 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 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

Downloads & links

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Assembly

Deposited unit
A: endoglucanase
B: endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1614
Polymers73,4762
Non-polymers6852
Water1,31573
1
A: endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0802
Polymers36,7381
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0802
Polymers36,7381
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.426, 236.399, 83.585
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein endoglucanase / Cellulase


Mass: 36738.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ganoderma lucidum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1A9TAJ1*PLUS
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Magnesium chloride hexahydrate, 0.1M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 21889 / % possible obs: 93.4 % / Redundancy: 7.8 % / Net I/σ(I): 20.41

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QR3

3qr3


Resolution: 2.7→25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.887 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 1.261 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1132 5.2 %RANDOM
Rwork0.179 ---
obs0.182 20753 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.03 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å20 Å20 Å2
2---4.22 Å20 Å2
3---2.36 Å2
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4864 0 46 74 4984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.025043
X-RAY DIFFRACTIONr_bond_other_d0.0010.024384
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.9156910
X-RAY DIFFRACTIONr_angle_other_deg0.908310056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7565646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.12325.984254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.88715662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3991510
X-RAY DIFFRACTIONr_chiral_restr0.0950.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026058
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021232
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_it3.0784.5312590
X-RAY DIFFRACTIONr_mcbond_other3.0724.5292589
X-RAY DIFFRACTIONr_mcangle_it4.7786.7933234
X-RAY DIFFRACTIONr_mcangle_other4.7786.7953235
X-RAY DIFFRACTIONr_scbond_it3.7474.8232453
X-RAY DIFFRACTIONr_scbond_other3.7394.8232453
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7217.1333677
X-RAY DIFFRACTIONr_long_range_B_refined7.837.145932
X-RAY DIFFRACTIONr_long_range_B_other7.76937.1245924
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 66 -
Rwork0.317 1389 -
obs--86.25 %

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