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- PDB-3x17: Crystal structure of metagenome-derived glycoside hydrolase famil... -

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Basic information

Entry
Database: PDB / ID: 3x17
TitleCrystal structure of metagenome-derived glycoside hydrolase family 9 endoglucanase
ComponentsEndoglucanase
KeywordsHYDROLASE / (alpha/alpha)6 barrel fold / Cellulase / Carbohydrate/Sugar Binding
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process / metal ion binding
Similarity search - Function
Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily ...Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsOkano, H. / Angkawidjaja, C. / Kanaya, S.
CitationJournal: Protein Sci. / Year: 2015
Title: Structure, activity, and stability of metagenome-derived glycoside hydrolase family 9 endoglucanase with an N-terminal Ig-like domain.
Authors: Okano, H. / Kanaya, E. / Ozaki, M. / Angkawidjaja, C. / Kanaya, S.
History
DepositionOct 30, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Endoglucanase
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,5048
Polymers122,2132
Non-polymers2916
Water7,152397
1
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2524
Polymers61,1071
Non-polymers1463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2524
Polymers61,1071
Non-polymers1463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.631, 89.913, 151.157
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 Endoglucanase / LC-CelG


Mass: 61106.598 Da / Num. of mol.: 2 / Fragment: UNP residues 20-577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pET25b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8PF21, cellulase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, 0.2M Magnesium chloride hexahydrate, 30% w/v Polyethylene glycol 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 13, 2013
RadiationMonochromator: Rotated-inclined double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 63355 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 14.9 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 28

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CLC

1clc


Resolution: 2.15→43.96 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.548 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24558 3208 5.1 %RANDOM
Rwork0.18693 ---
obs0.18978 60076 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.635 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---0.85 Å20 Å2
3---1.56 Å2
Refinement stepCycle: LAST / Resolution: 2.15→43.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8478 0 6 397 8881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228730
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.191.94811936
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.36251094
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92222.696408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.051151230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5061574
X-RAY DIFFRACTIONr_chiral_restr0.1040.21262
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0216954
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4461.55456
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.32528710
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8533274
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6144.53226
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 230 -
Rwork0.231 4300 -
obs--97.69 %

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