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- PDB-3wx5: Crystal structure of metagenome-derived glycoside hydrolase famil... -

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Basic information

Entry
Database: PDB / ID: 3wx5
TitleCrystal structure of metagenome-derived glycoside hydrolase family 12 endoglucanase
ComponentsCellulase
KeywordsHYDROLASE / Glycoside hydrolase family 12 endoglucanase / Cellulase / Carbohydrate binding / Sugar Binding
Function / homology
Function and homology information


cellulase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsOkano, H. / Angkawidjaja, C. / Kanaya, S.
CitationJournal: FEBS Open Bio / Year: 2014
Title: Structure and stability of metagenome-derived glycoside hydrolase family 12 cellulase (LC-CelA) a homolog of Cel12A from Rhodothermus marinus
Authors: Okano, H. / Ozaki, M. / Kanaya, E. / Kim, J.J. / Angkawidjaja, C. / Koga, Y. / Kanaya, S.
History
DepositionJul 17, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references / Derived calculations
Revision 1.2Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 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: Cellulase
B: Cellulase


Theoretical massNumber of molelcules
Total (without water)54,3242
Polymers54,3242
Non-polymers00
Water9,134507
1
A: Cellulase


Theoretical massNumber of molelcules
Total (without water)27,1621
Polymers27,1621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellulase


Theoretical massNumber of molelcules
Total (without water)27,1621
Polymers27,1621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.779, 59.576, 74.950
Angle α, β, γ (deg.)90.00, 122.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cellulase / LC-CelA


Mass: 27162.115 Da / Num. of mol.: 2 / Fragment: UNP residues 20-261
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: W8PWF3, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 0.2M sodium chloride, 23% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: May 26, 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: 1.85→50 Å / Num. obs: 41281 / % possible obs: 99.4 % / Observed criterion σ(I): 5 / Redundancy: 7.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 21.8

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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 1H0B

1h0b


Resolution: 1.85→33.36 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.476 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20008 2075 5 %RANDOM
Rwork0.1596 ---
obs0.16171 39135 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.678 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å2-0.93 Å2
2---1.13 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.85→33.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 0 507 4101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213704
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9045072
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7435456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39822.644174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55715524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3811532
X-RAY DIFFRACTIONr_chiral_restr0.1150.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212904
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_it1.5661.52258
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.50623612
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.73131446
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.584.51460
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: 1.848→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 155 -
Rwork0.173 2765 -
obs--95.99 %

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