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- PDB-4hu0: Crystal Structure of a metagenome-derived cellulase Cel5A in comp... -

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Basic information

Entry
Database: PDB / ID: 4hu0
TitleCrystal Structure of a metagenome-derived cellulase Cel5A in complex with cellotetraose
ComponentsCellulase
KeywordsHYDROLASE / (alpha/beta)8 barrel / Family 5 endoglucanase
Function / homology
Function and homology information


: / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
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-cellotetraose / Cellulase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.38 Å
AuthorsZhuang, N. / Lee, K.H.
CitationJournal: To be Published
Title: Crystal Structure of a metagenome-derived cellulase Cel5A in complex with cellotetraose
Authors: Zhuang, N. / Lee, K.H.
History
DepositionNov 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / 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.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8978
Polymers41,6781
Non-polymers1,2197
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.924, 136.924, 136.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-527-

HOH

21A-558-

HOH

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Components

#1: Protein Cellulase /


Mass: 41677.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: Cel5A / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I6PLH5
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotetraose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotetraose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 271 / 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

Crystal growTemperature: 291 K / pH: 6.5
Details: PEG 4000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23985
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 34430 / % possible obs: 100 %
Reflection shellResolution: 2.38→2.47 Å / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→43.3 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 7.838 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1725 5 %RANDOM
Rwork0.152 ---
obs0.154 34226 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.55 Å2
Refinement stepCycle: LAST / Resolution: 2.38→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 81 271 3056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0222884
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5281.9383920
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3165333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06823.784148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.61315445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6281518
X-RAY DIFFRACTIONr_chiral_restr0.1750.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212219
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_it1.3391.51649
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.34922668
X-RAY DIFFRACTIONr_scbond_it4.13331235
X-RAY DIFFRACTIONr_scangle_it6.2394.51250
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.38→2.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 113 -
Rwork0.231 2406 -
obs--99.45 %
Refinement TLS params.Method: refined / Origin x: -54.1611 Å / Origin y: -60.1265 Å / Origin z: -25.2994 Å
111213212223313233
T0.0289 Å20.0001 Å20.0054 Å2-0.0371 Å20.0379 Å2--0.051 Å2
L0.3102 °20.1199 °2-0.0847 °2-0.3671 °2-0.3025 °2--0.6198 °2
S0.0201 Å °0.002 Å °0.0118 Å °0.0114 Å °-0.0347 Å °-0.0627 Å °-0.0009 Å °-0.0532 Å °0.0146 Å °

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