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- PDB-4yzt: Crystal structure of a tri-modular GH5 (subfamily 4) endo-beta-1,... -

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Basic information

Entry
Database: PDB / ID: 4yzt
TitleCrystal structure of a tri-modular GH5 (subfamily 4) endo-beta-1, 4-glucanase from Bacillus licheniformis complexed with cellotetraose
ComponentsCellulose hydrolase
KeywordsHYDROLASE / Endoglucanase / GH5 / tri-modular / cellotetraose
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Glycoside hydrolase, family 5, endoglucanase B / Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily ...Glycoside hydrolase, family 5, endoglucanase B / Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
beta-cellotetraose / cellulase / cellulase
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.665 Å
AuthorsLiberato, M.V. / Popov, A. / Polikarpov, I.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2008/56255-9 Brazil
Sao Paulo Research Foundation (FAPESP)2009/52840-7 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)490022/2009-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)301981/2011-6 Brazil
CitationJournal: Sci Rep / Year: 2016
Title: Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism.
Authors: Liberato, M.V. / Silveira, R.L. / Prates, E.T. / de Araujo, E.A. / Pellegrini, V.O. / Camilo, C.M. / Kadowaki, M.A. / de O.Neto, M. / Popov, A. / Skaf, M.S. / Polikarpov, I.
History
DepositionMar 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Mar 8, 2017Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / 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_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellulose hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6534
Polymers60,8621
Non-polymers7913
Water13,295738
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.299, 91.299, 124.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1036-

HOH

21A-1625-

HOH

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Components

#1: Protein Cellulose hydrolase / ENDO-BETA-1 / 4-GLUCANASE


Mass: 60862.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: cel5C / Plasmid: pETTRXA-1a/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta2(DE3)
References: UniProt: D1L8C7, UniProt: Q65JI7*PLUS, cellulase
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 738 / 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: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 22.5 % PEG 4000, 14 % isopropanol and 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→73.66 Å / Num. obs: 62144 / % possible obs: 99.8 % / Redundancy: 5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.072 / Net I/σ(I): 6.9 / Num. measured all: 310788 / Scaling rejects: 73
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all
1.66-1.695.20.8022.21585830390.2860.381
9.12-73.664.80.03920.422584660.9890.02

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.7data scaling
PHASER2.5.7phasing
PHENIX1.9-1692refinement
PDB_EXTRACT3.15data extraction
MOSFLM7.1.3data reduction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YZP

4yzp


Resolution: 1.665→57.328 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2119 3073 4.95 %
Rwork0.1755 58999 -
obs0.1773 62072 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.66 Å2 / Biso mean: 21.345 Å2 / Biso min: 6.66 Å2
Refinement stepCycle: final / Resolution: 1.665→57.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4090 0 53 738 4881
Biso mean--22.2 32.76 -
Num. residues----512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074275
X-RAY DIFFRACTIONf_angle_d1.0855831
X-RAY DIFFRACTIONf_chiral_restr0.046643
X-RAY DIFFRACTIONf_plane_restr0.005741
X-RAY DIFFRACTIONf_dihedral_angle_d13.0581539
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.665-1.6910.35281620.316826352797100
1.691-1.71880.32941470.30726182765100
1.7188-1.74840.31531230.282326512774100
1.7484-1.78020.30931510.268426332784100
1.7802-1.81440.31631410.253726342775100
1.8144-1.85150.25711430.23812629277299
1.8515-1.89170.2791170.229326712788100
1.8917-1.93570.28271440.224426482792100
1.9357-1.98420.24111300.208426742804100
1.9842-2.03780.23721260.185426602786100
2.0378-2.09780.25081550.179726372792100
2.0978-2.16550.21591180.173126902808100
2.1655-2.24290.19511360.18262665280199
2.2429-2.33270.22161410.173426732814100
2.3327-2.43880.22011460.160626742820100
2.4388-2.56740.19651460.16126632809100
2.5674-2.72830.22641370.169527052842100
2.7283-2.93890.20541230.16422717284099
2.9389-3.23470.1811440.154127192863100
3.2347-3.70270.16241310.142227422873100
3.7027-4.66460.14371540.12382740289499
4.6646-57.3620.17541580.14662921307999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.76680.10440.09630.8704-0.19970.90530.0387-0.1601-0.12240.0769-0.0524-0.05180.07910.00640.01110.0905-0.0164-0.00230.12690.01570.09837.3485-21.030115.5961
21.4063-0.12420.12061.3137-0.10411.6158-0.01980.02060.0072-0.10730.0205-0.0003-0.0081-0.06070.00250.0758-0.01510.00020.088-0.00550.078830.5257-16.2717-0.1954
30.5028-0.29590.12551.8012-0.58180.57610.0771-0.01280.0531-0.29430.04290.582-0.0027-0.1201-0.08190.15130.0292-0.01670.17470.01710.229717.63850.5349-8.4665
42.1167-0.63270.42361.99030.7282.02340.0510.06720.2147-0.1099-0.0411-0.1689-0.13160.05450.010.116-0.00470.03410.0970.01810.100540.810411.7016-1.2592
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 239 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 240 through 317 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 318 through 448 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 449 through 533 )A0

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