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

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Basic information

Entry
Database: PDB / ID: 4yzp
TitleCrystal structure of a tri-modular GH5 (subfamily 4) endo-beta-1, 4-glucanase from Bacillus licheniformis
ComponentsCellulose hydrolase
KeywordsHYDROLASE / Endoglucanase / GH5 / tri-modular
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
cellulase / cellulase
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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 1.2Feb 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 / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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
Item: _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: Cellulose hydrolase


Theoretical massNumber of molelcules
Total (without water)60,8621
Polymers60,8621
Non-polymers00
Water10,683593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.700, 90.700, 120.630
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-784-

HOH

21A-956-

HOH

31A-992-

HOH

41A-1150-

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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.05 Å3/Da / Density % sol: 39.91 %
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: 0.9724 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: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.7→64.13 Å / Num. obs: 52079 / % possible obs: 94.1 % / Redundancy: 2.5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.058 / Net I/σ(I): 7.1 / Num. measured all: 127819 / Scaling rejects: 167
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.7-1.732.50.5521.7689727790.5710.41795.9
9-64.132.70.03517.410764040.9960.02591.4

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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: 3NDY

3ndy


Resolution: 1.7→64.13 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1976 2577 4.96 %
Rwork0.1663 49394 -
obs0.1678 51971 92.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.1 Å2 / Biso mean: 23.5962 Å2 / Biso min: 8.57 Å2
Refinement stepCycle: final / Resolution: 1.7→64.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4015 0 0 593 4608
Biso mean---35.22 -
Num. residues----509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074153
X-RAY DIFFRACTIONf_angle_d1.0555676
X-RAY DIFFRACTIONf_chiral_restr0.041622
X-RAY DIFFRACTIONf_plane_restr0.005730
X-RAY DIFFRACTIONf_dihedral_angle_d12.231486
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.73270.26331550.24212747290295
1.7327-1.76810.27091430.23662746288995
1.7681-1.80660.23691400.2222800294096
1.8066-1.84860.23671460.20452782292895
1.8486-1.89480.24141500.19312607275790
1.8948-1.94610.24461410.20782706284793
1.9461-2.00330.21441540.17972773292796
2.0033-2.0680.24631420.1792827296996
2.068-2.14190.2011520.16742779293196
2.1419-2.22770.22991480.17532736288493
2.2277-2.32910.21321460.17412544269087
2.3291-2.45190.17681360.16242759289594
2.4519-2.60550.21431340.17082758289293
2.6055-2.80670.22951420.17412785292794
2.8067-3.08910.18821270.15922648277589
3.0891-3.53610.18291520.15572830298295
3.5361-4.45490.14011330.13212719285289
4.4549-64.180.17181360.1482848298488
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)
10.8656-0.0928-0.06590.99280.10160.7035-0.0074-0.02060.02340.0331-0.01570.0292-0.01020.04470.02170.0904-0.009-0.01120.10890.01370.1026190.5301155.3535131.8656
20.3897-0.0083-0.02420.63080.25370.6170.02460.1202-0.1472-0.04650.02050.00850.15360.1617-0.02820.19660.0599-0.01760.251-0.03940.1876209.5848135.3669112.5662
31.083-0.209-0.02851.1106-0.20341.60410.0514-0.0319-0.10260.14970.04130.40340.3624-0.0486-0.08220.3047-0.01410.00160.1968-0.01720.3695186.2842123.677119.423
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 317 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 318 through 448 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 449 through 532 )A0

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