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- PDB-4lx4: Crystal Structure Determination of Pseudomonas stutzeri endogluca... -

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Basic information

Entry
Database: PDB / ID: 4lx4
TitleCrystal Structure Determination of Pseudomonas stutzeri endoglucanase Cel5A using a Twinned Data Set
ComponentsEndoglucanase(Endo-1,4-beta-glucanase)protein
KeywordsHYDROLASE / GLYCOSYL HYDROLASE FAMILY 5 / CELLULASE / TIM BARREL / BETA-1 / 4-ENDOGLUCANASE
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Endoglucanase(Endo-1,4-beta-glucanase)protein
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.556 Å
AuthorsDutoit, R. / Delsaute, M. / Berlemont, R. / Van Elder, D. / Galleni, M. / Bauvois, C.
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Crystal structure determination of Pseudomonas stutzeri A1501 endoglucanase Cel5A: the search for a molecular basis for glycosynthesis in GH5_5 enzymes.
Authors: Dutoit, R. / Delsaute, M. / Collet, L. / Vander Wauven, C. / Van Elder, D. / Berlemont, R. / Richel, A. / Galleni, M. / Bauvois, C.
#1: Journal: ISME J / Year: 2009
Title: Insights into bacterial cellulose biosynthesis by functional metagenomics on Antarctic soil samples.
Authors: Berlemont, R. / Delsaute, M. / Pipers, D. / D'Amico, S. / Feller, G. / Galleni, M. / Power, P.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501.
Authors: Yan, Y. / Yang, J. / Dou, Y. / Chen, M. / Ping, S. / Peng, J. / Lu, W. / Zhang, W. / Yao, Z. / Li, H. / Liu, W. / He, S. / Geng, L. / Zhang, X. / Yang, F. / Yu, H. / Zhan, Y. / Li, D. / Lin, ...Authors: Yan, Y. / Yang, J. / Dou, Y. / Chen, M. / Ping, S. / Peng, J. / Lu, W. / Zhang, W. / Yao, Z. / Li, H. / Liu, W. / He, S. / Geng, L. / Zhang, X. / Yang, F. / Yu, H. / Zhan, Y. / Li, D. / Lin, Z. / Wang, Y. / Elmerich, C. / Lin, M. / Jin, Q.
History
DepositionJul 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase(Endo-1,4-beta-glucanase)protein
B: Endoglucanase(Endo-1,4-beta-glucanase)protein
C: Endoglucanase(Endo-1,4-beta-glucanase)protein
D: Endoglucanase(Endo-1,4-beta-glucanase)protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,3568
Polymers148,8674
Non-polymers4894
Water20,3751131
1
A: Endoglucanase(Endo-1,4-beta-glucanase)protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3392
Polymers37,2171
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoglucanase(Endo-1,4-beta-glucanase)protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3392
Polymers37,2171
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Endoglucanase(Endo-1,4-beta-glucanase)protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3392
Polymers37,2171
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Endoglucanase(Endo-1,4-beta-glucanase)protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3392
Polymers37,2171
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.390, 82.900, 104.740
Angle α, β, γ (deg.)90.00, 92.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Endoglucanase(Endo-1,4-beta-glucanase)protein


Mass: 37216.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Strain: A1501 / Gene: PST_2494 / Plasmid: pET-22b:Ps_Cel5A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4VME5, cellulase
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1131 / 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: 40.04 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ps_Cel5A (27 microM) in 50 mM sodium phosphate pH 7.0, was mixed 1:1 with well buffer (100 mM tris pH 5.9 with 22.5 % v/v polyethylene glycol 600) using the hanging drop method with 500 uL ...Details: Ps_Cel5A (27 microM) in 50 mM sodium phosphate pH 7.0, was mixed 1:1 with well buffer (100 mM tris pH 5.9 with 22.5 % v/v polyethylene glycol 600) using the hanging drop method with 500 uL well buffer in the well of the crystallization tray. Crystals obtained by this method were soaked 1 hour in 100 mM Tris pH 5.9 with 30% v/v polyethylene glycol 600., VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979639 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979639 Å / Relative weight: 1
ReflectionResolution: 1.556→48.279 Å / Num. all: 157788 / Num. obs: 157658 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.07 / Net I/σ(I): 17.9
Reflection shellResolution: 1.56→1.6 Å / Redundancy: 7.07 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 5.9 / Num. unique all: 12421 / Rsym value: 0.314 / % possible all: 97.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASER(phenix.automr: 1.8.2_1309)phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EE9

4ee9


Resolution: 1.556→48.279 Å / Isotropic thermal model: Isotropic / σ(F): 1.36 / Phase error: 27.74 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 8444 5.36 %INHERITED
Rwork0.2196 ---
obs0.2236 157658 91.58 %-
all-157658 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.4 Å2
Refinement stepCycle: LAST / Resolution: 1.556→48.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10315 0 32 1131 11478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710667
X-RAY DIFFRACTIONf_angle_d1.17714487
X-RAY DIFFRACTIONf_dihedral_angle_d13.0843868
X-RAY DIFFRACTIONf_chiral_restr0.081448
X-RAY DIFFRACTIONf_plane_restr0.0061908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5565-1.58340.30734190.29467952X-RAY DIFFRACTION93
1.5834-1.61220.28854300.27898160X-RAY DIFFRACTION95
1.6122-1.64320.29064290.2758162X-RAY DIFFRACTION95
1.6432-1.67670.27854290.2718151X-RAY DIFFRACTION95
1.6767-1.71320.27354260.2738083X-RAY DIFFRACTION95
1.7132-1.7530.2944290.26128160X-RAY DIFFRACTION95
1.753-1.79690.2684290.26088147X-RAY DIFFRACTION95
1.7969-1.84540.25064280.25348145X-RAY DIFFRACTION95
1.8454-1.89980.29061820.25683440X-RAY DIFFRACTION40
1.8998-1.96110.29312080.26043971X-RAY DIFFRACTION46
1.9611-2.03120.25764280.24798126X-RAY DIFFRACTION95
2.0312-2.11250.27074280.24748129X-RAY DIFFRACTION95
2.1125-2.20860.24484310.23138183X-RAY DIFFRACTION95
2.2086-2.32510.24321920.23243661X-RAY DIFFRACTION43
2.3251-2.47070.2334300.22068172X-RAY DIFFRACTION95
2.4707-2.66150.24724310.22348183X-RAY DIFFRACTION95
2.6615-2.92930.23794310.21058193X-RAY DIFFRACTION95
2.9293-3.35310.23184320.20428192X-RAY DIFFRACTION95
3.3531-4.22410.19484320.18078223X-RAY DIFFRACTION95
4.2241-47.22860.19354390.17938325X-RAY DIFFRACTION94

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