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- PDB-4nf7: Crystal structure of the GH5 family catalytic domain of Endo-1,4-... -

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Basic information

Entry
Database: PDB / ID: 4nf7
TitleCrystal structure of the GH5 family catalytic domain of Endo-1,4-beta-glucanase Cel5C from Butyrivibrio proteoclasticus.
ComponentsEndo-1,4-beta-glucanase Cel5C
KeywordsHYDROLASE / alpha/beta TIM barrel / Glycosyl hydrolase / Polysaccharide binding / Secreted
Function / homology
Function and homology information


cellulase / beta-glucosidase activity / cellulase activity / polysaccharide binding / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / : / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. ...Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / : / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesButyrivibrio proteoclasticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.111 Å
AuthorsLott, J.S. / Colbert, D.A.
CitationJournal: To be Published
Title: Structural and functional characterisation of endo-1,4-beta-glucanase Cel5C from bovine rumen microbe Butyrivibrio proteoclasticus
Authors: Lott, J.S. / Colbert, D.A.
History
DepositionOct 30, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Dec 4, 2019Group: Data collection / Database references / Category: reflns / struct_ref_seq_dif / Item: _reflns.pdbx_Rsym_value / _struct_ref_seq_dif.details
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endo-1,4-beta-glucanase Cel5C


Theoretical massNumber of molelcules
Total (without water)41,5341
Polymers41,5341
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.890, 68.890, 175.640
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-469-

HOH

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Components

#1: Protein Endo-1,4-beta-glucanase Cel5C


Mass: 41533.891 Da / Num. of mol.: 1 / Fragment: Catalytic domain, UNP residues 32-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Butyrivibrio proteoclasticus (bacteria)
Strain: ATCC 51982 / DSM 14932 / B316 / Gene: bpr_I1710, cel5C / Plasmid: pDEST566 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: E0RXM0, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.51 Å3/Da / Density % sol: 50.97 % / Mosaicity: 1.22 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 20% PEG3350, 0.2M Ammonium formate pH 6.6, 20% PEG550 mme., VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 2, 2012
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.11→64.133 Å / Num. all: 24672 / Num. obs: 24672 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 27 % / Biso Wilson estimate: 18.81 Å2 / Rsym value: 0.0374 / Net I/σ(I): 11.8
Reflection shell

Rmerge(I) obs: 0.015 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.11-2.2324.21.5280.58326834460.3011.5280.014962.596
2.23-2.3627.31.2320.69057233130.2311.2320.01213.598.6
2.36-2.5227.90.9650.88829631600.1790.9650.009484.698.6
2.52-2.7328.10.76618292329520.1420.7660.00753698.8
2.73-2.99280.5191.57705127480.0960.5190.00518.898.9
2.99-3.3427.80.3112.56924224900.0580.3110.0030614.199
3.34-3.8527.40.1814.36119622300.0340.1810.0017822.499
3.85-4.72270.1216.45120318940.0230.1210.0011930.599.2
4.72-6.6826.20.1246.33996415270.0240.1240.0012227.299.2
6.68-37.44623.30.0819.1212179120.0160.0810.000793298.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.11 Å37.46 Å
Translation2.11 Å37.46 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASER2.4.0phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
Blu-Ice(McPhillipsdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.111→37.446 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.85 / SU ML: 0.26 / σ(F): 0 / Phase error: 21.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 1262 5.12 %Random
Rwork0.1899 ---
all0.1921 24655 --
obs0.1921 24655 97.92 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.362 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso max: 55.05 Å2 / Biso mean: 18.7319 Å2 / Biso min: 7.99 Å2
Baniso -1Baniso -2Baniso -3
1-3.5618 Å20 Å2-0 Å2
2--3.5618 Å20 Å2
3----7.1236 Å2
Refinement stepCycle: LAST / Resolution: 2.111→37.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2903 0 0 113 3016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082983
X-RAY DIFFRACTIONf_angle_d1.0324061
X-RAY DIFFRACTIONf_chiral_restr0.072424
X-RAY DIFFRACTIONf_plane_restr0.005533
X-RAY DIFFRACTIONf_dihedral_angle_d12.3651056
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.111-2.19560.28291380.22912434257294
2.1956-2.29560.30021400.2152543268398
2.2956-2.41660.27151230.19872555267898
2.4166-2.56790.28311350.19372592272798
2.5679-2.76610.2541460.20292567271398
2.7661-3.04440.23931400.19912601274198
3.0444-3.48470.23271470.20452611275898
3.4847-4.38920.17951500.16072656280699
4.3892-37.45190.2021430.17132834297799

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