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- PDB-4yhe: NATIVE BACTEROIDETES-AFFILIATED GH5 CELLULASE LINKED WITH A POLYS... -

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Basic information

Entry
Database: PDB / ID: 4yhe
TitleNATIVE BACTEROIDETES-AFFILIATED GH5 CELLULASE LINKED WITH A POLYSACCHARIDE UTILIZATION LOCUS
ComponentsGH5
KeywordsHYDROLASE / beta alpha barrel / glycoside hydrolase / metagenomics
Function / homology
Function and homology information


organic substance metabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacteroidetes bacterium AC2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNaas, A.E. / MacKenzie, A.K. / Dalhus, B. / Eijsink, V.G.H. / Pope, P.B.
Funding support Norway, Belgium, 6items
OrganizationGrant numberCountry
The Research Council of Norway214042 Norway
The Research Council of Norway216625/F50 Norway
The Research Council of Norway190965 Norway
European Research Council336355 Belgium
South-Eastern Norway Regional Health Authority2012085 Norway
South-Eastern Norway Regional Health Authority2015095 Norway
CitationJournal: Sci Rep / Year: 2015
Title: Structural Features of a Bacteroidetes-Affiliated Cellulase Linked with a Polysaccharide Utilization Locus.
Authors: Naas, A.E. / MacKenzie, A.K. / Dalhus, B. / Eijsink, V.G. / Pope, P.B.
History
DepositionFeb 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GH5
B: GH5


Theoretical massNumber of molelcules
Total (without water)87,3632
Polymers87,3632
Non-polymers00
Water17,204955
1
A: GH5


Theoretical massNumber of molelcules
Total (without water)43,6821
Polymers43,6821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GH5


Theoretical massNumber of molelcules
Total (without water)43,6821
Polymers43,6821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.510, 100.680, 101.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 5 / Auth seq-ID: 9 - 397 / Label seq-ID: 1 - 389

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.839827, -0.542834, -0.004644), (-0.542666, 0.83973, -0.01916), (0.0143, -0.013571, -0.999806)67.642014, 21.08563, 150.31955

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Components

#1: Protein GH5 / Glycoside Hydrolase 5 / Endoglucanase


Mass: 43681.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Synthetic DNA
Source: (gene. exp.) Bacteroidetes bacterium AC2a (bacteria)
Plasmid: pNIC-CH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A076MPD7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 955 / 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: 51.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Sodium Cacodylate,40% v/v 2-Methyl-2,4-pentanediol, 5% w/v PEG8000
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.85→65.51 Å / Num. obs: 74499 / % possible obs: 98.6 % / Redundancy: 3.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.047 / Net I/σ(I): 8.9 / Num. measured all: 273972 / Scaling rejects: 51
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
1.85-1.892.90.32.91149040270.910.20190.8
9.25-65.513.50.0616.523476780.990.03797.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Aimless0.1.26data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→65.51 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.267 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2118 3672 5 %RANDOM
Rwork0.1776 ---
obs0.1793 69260 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.81 Å2 / Biso mean: 25.762 Å2 / Biso min: 11.48 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.85→65.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6154 0 0 955 7109
Biso mean---35.52 -
Num. residues----778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196315
X-RAY DIFFRACTIONr_bond_other_d0.0020.025736
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9158568
X-RAY DIFFRACTIONr_angle_other_deg0.836313100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1775776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16223.765340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48115976
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2671552
X-RAY DIFFRACTIONr_chiral_restr0.0870.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027454
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021630
X-RAY DIFFRACTIONr_mcbond_it1.4412.3663110
X-RAY DIFFRACTIONr_mcbond_other1.4382.3653109
X-RAY DIFFRACTIONr_mcangle_it2.0423.5423884
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2271MEDIUM POSITIONAL0.10.5
3666LOOSE POSITIONAL0.425
2271MEDIUM THERMAL3.62
3666LOOSE THERMAL3.8510
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 224 -
Rwork0.271 4438 -
all-4662 -
obs--84 %

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