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

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Basic information

Entry
Database: PDB / ID: 4yhg
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


beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
: / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-cellotriose / GH5
Similarity search - Component
Biological speciesBacteroidetes bacterium AC2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNaas, A.E. / MacKenzie, A.K. / Dalhus, B. / Eijsink, V.G.H. / Pope, P.B.
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 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / 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 / 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_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7523
Polymers87,2472
Non-polymers5041
Water4,179232
1
A: GH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1282
Polymers43,6241
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GH5


Theoretical massNumber of molelcules
Total (without water)43,6241
Polymers43,6241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.326, 99.553, 102.462
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: 1 / 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(-0.8602, -0.509266, 0.026533), (-0.50974, 0.860187, -0.015614), (-0.014871, -0.026956, -0.999526)66.485184, 17.652531, -55.151932

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Components

#1: Protein GH5 / Glycoside Hydrolase 5 / Endoglucanase


Mass: 43623.602 Da / Num. of mol.: 2 / Mutation: E172A
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, cellulase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.2 M potassium nitrate, 20 % w/v PEG 3350, 5mM Cellotetraose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791 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: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→71.401 Å / Num. all: 34325 / Num. obs: 34325 / % possible obs: 99.8 % / Redundancy: 5.2 % / Rpim(I) all: 0.048 / Rrim(I) all: 0.116 / Rsym value: 0.105 / Net I/av σ(I): 5.405 / Net I/σ(I): 10.2 / Num. measured all: 180101
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.4-2.535.10.4961.52501849270.2340.4963.199.8
2.53-2.685.40.3761.92517046690.1710.3764.299.7
2.68-2.875.40.2512.92367244210.1140.2515.799.9
2.87-3.15.10.17442113441180.0810.1747.799.9
3.1-3.395.30.1255.62006337990.0570.12510.599.9
3.39-3.795.50.0867.41900534560.0380.08615.399.7
3.79-4.385.30.0718.71609230570.0320.07118.299.9
4.38-5.375.10.0629.41335926240.0290.06218.899.7
5.37-7.595.30.06101086620550.0280.0617.799.5
7.59-49.7774.80.0567.4572211990.0280.05621.199.3

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YHE

4yhe


Resolution: 2.4→71.4 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 15.315 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.405 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 1733 5.1 %RANDOM
Rwork0.1848 ---
obs0.1869 32543 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.05 Å2 / Biso mean: 42.408 Å2 / Biso min: 20.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0 Å2
2--0.05 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2.4→71.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5941 0 34 232 6207
Biso mean--55.23 34.96 -
Num. residues----750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196126
X-RAY DIFFRACTIONr_bond_other_d0.0020.025596
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.9248312
X-RAY DIFFRACTIONr_angle_other_deg0.847312778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8715746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06123.731327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38315950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7991552
X-RAY DIFFRACTIONr_chiral_restr0.0760.2851
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027168
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021570
X-RAY DIFFRACTIONr_mcbond_it1.22.3982996
X-RAY DIFFRACTIONr_mcbond_other1.1872.3972995
X-RAY DIFFRACTIONr_mcangle_it1.8853.5923738
Refine LS restraints NCSNumber: 5576 / Type: TIGHT THERMAL / Rms dev position: 3.11 Å / Weight position: 0.5
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 109 -
Rwork0.262 2412 -
all-2521 -
obs--99.6 %
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)
11.5768-0.7687-0.35222.6861-0.35371.603-0.2081-0.1881-0.1230.37320.1879-0.04510.13950.0830.02020.07740.0476-0.00380.0531-0.01310.035416.597422.953-6.6671
22.1631-0.4501-0.67573.1760.80631.626-0.07660.3151-0.3297-0.3286-0.00720.0240.0784-0.04910.08390.0543-0.01280.01690.0726-0.02360.077638.864828.468-48.9207
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 397
2X-RAY DIFFRACTION2B9 - 397

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