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- PDB-5nrk: Crystal structure of the sixth cohesin from Acetivibrio celluloly... -

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Basic information

Entry
Database: PDB / ID: 5nrk
TitleCrystal structure of the sixth cohesin from Acetivibrio cellulolyticus' scaffoldin B in complex with Cel5 dockerin S15I, I16N mutant
Components
  • DocCel5: Type I dockerin repeat domain from A. cellulolyticus family 5 endoglucanase WP_010249057 S15I, I16N mutant
  • Endoglucanase
KeywordsPROTEIN BINDING / cellulosome / cohesin / dockerin / type I cohesin-dockerin / Coh-Doc / protein-protein interaction
Function / homology
Function and homology information


cellulase / cellulose binding / cellulase activity / polysaccharide catabolic process / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / extracellular region / metal ion binding
Similarity search - Function
Carboxypeptidase regulatory-like domain / Type 1 dockerin domain / Dockerin domain / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Carboxypeptidase-like, regulatory domain superfamily / Cellulose binding domain / Carbohydrate-binding module 3 ...Carboxypeptidase regulatory-like domain / Type 1 dockerin domain / Dockerin domain / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Carboxypeptidase-like, regulatory domain superfamily / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
THIOCYANATE ION / DocCel5: Type I dockerin repeat domain from A. cellulolyticus family 5 endoglucanase WP_010249057 S15I, I16N mutant / Endoglucanase
Similarity search - Component
Biological speciesAcetivibrio cellulolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBule, P. / Najmudin, S. / Fontes, C.M.G.A. / Alves, V.D.
Funding support Portugal, 3items
OrganizationGrant numberCountry
Fundacao para a Ciencia e TecnologiaEXPL/BIA-MIC/1176/2012 Portugal
Fundacao para a Ciencia e TecnologiaPTDC/BIA-PRO/103980/2008 Portugal
Fundacao para a Ciencia e TecnologiaPTDC/BIA-MIC/5947/2014 Portugal
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structure-function analyses generate novel specificities to assemble the components of multienzyme bacterial cellulosome complexes.
Authors: Bule, P. / Cameron, K. / Prates, J.A.M. / Ferreira, L.M.A. / Smith, S.P. / Gilbert, H.J. / Bayer, E.A. / Najmudin, S. / Fontes, C.M.G.A. / Alves, V.D.
History
DepositionApr 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 17, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase
B: DocCel5: Type I dockerin repeat domain from A. cellulolyticus family 5 endoglucanase WP_010249057 S15I, I16N mutant
C: Endoglucanase
D: DocCel5: Type I dockerin repeat domain from A. cellulolyticus family 5 endoglucanase WP_010249057 S15I, I16N mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,07715
Polymers44,4784
Non-polymers59911
Water10,449580
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-82 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.539, 79.809, 112.159
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Endoglucanase / scaffoldin


Mass: 14747.412 Da / Num. of mol.: 2 / Fragment: ScaB Type I cohesin domain UNP residues 1472-1611
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio cellulolyticus (bacteria) / Gene: cipV / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RPL0, cellulase
#2: Protein DocCel5: Type I dockerin repeat domain from A. cellulolyticus family 5 endoglucanase WP_010249057 S15I, I16N mutant


Mass: 7491.539 Da / Num. of mol.: 2 / Fragment: Type I dockerin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio cellulolyticus (bacteria) / Gene: BglC / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2R2JFJ6*PLUS

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Non-polymers , 4 types, 591 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / 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: 2.34 Å3/Da / Density % sol: 47.47 % / Mosaicity: 0.18 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 0.2 M sodium thiocyanate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→27.38 Å / Num. obs: 74140 / % possible obs: 99.2 % / Redundancy: 4.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.028 / Rrim(I) all: 0.064 / Net I/σ(I): 14.9 / Num. measured all: 327094 / Scaling rejects: 108
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.45-1.472.60.203880733950.9120.1410.254.193.8
7.94-27.384.60.04124235230.9970.020.04630.297.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ccl

2ccl


Resolution: 1.45→65.03 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.645 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1699 3641 4.9 %RANDOM
Rwork0.144 ---
obs0.1453 70443 98.98 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.86 Å2 / Biso mean: 14.99 Å2 / Biso min: 4.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0 Å2
2--0.19 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.45→65.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3114 0 27 580 3721
Biso mean--23.46 26.94 -
Num. residues----421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023331
X-RAY DIFFRACTIONr_bond_other_d0.0050.023240
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9844527
X-RAY DIFFRACTIONr_angle_other_deg1.0937526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5275465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16826.585123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.79315593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.311154
X-RAY DIFFRACTIONr_chiral_restr0.0880.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023820
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02680
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 269 -
Rwork0.183 4859 -
all-5128 -
obs--94.32 %
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)
10.3974-0.2404-0.13770.43240.11320.7002-0.01490.0221-0.0074-0.0419-0.00890.00720.0111-0.02760.02380.025-0.0095-0.00070.0139-0.00780.007812.20673.083-48.846
22.0191-0.15970.2940.89710.37711.17150.0153-0.2251-0.13380.0948-0.00830.02450.088-0.092-0.0070.0364-0.01410.00280.05590.00280.01397.49875.371-25.918
30.6245-0.16030.27391.08390.29161.9425-0.0065-0.048-0.11070.1223-0.0130.02630.3867-0.00850.01940.11440.00410.01130.0289-0.00650.03330.28473.289-10.572
41.70310.35220.76080.8090.17722.2505-0.07990.16580.0747-0.10150.05120.0109-0.1250.13880.02880.0373-0.0083-0.00320.0542-0.01030.018427.98784.585-31.413
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 142
2X-RAY DIFFRACTION2B3 - 70
3X-RAY DIFFRACTION3C0 - 142
4X-RAY DIFFRACTION4D3 - 69

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