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

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Basic information

Entry
Database: PDB / ID: 5nrm
TitleCrystal structure of the sixth cohesin from Acetivibrio cellulolyticus' scaffoldin B in complex with Cel5 dockerin S51I, L52N mutant
Components
  • DocCel5: Type I dockerin repeat domain from A. cellulolyticus family 5 endoglucanase WP_010249057 S51I, L52N mutant
  • EndoglucanaseCellulase
KeywordsCELL ADHESION / cellulosome / cohesin / dockerin / type I cohesin-dockerin / Coh-Doc / protein-protein interaction
Function / homology
Function and homology information


cellulose binding / cellulase / cellulase activity / cellulose catabolic process / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / extracellular region / metal ion binding
Similarity search - Function
Type 1 dockerin domain / Dockerin domain / CarboxypepD_reg-like 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 / Cellulose binding domain ...Type 1 dockerin domain / Dockerin domain / CarboxypepD_reg-like 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 / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / 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
DocCel5: Type I dockerin repeat domain from A. cellulolyticus family 5 endoglucanase WP_010249057 S51I, L52N mutant / Endoglucanase
Similarity search - Component
Biological speciesAcetivibrio cellulolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsBule, P. / Najmudin, S. / Fontes, C.M.G.A. / Alves, V.D.
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 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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 S51I, L52N mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9145
Polymers21,7932
Non-polymers1203
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-34 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.490, 59.950, 51.260
Angle α, β, γ (deg.)90.000, 106.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endoglucanase / Cellulase / scaffoldin


Mass: 14488.091 Da / Num. of mol.: 1 / 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 S51I, L52N mutant


Mass: 7305.331 Da / Num. of mol.: 1 / 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: A0A2R2JFJ7*PLUS
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.03 Å3/Da / Density % sol: 39.49 % / Mosaicity: 0.45 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 28% PEG400

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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: 1.4→18.98 Å / Num. obs: 33539 / % possible obs: 96.6 % / Redundancy: 2.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.059 / Rrim(I) all: 0.095 / Net I/σ(I): 6.5 / Num. measured all: 76946 / Scaling rejects: 0
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
1.4-1.422.30.438368616330.5030.3560.5661.895.1
7.67-18.982.50.045082030.9950.0310.0518.792.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
PHASERphasing
RefinementResolution: 1.4→49.05 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.053 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2052 1590 4.7 %RANDOM
Rwork0.1783 ---
obs0.1796 31929 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.15 Å2 / Biso mean: 17.362 Å2 / Biso min: 7.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.09 Å2
2--0.12 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 1.4→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1530 0 3 199 1732
Biso mean--15.89 24.68 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021588
X-RAY DIFFRACTIONr_bond_other_d0.0010.021521
X-RAY DIFFRACTIONr_angle_refined_deg1.961.9732161
X-RAY DIFFRACTIONr_angle_other_deg0.90233521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9075217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61326.61362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58615269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.937152
X-RAY DIFFRACTIONr_chiral_restr0.1260.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211843
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02331
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 128 -
Rwork0.305 2305 -
all-2433 -
obs--94.71 %
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)
11.5690.01490.51080.4496-0.22870.87180.00120.0767-0.0279-0.0328-0.0057-0.00520.03840.05140.00450.0121-0.0017-0.01180.061-0.00250.019-42.244-57.09154.38
23.6587-0.6021.79411.66240.25083.0102-0.305-0.60680.48980.16640.0824-0.1227-0.3632-0.36260.22260.07710.0581-0.05970.164-0.08520.0961-29.048-46.21670.77
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 142
2X-RAY DIFFRACTION2B4 - 69

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