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- PDB-4wi0: Crystal structure of Coh3ScaB-XDoc_M2ScaA complex: A C-terminal i... -

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Basic information

Entry
Database: PDB / ID: 4wi0
TitleCrystal structure of Coh3ScaB-XDoc_M2ScaA complex: A C-terminal interface mutant of type II Cohesin-X-Dockerin complex from Acetivibrio cellulolyticus
Components
  • Cellulosomal scaffoldin
  • Cellulosomal scaffoldin adaptor protein B
KeywordsSTRUCTURAL PROTEIN / cellulosome / cohesin / dockerin / type II cohesin-dockerin / Coh-XDoc / 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 / carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
Carboxypeptidase regulatory-like domain / Carboxypeptidase-like, regulatory domain / Type 1 dockerin domain / Dockerin domain / CarboxypepD_reg-like domain / Immunoglobulin-like - #680 / 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 regulatory-like domain / Carboxypeptidase-like, regulatory domain / Type 1 dockerin domain / Dockerin domain / CarboxypepD_reg-like domain / Immunoglobulin-like - #680 / 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. / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Cellulosomal scaffoldin adaptor protein B / Endoglucanase
Similarity search - Component
Biological speciesAcetivibrio cellulolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å
AuthorsAlves, V.D. / Cameron, K. / Najmudin, S.H. / Fontes, C.M.G.A.
Funding support Portugal, 1items
OrganizationGrant numberCountry
FCTEXPL/BIA-MIC/1176/2012 Portugal
CitationJournal: To Be Published
Title: Crystal structure of Coh3ScaB-XDoc_M1ScaA complex: A C-terminal interface mutant of type II Cohesin-X-Dockerin complex from Acetivibrio cellulolyticus
Authors: Alves, V.D. / Cameron, K. / Najmudin, S.H. / Fontes, C.M.G.A.
History
DepositionSep 24, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / 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: Cellulosomal scaffoldin adaptor protein B
B: Cellulosomal scaffoldin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8864
Polymers34,8062
Non-polymers802
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-36 kcal/mol
Surface area14130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.540, 88.300, 92.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Cellulosomal scaffoldin adaptor protein B


Mass: 18318.576 Da / Num. of mol.: 1
Fragment: Third Type II cohesin domain, UNP residues 407-573
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio cellulolyticus (bacteria) / Gene: scaB / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Tuner / References: UniProt: Q7WYN3
#2: Protein Cellulosomal scaffoldin


Mass: 16487.424 Da / Num. of mol.: 1 / Fragment: UNP residues 1760-1915 / Mutation: N178G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio cellulolyticus (bacteria) / Gene: cipV / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Tuner / References: UniProt: Q9RPL0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 25% PEG 3350, 0.1 M Bis_tris pH 5.5, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.93→92.02 Å / Num. obs: 29281 / % possible obs: 90.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.93-1.983.10.4972447614550.5610.30492.3
9.05-46.013.50.06511.28152330.9930.03583.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimlessdata scaling
MOSFLMdata reduction
BALBESphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2b59

2b59


Resolution: 1.93→63.71 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 9.071 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2412 1123 5.2 %RANDOM
Rwork0.1968 20653 --
obs0.1992 21766 89.41 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 58.26 Å2 / Biso mean: 23.779 Å2 / Biso min: 14.55 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å20 Å2-0 Å2
2--0.38 Å2-0 Å2
3---1.31 Å2
Refinement stepCycle: final / Resolution: 1.93→63.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2447 0 2 219 2668
Biso mean--19.76 29.89 -
Num. residues----324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022501
X-RAY DIFFRACTIONr_bond_other_d0.0010.022377
X-RAY DIFFRACTIONr_angle_refined_deg1.0961.9563406
X-RAY DIFFRACTIONr_angle_other_deg0.70735488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3835326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.51825.91898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54415420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.704155
X-RAY DIFFRACTIONr_chiral_restr0.0680.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022847
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02524
X-RAY DIFFRACTIONr_mcbond_it0.7280.9191298
X-RAY DIFFRACTIONr_mcbond_other0.7270.9191297
X-RAY DIFFRACTIONr_mcangle_it1.2321.3721620
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 88 -
Rwork0.275 1485 -
all-1573 -
obs--90.82 %
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)
10.83260.2605-0.28121.3747-0.53811.3893-0.00810.05760.0145-0.05420.07160.0648-0.1024-0.0698-0.06350.25280.0055-0.00340.15650.02450.00715.55321.402-15.786
20.98330.6219-0.26813.4737-0.77750.69360.00810.0389-0.07-0.1142-0.0614-0.17390.04990.02290.05330.19290.0032-0.00120.10230.00670.011110.585-9.865-6.64
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 168
2X-RAY DIFFRACTION2B29 - 184

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