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- PDB-4u3s: Crystal structure of Coh3ScaB-XDoc_M1ScaA complex: A N-terminal i... -

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Basic information

Entry
Database: PDB / ID: 4u3s
TitleCrystal structure of Coh3ScaB-XDoc_M1ScaA complex: A N-terminal interface mutant of type II Cohesin-X-Dockerin complex from Acetivibrio cellulolyticus
Components
  • Cellulosomal scaffoldin
  • Cellulosomal scaffoldin adaptor protein B
KeywordsPROTEIN BINDING / 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 / Resolution: 1.64 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 N-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
DepositionJul 22, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)38,4547
Polymers37,7522
Non-polymers7025
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-30 kcal/mol
Surface area14620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.320, 72.320, 231.490
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-201-

NHE

21A-339-

HOH

31A-368-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Cellulosomal scaffoldin adaptor protein B / Coh3ScaB


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 / XDoc_M1ScaA


Mass: 19433.686 Da / Num. of mol.: 1 / Fragment: UNP residues 1755-1955 / Mutation: N145G
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-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 0.1 M CHES pH 9.5, 20% v/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionNumber: 1230010 / Rmerge(I) obs: 0.113 / Χ2: 1.04 / D res high: 1.64 Å / Num. obs: 83112 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
7.3362.6394910.043
5.197.33171110.057
4.235.19221310.073
3.674.23260110.089
3.283.67295310.097
2.993.28326210.104
2.772.99355910.115
2.592.77384410.124
2.442.59406010.138
2.322.44427110.154
2.212.32454910.167
2.122.21470010.189
2.032.12493810.218
1.962.03507610.258
1.891.96533710.314
1.831.89548710.375
1.781.83565710.443
1.731.78581610.494
1.681.73596310.619
1.641.68616610.702
ReflectionResolution: 1.64→62.63 Å / Num. obs: 45113 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 26.7 % / Biso Wilson estimate: 29.66 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.117 / Χ2: 1.04 / Net I/σ(I): 13.46 / Num. measured all: 1230010
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.64-1.680.8560.7023.2496281616661660.725100
1.68-1.730.8780.6193.9390688596359630.64100
1.73-1.780.9210.4945.2793437581658160.51100
1.78-1.830.9260.4436.3789463565756570.458100
1.83-1.890.9540.3757.9282053548754870.388100
1.89-1.960.9710.3149.7180420533953370.325100
1.96-2.030.9810.25811.6774916507650760.268100
2.03-2.120.9840.21813.4470629493949380.227100
2.12-2.210.990.18915.2468431470147000.196100
2.21-2.320.990.16716.564869454945490.174100
2.32-2.440.990.15417.2257953427142710.16100
2.44-2.590.9920.13819.0457375406040600.143100
2.59-2.770.9930.12420.2552383384438440.128100
2.77-2.990.9940.11522.0551456355935590.119100
2.99-3.280.9950.10422.6945262326232620.108100
3.28-3.670.9960.09723.8241053295329530.1100
3.67-4.230.9970.08924.6137044260226010.092100
4.23-5.190.9980.07325.7834574221422130.075100
5.19-7.330.9990.05725.4826595171217110.05999.9
7.33-62.630.9980.04326.35151289529490.04599.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0073refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2b59, 3l8q, 3fnk

2b59

3l8q

3fnk


Resolution: 1.64→62.63 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.309 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2061 2272 5 %RANDOM
Rwork0.1709 42730 --
obs0.1726 45002 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.83 Å2 / Biso mean: 27.367 Å2 / Biso min: 14.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å2-0 Å2
2---0.16 Å20 Å2
3---0.52 Å2
Refinement stepCycle: final / Resolution: 1.64→62.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 41 341 2821
Biso mean--55.44 31.9 -
Num. residues----323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022544
X-RAY DIFFRACTIONr_bond_other_d0.0020.022433
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.973466
X-RAY DIFFRACTIONr_angle_other_deg0.75535627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3955329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10225.9699
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.17215421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.618155
X-RAY DIFFRACTIONr_chiral_restr0.0860.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022871
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02532
X-RAY DIFFRACTIONr_mcbond_it1.5881.3461298
X-RAY DIFFRACTIONr_mcbond_other1.5861.3451297
X-RAY DIFFRACTIONr_mcangle_it2.3262.011621
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 137 -
Rwork0.22 3117 -
all-3254 -
obs--100 %
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)
10.9524-0.3132-0.04281.5218-0.36180.7421-0.0768-0.0752-0.1366-0.05640.15340.07460.1392-0.1847-0.07660.083-0.0708-0.02720.16650.07230.0456-31.358.42-12.71
22.18070.45090.38131.0513-0.04261.1177-0.03780.0542-0.1125-0.08260.0612-0.2099-0.01270.1155-0.02340.0363-0.0288-0.01530.10530.00710.0801-4.16920.992-7.978
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 167
2X-RAY DIFFRACTION2B29 - 184

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