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- PDB-3kmv: Crystal structure of CBM42A from Clostridium thermocellum -

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Basic information

Entry
Database: PDB / ID: 3kmv
TitleCrystal structure of CBM42A from Clostridium thermocellum
ComponentsAlpha-L-arabinofuranosidase B
KeywordsSUGAR BINDING PROTEIN / protein:carboydrate interactions / carbohydrate-binding module / beta-trefoil fold / CBM42
Function / homology
Function and homology information


L-arabinose metabolic process / alpha-L-arabinofuranosidase activity / polysaccharide catabolic process / metal ion binding
Similarity search - Function
Alpha-L-arabinofuranosidase B, arabinose-binding domain / Alpha-L-arabinofuranosidase B, arabinose-binding domain superfamily / Alpha-L-arabinofuranosidase B (ABFB) domain / Extracellular endo-alpha-(1->5)-L-arabinanase, C-terminal / C-terminal lipocalin-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. ...Alpha-L-arabinofuranosidase B, arabinose-binding domain / Alpha-L-arabinofuranosidase B, arabinose-binding domain superfamily / Alpha-L-arabinofuranosidase B (ABFB) domain / Extracellular endo-alpha-(1->5)-L-arabinanase, C-terminal / C-terminal lipocalin-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / Alpha-L-arabinofuranosidase B
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSantos-Silva, T. / Alves, V.D. / Prates, J.A.M. / Fontes, C.M.G.A. / Romao, M.J.
CitationJournal: Biochim.Biophys.Acta / Year: 2010
Title: Family 42 carbohydrate-binding modules display multiple arabinoxylan-binding interfaces presenting different ligand affinities.
Authors: Ribeiro, T. / Santos-Silva, T. / Alves, V.D. / Dias, F.M. / Luis, A.S. / Prates, J.A. / Ferreira, L.M. / Romao, M.J. / Fontes, C.M.
History
DepositionNov 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 6, 2023Group: 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 / struct_site
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.pdbx_ptnr1_label_alt_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-L-arabinofuranosidase B
B: Alpha-L-arabinofuranosidase B
C: Alpha-L-arabinofuranosidase B
D: Alpha-L-arabinofuranosidase B
E: Alpha-L-arabinofuranosidase B
F: Alpha-L-arabinofuranosidase B
G: Alpha-L-arabinofuranosidase B
H: Alpha-L-arabinofuranosidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,80742
Polymers146,0008
Non-polymers1,80734
Water15,547863
1
A: Alpha-L-arabinofuranosidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5667
Polymers18,2501
Non-polymers3166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-L-arabinofuranosidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4746
Polymers18,2501
Non-polymers2245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Alpha-L-arabinofuranosidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5667
Polymers18,2501
Non-polymers3166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Alpha-L-arabinofuranosidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3823
Polymers18,2501
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Alpha-L-arabinofuranosidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4745
Polymers18,2501
Non-polymers2244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Alpha-L-arabinofuranosidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4284
Polymers18,2501
Non-polymers1783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Alpha-L-arabinofuranosidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4876
Polymers18,2501
Non-polymers2375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Alpha-L-arabinofuranosidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4284
Polymers18,2501
Non-polymers1783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.370, 106.370, 237.564
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Alpha-L-arabinofuranosidase B


Mass: 18250.061 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / Gene: Cthe_0015 / Plasmid: Pet21A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: A3DBC8

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Non-polymers , 5 types, 897 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 863 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate, 2.1M sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2007 / Details: mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→237.564 Å / Num. obs: 144547 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 19.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2 / Num. measured all: 191837 / Num. unique all: 20870 / Rsym value: 0.381 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 52.32 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.22 Å
Translation2.5 Å45.22 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WD3

1wd3


Resolution: 1.8→45.22 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.192 / WRfactor Rwork: 0.162 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.899 / SU B: 4.186 / SU ML: 0.06 / SU R Cruickshank DPI: 0.095 / SU Rfree: 0.096 / Isotropic thermal model: isotropic and anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.192 7239 5 %RANDOM
Rwork0.158 ---
all0.192 ---
obs0.16 144449 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.8 Å2 / Biso mean: 9.877 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9058 0 105 863 10026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0229712
X-RAY DIFFRACTIONr_angle_refined_deg2.1211.95213244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.31951194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.47424.1539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15151551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7621563
X-RAY DIFFRACTIONr_chiral_restr0.1910.21385
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0217719
X-RAY DIFFRACTIONr_mcbond_it1.2931.55717
X-RAY DIFFRACTIONr_mcangle_it2.01929268
X-RAY DIFFRACTIONr_scbond_it3.23333995
X-RAY DIFFRACTIONr_scangle_it4.8324.53923
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 529 -
Rwork0.201 9964 -
all-10493 -
obs--99.66 %
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)
12.961-1.38490.66361.293-0.40142.33260.0049-0.1113-0.011-0.03360.0190.0069-0.04250.0694-0.0240.01310.0037-0.01470.0548-0.00670.0373-10.829-22.648-27.966
20.83170.13930.42363.92450.82522.6428-0.0713-0.021-0.0096-0.18440.1473-0.0026-0.0841-0.0298-0.0760.0446-0.0112-0.01580.02320.00380.0249-28.282-4.06-51.196
33.8762-1.04340.30171.3232-0.03012.47620.0198-0.10470.0376-0.048-0.00020.0397-0.0985-0.0838-0.01970.02450.0283-0.02240.0623-0.01320.0451-35.92920.637-28.062
43.8004-0.92560.83742.36-1.47733.5948-0.0309-0.3091-0.05750.1459-0.04310.01040.14790.01090.0740.0354-0.01610.00010.1275-0.02460.0498-63.18818.379-7.81
55.2466-1.27852.57742.463-2.1295.07780.0909-0.3894-0.32460.06270.05070.08990.0439-0.2302-0.14160.0094-0.012-0.01390.11640.03610.0478-9.78918.912-8.265
65.062-0.96730.49082.763-1.53143.9372-0.1353-0.3519-0.22130.21370.05980.13470.1522-0.17930.07560.0490.00110.02640.12510.03220.0738-38.432-26.262-8.511
73.1934-1.2171.46951.4442-0.74913.79120.0837-0.1636-0.0922-0.0908-0.0146-0.04220.1165-0.0283-0.06910.06360.0164-0.00950.0531-0.00690.0817-64.02-21.168-28.275
83.3792-2.03892.33494.94030.16163.34790.18140.21610.003-0.2272-0.1999-0.06070.01370.03970.01840.07970.03920.00280.07410.03850.0703-30.0170.2828.243
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 146
2X-RAY DIFFRACTION2B9 - 146
3X-RAY DIFFRACTION3C8 - 145
4X-RAY DIFFRACTION4D9 - 145
5X-RAY DIFFRACTION5E7 - 145
6X-RAY DIFFRACTION6F9 - 145
7X-RAY DIFFRACTION7G8 - 146
8X-RAY DIFFRACTION8H7 - 145

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