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- PDB-5a8c: The ultra high resolution structure of a novel alpha-L-arabinofur... -

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Basic information

Entry
Database: PDB / ID: 5a8c
TitleThe ultra high resolution structure of a novel alpha-L-arabinofuranosidase (CtGH43) from Clostridium thermocellum ATCC 27405 with bound trimethyl N-Oxide (TRS)
ComponentsCARBOHYDRATE BINDING FAMILY 6
KeywordsHYDROLASE / G CTGH43 / ALPHA-L-ARABINOFURANOSIDASE / 5-FOLD-BETA-PROPELLER
Function / homology
Function and homology information


xylan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / metal ion binding
Similarity search - Function
: / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Clostridium cellulosome enzymes repeated domain signature. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Dockerin domain ...: / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Clostridium cellulosome enzymes repeated domain signature. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Dockerin domain superfamily / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Galactose-binding-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Mainly Beta
Similarity search - Domain/homology
Carbohydrate binding family 6
Similarity search - Component
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å
AuthorsGoyal, A. / Ahmed, S. / Sharma, K. / Fontes, C.M.G.A. / Najmudin, S.
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Molecular determinants of substrate specificity revealed by the structure of Clostridium thermocellum arabinofuranosidase 43A from glycosyl hydrolase family 43 subfamily 16.
Authors: Goyal, A. / Ahmed, S. / Sharma, K. / Gupta, V. / Bule, P. / Alves, V.D. / Fontes, C.M. / Najmudin, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Crystallization and Preliminary X-Ray Crystallographic Analysis of a Novel Alpha-L-Arabinofuranosidase (Ctgh43) Fr Clostridium Thermocellum Atcc 27405.
Authors: Goyal, A. / Ahmed, S. / Fontes, C.M.G.A. / Najmudin, S.
History
DepositionJul 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Mar 1, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_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: CARBOHYDRATE BINDING FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6153
Polymers36,4521
Non-polymers1622
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.440, 67.700, 51.010
Angle α, β, γ (deg.)90.00, 113.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CARBOHYDRATE BINDING FAMILY 6 / ALPHA-L-ARABINOFURANOSIDASE


Mass: 36452.402 Da / Num. of mol.: 1 / Fragment: FAMILY 43 GLYCOSIDE HYDROLASE, RESIDUES 30-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: A3DEX4, non-reducing end alpha-L-arabinofuranosidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCALCIUM ION (CA): FROM THE STORAGE BUFFER 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS): FROM THE ...CALCIUM ION (CA): FROM THE STORAGE BUFFER 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS): FROM THE CRYSTALLISATION BUFFER

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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 Å3/Da / Density % sol: 39 %
Description: THE RESOLUTION CUT-OFF TO GET OVER 90 PER CENT COMPLETENESS IS 1.1A BUT ALL THE DATA WAS USED FOR REFINEMENT.
Crystal growpH: 8.5
Details: 0.1 M TRIS PH 8.5, 20% PEG 2000 MONOMETHYL ETHER, 0.2 M TRIMETHYL N-OXIDE, WITH PARATONE-N USED AS CRYOPROTECTANT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 0.97→67.76 Å / Num. obs: 119795 / % possible obs: 71.5 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.5
Reflection shellResolution: 0.97→1 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2 / % possible all: 6.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
xia2data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C7E

3c7e


Resolution: 0.97→39.95 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.475 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.12384 5972 5 %RANDOM
Rwork0.1031 ---
obs0.10413 113299 71.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.6 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0.16 Å2
2---0.27 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 0.97→39.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2365 0 9 564 2938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022506
X-RAY DIFFRACTIONr_bond_other_d0.0020.022241
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.9273430
X-RAY DIFFRACTIONr_angle_other_deg1.0635170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8115319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64524.355124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.09515372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7811510
X-RAY DIFFRACTIONr_chiral_restr0.1250.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212937
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02629
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8910.8421218
X-RAY DIFFRACTIONr_mcbond_other0.8580.841216
X-RAY DIFFRACTIONr_mcangle_it1.2571.2761525
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2711.011288
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.87334747
X-RAY DIFFRACTIONr_sphericity_free21.023592
X-RAY DIFFRACTIONr_sphericity_bonded6.37355146
LS refinement shellResolution: 0.97→0.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 31 -
Rwork0.242 760 -
obs--6.42 %

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