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- PDB-5a8d: The high resolution structure of a novel alpha-L-arabinofuranosid... -

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Basic information

Entry
Database: PDB / ID: 5a8d
TitleThe high resolution structure of a novel alpha-L-arabinofuranosidase (CtGH43) from Clostridium thermocellum ATCC 27405
ComponentsCARBOHYDRATE BINDING FAMILY 6
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / CTGH43 / ALPHA-L-ARABINOFURANOSIDASE / C. THERMOCELLUM / 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 / Dockerin domain superfamily / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / 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
ACETATE ION / Carbohydrate binding family 6
Similarity search - Component
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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) from 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 1.3Sep 18, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / reflns / reflns_shell
Item: _exptl_crystal_grow.method / _reflns.pdbx_Rmerge_I_obs ..._exptl_crystal_grow.method / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_Rpim_I_all
Revision 1.4Jan 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 / 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 / _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)37,41912
Polymers36,4521
Non-polymers96711
Water4,179232
1
A: CARBOHYDRATE BINDING FAMILY 6
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)898,060288
Polymers874,85824
Non-polymers23,203264
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_775-z+2,-x+2,y1
crystal symmetry operation18_855-x+3,z,y1
crystal symmetry operation12_764-y+2,-z+1,x-11
crystal symmetry operation9_654y+1,z,x-11
crystal symmetry operation3_856-x+3,y,-z+11
crystal symmetry operation20_565x,-z+1,y1
crystal symmetry operation10_757-y+2,z,-x+21
crystal symmetry operation15_675y+1,-x+2,z1
crystal symmetry operation2_865-x+3,-y+1,z1
crystal symmetry operation14_776-y+2,-x+2,-z+11
crystal symmetry operation8_746-z+2,x-1,-y+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation22_664z+1,-y+1,x-11
crystal symmetry operation19_866-x+3,-z+1,-y+11
crystal symmetry operation24_767-z+2,-y+1,-x+21
crystal symmetry operation13_646y+1,x-1,-z+11
crystal symmetry operation23_754-z+2,y,x-11
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation11_667y+1,-z+1,-x+21
crystal symmetry operation6_676z+1,-x+2,-y+11
crystal symmetry operation16_745-y+2,x-1,z1
crystal symmetry operation5_645z+1,x-1,y1
crystal symmetry operation21_657z+1,y,-x+21
Buried area104010 Å2
ΔGint-1563 kcal/mol
Surface area246440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.990, 139.990, 139.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-2208-

HOH

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSULFATE ION (SO4): FROM THE CRYSTALLISATION BUFFER. GLYCEROL (GOL): FROM THE CRYOPROTECTANT ACETATE ...SULFATE ION (SO4): FROM THE CRYSTALLISATION BUFFER. GLYCEROL (GOL): FROM THE CRYOPROTECTANT ACETATE ION (ACT): FROM THE CRYSTALLISATION BUFFER.
Sequence detailsTHE N-TERMINAL CONTAINS THE HIS6 TAG.

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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: 3.17 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.5
Details: 120 MG ML-1 PROTEIN IN: 0.1 M SODIUM ACETATE PH 4.5, 2.0 M AMMONIUM SULPHATE CRYOPROTECTANT 30% GLYCEROL ADDED TO ABOVE BUFFER.

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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: 1.65→57.15 Å / Num. obs: 56751 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 20.7 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.02 / Net I/σ(I): 20
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.15 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5554 / Rpim(I) all: 0.36 / % possible all: 100

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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: 1.65→139.99 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.998 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. FOR 7 SEGMENTS DUE TO THE HIGHLY FLEXIBLE LOOPS BETWEEN RESIDUES 62 AND 72, 261 AND 268 AND 294 AND 303 DISORDERED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. FOR 7 SEGMENTS DUE TO THE HIGHLY FLEXIBLE LOOPS BETWEEN RESIDUES 62 AND 72, 261 AND 268 AND 294 AND 303 DISORDERED REGIONS IN THE LOOPS 62 TO 72, 261 TO 268 AND 294 TO 303 WERE MODELED STEREOCHEMICALLY IN THE SPURRIOUS ELECTRON DENSITY USING AUTOBUILD IN PHENIX WITH SIMULATED ANNEALING ON.
RfactorNum. reflection% reflectionSelection details
Rfree0.19327 2874 5.1 %RANDOM
Rwork0.1693 ---
obs0.17053 53797 99.86 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.453 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→139.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 57 232 2678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022603
X-RAY DIFFRACTIONr_bond_other_d0.0030.022310
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.9353559
X-RAY DIFFRACTIONr_angle_other_deg1.1135326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7915322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.82824.341129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29615379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8231510
X-RAY DIFFRACTIONr_chiral_restr0.1220.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213011
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02649
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_it4.0792.4371235
X-RAY DIFFRACTIONr_mcbond_other4.0582.4271232
X-RAY DIFFRACTIONr_mcangle_it6.8513.6461547
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1252.731362
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 201 -
Rwork0.263 3894 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 159.4072 Å / Origin y: 86.9802 Å / Origin z: 46.961 Å
111213212223313233
T0.0227 Å2-0.0204 Å20.0098 Å2-0.0251 Å2-0.0067 Å2--0.0324 Å2
L1.2324 °2-0.209 °20.099 °2-0.7921 °20.0201 °2--1.0611 °2
S-0.0177 Å °0.0092 Å °-0.0681 Å °0.0069 Å °-0.0151 Å °0.0523 Å °0.0214 Å °-0.0974 Å °0.0329 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 61
2X-RAY DIFFRACTION1A62 - 72
3X-RAY DIFFRACTION1A73 - 260
4X-RAY DIFFRACTION1A261 - 268
5X-RAY DIFFRACTION1A269 - 293
6X-RAY DIFFRACTION1A294 - 303
7X-RAY DIFFRACTION1A304 - 330

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