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- PDB-2c7f: The Structure of a family 51 arabinofuranosidase, Araf51, from Cl... -

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Basic information

Entry
Database: PDB / ID: 2c7f
TitleThe Structure of a family 51 arabinofuranosidase, Araf51, from Clostridium thermocellum in complex with 1,5-alpha-L-Arabinotriose.
ComponentsALPHA-L-ARABINOFURANOSIDASE
KeywordsHYDROLASE / ARABINOFURANOSIDASE / GLYCOSIDASE / XYLAN / ARABINAN
Function / homology
Function and homology information


arabinan catabolic process / L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / cytoplasm
Similarity search - Function
Alpha-L-arabinofuranosidase, C-terminal / Alpha-L-arabinofuranosidase C-terminal domain / Alpha-L-arabinofuranosidase C-terminus / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like ...Alpha-L-arabinofuranosidase, C-terminal / Alpha-L-arabinofuranosidase C-terminal domain / Alpha-L-arabinofuranosidase C-terminus / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Intracellular exo-alpha-(1->5)-L-arabinofuranosidase / :
Similarity search - Component
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.7 Å
AuthorsTaylor, E.J. / Smith, N.L. / Turkenburg, J.P. / D'Souza, S. / Gilbert, H.J. / Davies, G.J.
CitationJournal: Biochem.J. / Year: 2006
Title: Structural Insight Into the Ligand Specificity of a Thermostable Family 51 Arabinofuranosidase, Araf51, from Clostridium Thermocellum.
Authors: Taylor, E.J. / Smith, N.L. / Turkenburg, J.P. / D'Souza, S. / Gilbert, H.J. / Davies, G.J.
History
DepositionNov 23, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jun 14, 2017Group: Advisory / Atomic model / Derived calculations
Category: atom_site / database_PDB_caveat ...atom_site / database_PDB_caveat / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _struct_conf.pdbx_PDB_helix_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sense / _struct_sheet_order.sheet_id
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-L-ARABINOFURANOSIDASE
B: ALPHA-L-ARABINOFURANOSIDASE
C: ALPHA-L-ARABINOFURANOSIDASE
D: ALPHA-L-ARABINOFURANOSIDASE
E: ALPHA-L-ARABINOFURANOSIDASE
F: ALPHA-L-ARABINOFURANOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)356,23921
Polymers353,4586
Non-polymers2,78115
Water2,108117
1
A: ALPHA-L-ARABINOFURANOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5105
Polymers58,9101
Non-polymers6014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ALPHA-L-ARABINOFURANOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2543
Polymers58,9101
Non-polymers3442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ALPHA-L-ARABINOFURANOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3863
Polymers58,9101
Non-polymers4762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: ALPHA-L-ARABINOFURANOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3863
Polymers58,9101
Non-polymers4762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: ALPHA-L-ARABINOFURANOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4484
Polymers58,9101
Non-polymers5383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: ALPHA-L-ARABINOFURANOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2543
Polymers58,9101
Non-polymers3442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)173.341, 173.341, 272.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 1000
2111B1 - 1000
3111C1 - 1000
4111D1 - 1000
5111E1 - 1000
6111F1 - 1000

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Components

#1: Protein
ALPHA-L-ARABINOFURANOSIDASE / / ARABINOFURANOSIDASE


Mass: 58909.719 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Strain: F1 / YS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q4CJG5, UniProt: A3DIH0*PLUS, non-reducing end alpha-L-arabinofuranosidase
#2: Polysaccharide
alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose


Type: oligosaccharide / Mass: 414.360 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-5LArafa1-5LArafa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a211h-1a_1-4]/1-1-1/a5-b1_b5-c1WURCSPDB2Glycan 1.1.0
[][<C5O4>]{[(1+1)][a-L-Araf]{[(5+1)][a-L-Araf]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose


Type: oligosaccharide / Mass: 282.245 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-5LArafa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a211h-1a_1-4]/1-1/a5-b1WURCSPDB2Glycan 1.1.0
[][a-L-Araf]{[(5+1)][a-L-Araf]{}}LINUCSPDB-CARE
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 173 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 173 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, GLU 173 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 173 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 173 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLU 173 TO ALA ENGINEERED RESIDUE IN CHAIN E, GLU 173 TO ALA ENGINEERED RESIDUE IN CHAIN F, GLU 173 TO ALA
Sequence detailsTHE SEQUENCE SHOWN HERE IS DERIVED FROM AN EMBL/GENBANK/DDBJ WHOLE GENOME SHOTGUN (WGS) ENTRY WHICH ...THE SEQUENCE SHOWN HERE IS DERIVED FROM AN EMBL/GENBANK/DDBJ WHOLE GENOME SHOTGUN (WGS) ENTRY WHICH IS PRELIMINARY DATA. THE N-TERMINAL MGSSHHHHHH IS DERIVED FROM THE CLONING VECTOR PET 28A. THE PBD IS NUMBERED AS THE UNIPROT SEQUENCE Q4CJG5 BEGINNING AT RESIDUES MKKARMTVDKDY

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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: 3.04 Å3/Da / Density % sol: 59.22 %
Crystal growDetails: 5.0M SODIUM ACETATE,0.1M SODIUM CACODYLATE PH 6.5,5% DIOXANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD / Date: May 7, 2005 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND MONOCHROMATORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.7→59.76 Å / Num. obs: 113914 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.7→145.86 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.902 / SU B: 29.895 / SU ML: 0.277 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.955 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 5684 5 %RANDOM
Rwork0.242 ---
obs0.243 108059 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.7→145.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23734 0 186 117 24037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02224514
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.95333210
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg16.82852968
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36824.551189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.982154197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.12115138
X-RAY DIFFRACTIONr_chiral_restr0.1550.23602
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218614
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.211577
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.216342
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2943
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4170.215
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0411.515295
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.064223927
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.163310689
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.2974.59283
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 3852 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.040.05
2Btight positional0.050.05
3Ctight positional0.040.05
4Dtight positional0.040.05
5Etight positional0.040.05
6Ftight positional0.040.05
1Atight thermal0.010.5
2Btight thermal0.010.5
3Ctight thermal0.010.5
4Dtight thermal0.010.5
5Etight thermal0.010.5
6Ftight thermal0.010.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 412 -
Rwork0.35 7841 -
obs--98.9 %
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)
11.31150.26110.2571.7434-0.56642.2877-0.0191-0.2297-0.02230.55830.04280.0104-0.0992-0.078-0.0237-0.01510.0622-0.0006-0.20590.0415-0.192724.6731.32-36.303
23.0268-0.0549-0.12871.6412-0.18281.00170.10180.44120.5205-0.2340.0680.1952-0.2018-0.3127-0.1698-0.1280.0577-0.06810.01810.0415-0.109710.51443.597-88.34
32.06770.1852-0.58261.31740.36272.86180.05630.6352-0.0084-0.2439-0.0516-0.0339-0.1351-0.1308-0.0047-0.16440.03190.0314-0.0380.0091-0.17352.72860.99-100.103
41.50280.0253-0.34872.7916-0.02011.09380.0077-0.18230.21620.41650.11010.4074-0.3728-0.1713-0.11780.07380.0656-0.0092-0.1895-0.0573-0.118243.08773.116-47.387
51.71820.19990.78071.9455-0.39032.68220.1383-0.052-0.18680.281-0.0302-0.50650.53580.5165-0.1081-0.07520.1243-0.1459-0.0171-0.1054-0.046380.24834.822-60.335
61.81380.1754-0.58961.61330.90612.8361-0.06150.2653-0.4672-0.09870.1651-0.16640.37250.4051-0.1036-0.01570.0798-0.0917-0.1683-0.1217-0.068148.2814.355-78.612
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 502
2X-RAY DIFFRACTION1A1503 - 1506
3X-RAY DIFFRACTION2B3 - 502
4X-RAY DIFFRACTION2B1503 - 1506
5X-RAY DIFFRACTION3C4 - 502
6X-RAY DIFFRACTION3C1503 - 1506
7X-RAY DIFFRACTION4D4 - 502
8X-RAY DIFFRACTION4D1503 - 1507
9X-RAY DIFFRACTION5E3 - 502
10X-RAY DIFFRACTION5E1503 - 1507
11X-RAY DIFFRACTION6F3 - 501
12X-RAY DIFFRACTION6F1503 - 1505

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