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- PDB-1gye: Structure of Cellvibrio cellulosa alpha-L-arabinanase complexed w... -

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Basic information

Entry
Database: PDB / ID: 1gye
TitleStructure of Cellvibrio cellulosa alpha-L-arabinanase complexed with Arabinohexaose
ComponentsARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
KeywordsHYDROLASE / ARABINANASE / PROPELLER / CATALYSIS / CELLVIBRIO / PSEUDOMONAS
Function / homology
Function and homology information


arabinan endo-1,5-alpha-L-arabinosidase activity / arabinan catabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / extracellular region / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 43, endo-1, 5-alpha-L-arabinosidase / : / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
Extracellular exo-alpha-(1->5)-L-arabinofuranosidase ArbA
Similarity search - Component
Biological speciesCELLVIBRIO CELLULOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNurizzo, D. / Turkenburg, J.P. / Charnock, S.J. / Roberts, S.M. / Dodson, E.J. / McKie, V.A. / Taylor, E.J. / Gilbert, H.J. / Davies, G.J.
CitationJournal: Nat. Struct. Biol. / Year: 2002
Title: Cellvibrio japonicus alpha-L-arabinanase 43A has a novel five-blade beta-propeller fold.
Authors: Nurizzo, D. / Turkenburg, J.P. / Charnock, S.J. / Roberts, S.M. / Dodson, E.J. / McKie, V.A. / Taylor, E.J. / Gilbert, H.J. / Davies, G.J.
History
DepositionApr 23, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2002Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 28, 2018Group: Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity_src_gen / struct
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant / _struct.title
Revision 2.0Jul 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 / pdbx_struct_special_symmetry / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6913
Polymers35,8451
Non-polymers8462
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)90.605, 90.605, 177.554
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-2022-

HOH

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Components

#1: Protein ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A / ALPHA-L-ARABINANASE / ABN A / ENDO-1 / 5-ALPHA-L-ARABINANASE A


Mass: 35845.191 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CELLVIBRIO CELLULOSA (bacteria) / Plasmid: PVM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: P95470*PLUS, arabinan endo-1,5-alpha-L-arabinanase
#2: Polysaccharide alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L- ...alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose


Type: oligosaccharide / Mass: 810.704 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-5LArafa1-5LArafa1-5LArafa1-5LArafa1-5LArafa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a211h-1a_1-4]/1-1-1-1-1-1/a5-b1_b5-c1_c5-d1_d5-e1_e5-f1WURCSPDB2Glycan 1.1.0
[][a-L-Araf]{[(5+1)][a-L-Araf]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsENGINEERED MUTATION: ASP(158)ALA

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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: 2.6 Å3/Da / Density % sol: 52.2 %
Crystal growpH: 8
Details: 10% PEG8000, 100MM TRIS-HCL PH8.0, 20% GLYCEROL, 100MM ARABINOTRIOSE, pH 8.00
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %(w/v)PEG800011
2100 mMTris-HCl11pH8.0
320 %(v/v)glycerol11
420 mg/mlprotein11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 15610 / % possible obs: 100 % / Redundancy: 10.47 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 30.1
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 10.74 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 6.1 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 100 % / Redundancy: 10.5 %
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 10.7 %

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Processing

Software
NameVersionClassification
REFMAC5.1.13refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE STRUCTURE SOLVED PREVIOUSLY

Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.491 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.372 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.238 484 3.1 %RANDOM
Rwork0.188 ---
obs0.19 15073 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.9 Å21.45 Å20 Å2
2--2.9 Å20 Å2
3----4.36 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2537 0 56 77 2670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212683
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.7631.9483655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr7.2845314
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022043
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21158
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6721.51560
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22122502
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.24931123
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.34.51153
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: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.285 43
Rwork0.217 1063
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)
13.3785-0.6591.4383.4078-2.09851.1145-0.3776-1.423700.6320.30840.4219-0.1688-1.29920.06920.14960.21480.11981.0864-0.04860.308657.298632.828357.8518
22.9204-1.1098-0.70192.61311.21935.8163-0.0735-0.68960.30150.0870.04440.3893-0.5243-1.14140.02920.05810.1638-0.0240.5484-0.14120.291959.743237.371745.5901
33.2305-0.12311.00251.96971.52264.0007-0.2105-0.4280.3641-0.10040.1284-0.0049-0.4887-0.23960.08210.0230.052-0.0460.1457-0.06030.160673.762434.592939.8114
44.78950.58291.95283.37890.91193.5573-0.0103-0.8539-0.35920.25390.09720.0410.2444-0.4209-0.08690.05510.012-0.01140.26940.05980.112677.377323.169949.2509
57.11111.57690.35992.4082-0.15682.72660.1243-1.7407-0.3430.58760.04080.16980.1782-0.7942-0.16510.21630.05010.06310.8890.15240.226569.670822.821962.1836
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B32 - 83
2X-RAY DIFFRACTION2B84 - 152
3X-RAY DIFFRACTION3B153 - 211
4X-RAY DIFFRACTION4B212 - 285
5X-RAY DIFFRACTION5B286 - 346
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.019
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.7

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