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- PDB-5ho9: Structure of truncated AbnA (domains 1-3), a GH43 arabinanase fro... -

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Basic information

Entry
Database: PDB / ID: 5ho9
TitleStructure of truncated AbnA (domains 1-3), a GH43 arabinanase from Geobacilllus stearothermophilus, in complex with arabinooctaose
ComponentsExtracellular arabinanase
KeywordsHYDROLASE / GH43 / arabinanase / arabinooctaose / Geobacillus stearothermophilus
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Atrophied bacterial Ig domain / Atrophied bacterial Ig domain / Extracellular endo-alpha-(1->5)-L-arabinanase, C-terminal / C-terminal lipocalin-like domain / Lipocalin - #10 / LamG-like jellyroll fold / : / LamG-like jellyroll fold domain / Concanavalin A-like lectin/glucanases superfamily / Glycoside hydrolase, family 43 ...Atrophied bacterial Ig domain / Atrophied bacterial Ig domain / Extracellular endo-alpha-(1->5)-L-arabinanase, C-terminal / C-terminal lipocalin-like domain / Lipocalin - #10 / LamG-like jellyroll fold / : / LamG-like jellyroll fold domain / Concanavalin A-like lectin/glucanases superfamily / 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 / Lipocalin / Concanavalin A-like lectin/glucanase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Extracellular arabinanase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.845 Å
AuthorsLansky, S. / Salama, R. / Azoulai, D. / Shwartstien, O. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: Structure of truncated AbnA (domains 1-3), a GH43 arabinanase from Geobacilllus stearothermophilus, in complex with arabinooctaose
Authors: Lansky, S. / Salama, R. / Shwartstien, O. / Shoham, Y. / Shoham, G.
History
DepositionJan 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / pdbx_validate_close_contact / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extracellular arabinanase
B: Extracellular arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,80933
Polymers142,7832
Non-polymers5,02631
Water2,828157
1
A: Extracellular arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,04418
Polymers71,3921
Non-polymers2,65217
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Extracellular arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,76615
Polymers71,3921
Non-polymers2,37414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.172, 129.172, 488.364
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-853-

HOH

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Components

#1: Protein Extracellular arabinanase


Mass: 71391.531 Da / Num. of mol.: 2 / Fragment: domains 1-3, UNP residues 1-639
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: abnA / Production host: Escherichia coli (E. coli) / References: UniProt: B3EYN2
#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-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose


Type: oligosaccharide / Mass: 1074.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-5LArafa1-5LArafa1-5LArafa1-5LArafa1-5LArafa1-5LArafa1-5LArafa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,8,7/[a211h-1a_1-4]/1-1-1-1-1-1-1-1/a5-b1_b5-c1_c5-d1_d5-e1_e5-f1_f5-g1_g5-h1WURCSPDB2Glycan 1.1.0
[][a-L-Araf]{[(5+1)][a-L-Araf]{[(5+1)][a-L-Araf]{[(5+1)][a-L-Araf]{[(5+1)][a-L-Araf]{[(5+1)][a-L-Araf]{[(5+1)][a-L-Araf]{[(5+1)][a-L-Araf]{}}}}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 4.12 Å3/Da / Density % sol: 70.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.9 M AmSO4, 1% PEG 400, 0.1 M Hepes pH 7.5, 5mM arabinooctaose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.84→48.84 Å / Num. obs: 57801 / % possible obs: 99.9 % / Redundancy: 37.6 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 35.6
Reflection shellResolution: 2.84→3.02 Å / Redundancy: 39.1 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 7.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HO0

2ho0


Resolution: 2.845→48.822 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2418 2101 3.64 %
Rwork0.1827 --
obs0.1849 57737 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.845→48.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9398 0 309 157 9864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129968
X-RAY DIFFRACTIONf_angle_d2.29213558
X-RAY DIFFRACTIONf_dihedral_angle_d14.2283603
X-RAY DIFFRACTIONf_chiral_restr0.2251436
X-RAY DIFFRACTIONf_plane_restr0.0061705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8448-2.9110.33011360.26673596X-RAY DIFFRACTION99
2.911-2.98380.381370.27323619X-RAY DIFFRACTION100
2.9838-3.06440.35661370.26453633X-RAY DIFFRACTION100
3.0644-3.15460.34341380.25793643X-RAY DIFFRACTION100
3.1546-3.25640.31471360.24393624X-RAY DIFFRACTION100
3.2564-3.37270.28231380.22953639X-RAY DIFFRACTION100
3.3727-3.50770.27211380.21723669X-RAY DIFFRACTION100
3.5077-3.66730.24821390.19953670X-RAY DIFFRACTION100
3.6673-3.86060.23521380.18113670X-RAY DIFFRACTION100
3.8606-4.10240.22061390.16093685X-RAY DIFFRACTION100
4.1024-4.41890.22631410.14593722X-RAY DIFFRACTION100
4.4189-4.86330.17271410.12993738X-RAY DIFFRACTION100
4.8633-5.56610.19981430.13453789X-RAY DIFFRACTION100
5.5661-7.00940.18951450.16083837X-RAY DIFFRACTION100
7.0094-48.82930.22871550.17544102X-RAY DIFFRACTION100

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