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- PDB-5hp6: Structure of AbnA, a GH43 extracellular arabinanase from Geobacil... -

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Basic information

Entry
Database: PDB / ID: 5hp6
TitleStructure of AbnA, a GH43 extracellular arabinanase from Geobacillus stearothermophilus (a new conformational state)
ComponentsExtracellular arabinanase
KeywordsHYDROLASE / arabinanase / GH43 / extracellular / 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 / LamG-like jellyroll fold / LamG-like jellyroll fold domain / : / Concanavalin A-like lectin/glucanases superfamily / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 ...Atrophied bacterial Ig domain / Atrophied bacterial Ig domain / Extracellular endo-alpha-(1->5)-L-arabinanase, C-terminal / C-terminal lipocalin-like domain / 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, five-bladed beta-propellor domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Extracellular arabinanase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.093 Å
AuthorsLansky, S. / Salama, R. / Shwartstien, O. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: Structure of AbnA, a GH43 extracellular arabinanase from Geobacillus stearothermophilus (a new conformational state)
Authors: Lansky, S. / Salama, R. / Shwartstien, O. / Shoham, Y. / Shoham, G.
History
DepositionJan 20, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Extracellular arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4405
Polymers94,1321
Non-polymers3084
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-6 kcal/mol
Surface area31440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.847, 82.641, 132.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Extracellular arabinanase


Mass: 94131.516 Da / Num. of mol.: 1
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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / 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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 17%-19% PEG 6K, 0.2M NaCl, 0.1M HEPES buffer, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.093→48.93 Å / Num. obs: 45306 / % possible obs: 97.6 % / Redundancy: 11.34 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 23.2
Reflection shellResolution: 2.093→2.33 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.6 / % possible all: 86

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HO0

5ho0


Resolution: 2.093→48.925 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 2093 4.62 %
Rwork0.1924 --
obs0.1952 45306 94.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.093→48.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6268 0 17 275 6560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086478
X-RAY DIFFRACTIONf_angle_d1.1368827
X-RAY DIFFRACTIONf_dihedral_angle_d13.4092271
X-RAY DIFFRACTIONf_chiral_restr0.045925
X-RAY DIFFRACTIONf_plane_restr0.0061146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0929-2.14160.42091030.32032122X-RAY DIFFRACTION71
2.1416-2.19520.31781230.29342531X-RAY DIFFRACTION84
2.1952-2.25450.53081180.39252441X-RAY DIFFRACTION82
2.2545-2.32080.34341270.28172619X-RAY DIFFRACTION87
2.3208-2.39580.32921440.23952971X-RAY DIFFRACTION99
2.3958-2.48140.28581450.22212990X-RAY DIFFRACTION100
2.4814-2.58070.29161450.22463011X-RAY DIFFRACTION100
2.5807-2.69820.29951470.22743024X-RAY DIFFRACTION100
2.6982-2.84040.31721450.2213001X-RAY DIFFRACTION100
2.8404-3.01830.27791470.2183030X-RAY DIFFRACTION100
3.0183-3.25140.29661460.21333023X-RAY DIFFRACTION100
3.2514-3.57850.22781480.19013062X-RAY DIFFRACTION100
3.5785-4.0960.25011480.16743059X-RAY DIFFRACTION99
4.096-5.15970.16471500.13693092X-RAY DIFFRACTION100
5.1597-48.93840.19691570.15043234X-RAY DIFFRACTION100

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