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- PDB-5ho0: Crystal structure of AbnA (closed conformation), a GH43 extracell... -

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Basic information

Entry
Database: PDB / ID: 5ho0
TitleCrystal structure of AbnA (closed conformation), a GH43 extracellular arabinanase from Geobacillus stearothermophilus
ComponentsExtracellular arabinanase
KeywordsHYDROLASE / GH43 / arabinanase / Geobacillus stearothermophilus / extracellular
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
Extracellular arabinanase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLansky, S. / Shwartstien, S. / Salama, R. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: Crystal structure of AbnA (closed conformation), a GH43 extracellular arabinanase from Geobacillus stearothermophilus
Authors: Lansky, S. / Shwartstien, S. / Salama, R. / Shoham, Y. / Shoham, G.
History
DepositionJan 19, 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)94,6346
Polymers94,1321
Non-polymers5035
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-5 kcal/mol
Surface area31630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.715, 82.614, 131.704
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Extracellular arabinanase / GH43 extracelluar 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

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Non-polymers , 5 types, 432 molecules

#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
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: ESRF / Beamline: BM14 / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 33468 / % possible obs: 98 % / Redundancy: 6 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 8.4
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.2 / % possible all: 86

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X8T

2x8t


Resolution: 2.35→42.25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.907 / SU B: 8.578 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.515 / ESU R Free: 0.283 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25473 1661 5 %RANDOM
Rwork0.17847 ---
obs0.18237 31763 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.627 Å2
Baniso -1Baniso -2Baniso -3
1-3.02 Å20 Å20 Å2
2---0.52 Å20 Å2
3----2.5 Å2
Refinement stepCycle: 1 / Resolution: 2.35→42.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6294 0 29 427 6750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196517
X-RAY DIFFRACTIONr_bond_other_d0.0020.025889
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.938871
X-RAY DIFFRACTIONr_angle_other_deg0.805313573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5295804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88724.466309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22215997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3021524
X-RAY DIFFRACTIONr_chiral_restr0.0880.2924
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217525
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021573
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_it2.4813.5893208
X-RAY DIFFRACTIONr_mcbond_other2.483.5893206
X-RAY DIFFRACTIONr_mcangle_it3.8075.3724008
X-RAY DIFFRACTIONr_mcangle_other3.8075.3734009
X-RAY DIFFRACTIONr_scbond_it2.5353.7543309
X-RAY DIFFRACTIONr_scbond_other2.5353.7543309
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.965.5444862
X-RAY DIFFRACTIONr_long_range_B_refined6.25428.9747933
X-RAY DIFFRACTIONr_long_range_B_other6.25428.9797934
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.352→2.413 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 112 -
Rwork0.245 2022 -
obs--86.64 %

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