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- PDB-1uv4: Native Bacillus subtilis Arabinanase Arb43A -

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Basic information

Entry
Database: PDB / ID: 1uv4
TitleNative Bacillus subtilis Arabinanase Arb43A
ComponentsARABINAN-ENDO 1,5-ALPHA-L-ARABINASE
KeywordsHYDROLASE / PROPELLER / CATALYSIS
Function / homology
Function and homology information


arabinan endo-1,5-alpha-L-arabinanase / arabinan endo-1,5-alpha-L-arabinosidase activity / arabinan catabolic process / 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 endo-alpha-(1->5)-L-arabinanase 1
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNurizzo, D. / Taylor, E.J. / Gilbert, H.J. / Davies, G.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Tailored Catalysts for Plant Cell-Wall Degradation: Redesigning the Exo/Endo Preference of Cellvibrio Japonicus Arabinanase 43A
Authors: Proctor, M. / Taylor, E.J. / Nurizzo, D. / Turkenburg, J. / Lloyd, R. / Vardakou, M. / Davies, G.J. / Gilbert, H.J.
History
DepositionJan 14, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,5397
Polymers32,2111
Non-polymers3286
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.628, 46.153, 57.322
Angle α, β, γ (deg.)90.00, 98.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ARABINAN-ENDO 1,5-ALPHA-L-ARABINASE / ARABINASE


Mass: 32210.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Plasmid: PET 22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER DE3
References: UniProt: P94522, arabinan endo-1,5-alpha-L-arabinanase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growpH: 8
Details: 0.2M MGCL2, 15% PEG 3350 5MM CACL2, 10 MM TRIS PH 8.0, 25% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 15, 2002 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.5→28.3 Å / Num. obs: 40400 / % possible obs: 91 % / Redundancy: 4 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 18.2
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 4.3 / % possible all: 74.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GYD

1gyd


Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.327 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1840 5 %RANDOM
Rwork0.167 ---
obs0.169 34795 90.8 %-
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: 13.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20.08 Å2
2---0.13 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2263 0 18 302 2583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212345
X-RAY DIFFRACTIONr_bond_other_d0.0020.021961
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.9343184
X-RAY DIFFRACTIONr_angle_other_deg1.38834594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3415290
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_restr0.1390.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022636
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02481
X-RAY DIFFRACTIONr_nbd_refined0.2020.2380
X-RAY DIFFRACTIONr_nbd_other0.260.22274
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.21301
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3470.2189
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1010.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.861.51435
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40122294
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2463910
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2674.5890
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.235 110
Rwork0.231 1790
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)
115.1277-2.9629-1.49962.7664-0.0291.50480.0662-0.323-0.9042-0.088-0.03890.45170.02-0.0454-0.02740.1113-0.0184-0.01730.0850.02070.126924.31189.32348.5592
22.91970.6354-0.84452.03280.04871.5353-0.0347-0.0151-0.2786-0.04-0.02280.01720.1685-0.02310.05750.07030.0131-0.00360.0273-0.00860.029235.871611.808438.3782
32.58370.03380.40752.67420.15212.32320.02480.1506-0.0529-0.20970.0336-0.0470.08750.12-0.05840.03190.00740.02410.0339-0.00410.02140.203322.731734.9749
41.68120.20620.51261.39370.28152.837-0.01840.01170.1153-0.06910.03790.0158-0.2051-0.0576-0.01950.01980.00150.00970.03240.00060.033233.303933.814338.8191
51.6681-0.8186-0.4412.9524-0.79321.3198-0.005-0.17160.01410.14950.06320.0455-0.0939-0.0378-0.05820.0428-0.00220.01260.0705-0.01790.039125.353830.782850.2982
62.0094-1.4672-0.02573.3143-0.13751.15050.14250.146-0.1405-0.138-0.08680.3192-0.0169-0.0872-0.05570.0508-0.0055-0.00250.08540.01560.060823.383618.268349.2177
736.01570.691536.41742.3289-1.925961.86750.3819-0.1730.3611-0.0049-0.1549-0.06290.05440.1858-0.2270.0577-0.00220.03680.03290.00880.067330.88923.113841.553
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 11
2X-RAY DIFFRACTION2A12 - 64
3X-RAY DIFFRACTION3A65 - 127
4X-RAY DIFFRACTION4A128 - 181
5X-RAY DIFFRACTION5A182 - 250
6X-RAY DIFFRACTION6A251 - 293
7X-RAY DIFFRACTION7A502
8X-RAY DIFFRACTION7A1294

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