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- PDB-3c7e: Crystal structure of a glycoside hydrolase family 43 arabinoxylan... -

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Basic information

Entry
Database: PDB / ID: 3c7e
TitleCrystal structure of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase from Bacillus subtilis.
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / 5-bladed beta-propeller fold / beta-sandwich / Xylan degradation
Function / homology
Function and homology information


non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / xylan catabolic process / carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
: / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyl hydrolase domain; family 43 / 5 Propeller ...: / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / Arabinoxylan arabinofuranohydrolase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVandermarliere, E. / Bourgois, T.M. / Winn, M.D. / Van Campenhout, S. / Volckaert, G. / Strelkov, S.V. / Delcour, J.A. / Rabijns, A. / Courtin, C.M.
CitationJournal: Biochem.J. / Year: 2009
Title: Structural analysis of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase in complex with xylotetraose reveals a different binding mechanism compared with other members of the same family.
Authors: Vandermarliere, E. / Bourgois, T.M. / Winn, M.D. / van Campenhout, S. / Volckaert, G. / Delcour, J.A. / Strelkov, S.V. / Rabijns, A. / Courtin, C.M.
History
DepositionFeb 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Aug 30, 2023Group: 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9468
Polymers51,6761
Non-polymers2707
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.710, 74.430, 106.990
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 Endo-1,4-beta-xylanase / Xylanase D


Mass: 51676.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: xynD / Production host: Escherichia coli (E. coli)
References: UniProt: Q45071, non-reducing end alpha-L-arabinofuranosidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 4.0 M Na formate, 30% sucrose, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9785 Å
DetectorType: PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 35773 / % possible obs: 96.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.102 / Rsym value: 10.2 / Net I/σ(I): 14.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 3.9 / Num. unique all: 4966 / Rsym value: 33.3 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1w9t, 1gyh

1w9t

1gyh


Resolution: 2→28.61 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.434 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21333 1884 5.3 %RANDOM
Rwork0.16755 ---
obs0.16994 33849 95.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2---1.23 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 2→28.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3671 0 3 323 3997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223791
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9185169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8525492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13824.217166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75715521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2021512
X-RAY DIFFRACTIONr_chiral_restr0.1130.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023000
X-RAY DIFFRACTIONr_nbd_refined0.2080.21802
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22603
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2298
X-RAY DIFFRACTIONr_metal_ion_refined0.1390.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.217
X-RAY DIFFRACTIONr_mcbond_it0.8321.52413
X-RAY DIFFRACTIONr_mcangle_it1.40423849
X-RAY DIFFRACTIONr_scbond_it1.98431440
X-RAY DIFFRACTIONr_scangle_it2.8734.51317
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 113 -
Rwork0.191 2374 -
obs--92.01 %

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