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- PDB-3vzk: Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylan... -

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Basic information

Entry
Database: PDB / ID: 3vzk
TitleCrystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35E mutant
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / xylanase / GH-11 glycoside hydrolase
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 ...Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLudwiczek, M.L. / D'Angelo, I. / Yalloway, G.N. / Okon, M. / Nielsen, J.E. / Strynadka, N.C. / Withers, S.G. / McIntosh, L.P.
CitationJournal: Biochemistry / Year: 2013
Title: Strategies for modulating the pH-dependent activity of a family 11 glycoside hydrolase
Authors: Ludwiczek, M.L. / D'Angelo, I. / Yalloway, G.N. / Brockerman, J.A. / Okon, M. / Nielsen, J.E. / Strynadka, N.C. / Withers, S.G. / McIntosh, L.P.
History
DepositionOct 14, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Nov 8, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,0404
Polymers40,8482
Non-polymers1922
Water8,755486
1
A: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)20,4241
Polymers20,4241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6163
Polymers20,4241
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.327, 62.814, 64.126
Angle α, β, γ (deg.)90.00, 104.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endo-1,4-beta-xylanase / Xylanase / 1 / 4-beta-D-xylan xylanohydrolase


Mass: 20424.016 Da / Num. of mol.: 2 / Mutation: N35E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Gene: xlnA / Production host: Escherichia coli (E. coli) / References: UniProt: P09850, endo-1,4-beta-xylanase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 1.88 Å3/Da / Density % sol: 34.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.54→62 Å / Num. all: 68561 / Num. obs: 62680 / % possible obs: 97.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HV1

1hv1


Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.291 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19672 2148 5 %RANDOM
Rwork0.16162 ---
obs0.16343 40811 97.81 %-
all-42325 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.28 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.5 Å2
2--0.01 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2867 0 10 486 3363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0212997
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9441.8834120
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7795375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72423.571140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.1915394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.351513
X-RAY DIFFRACTIONr_chiral_restr0.1460.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212389
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.2151.51810
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.94522920
X-RAY DIFFRACTIONr_scbond_it2.69331187
X-RAY DIFFRACTIONr_scangle_it3.7144.51194
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 149 -
Rwork0.357 2906 -
obs--95.62 %

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