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- PDB-3vpl: Crystal structure of a 2-fluoroxylotriosyl complex of the Vibrio ... -

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Basic information

Entry
Database: PDB / ID: 3vpl
TitleCrystal structure of a 2-fluoroxylotriosyl complex of the Vibrio sp. AX-4 Beta-1,3-xylanase
ComponentsBeta-1,3-xylanase XYL4
KeywordsHYDROLASE / beta-1 / 3-xylanase / glycoside hydrolase / TIM barrel
Function / homology
Function and homology information


endo-1,3-beta-xylanase / xylan endo-1,3-beta-xylosidase activity / substituted mannan metabolic process / mannan endo-1,4-beta-mannosidase activity / xylan catabolic process / polysaccharide binding / cellulose catabolic process
Similarity search - Function
Beta-1,3-xylanase / Beta-1,3-xylanase, CBM31 domain superfamily / Family 31 carbohydrate binding protein / Glycoside hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
3,4-dinitrophenol / Beta-1,3-xylanase XYL4
Similarity search - Component
Biological speciesVibrio (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsWatanabe, N. / Sakaguchi, K.
Citation
Journal: To be Published
Title: The crystal structure of a 2-fluoroxylotriosyl complex of the Vibrio sp. AX-4 beta-1,3-xylanase at 1.2 A resolution
Authors: Sakaguchi, K. / Goddard-Borger, E.D. / Kawamura, T. / Kiyohara, M. / Tanaka, I. / Ito, M. / Withers, S.G. / Watanabe, N.
#1: Journal: J.Am.Chem.Soc. / Year: 2012
Title: Mechanistic insights into the 1,3-xylanases: useful enzymes for manipulation of algal biomass
Authors: Goddard-Borger, E.D. / Sakaguchi, K. / Reitinger, S. / Watanabe, N. / Ito, M. / Withers, S.G.
History
DepositionMar 5, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-1,3-xylanase XYL4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9534
Polymers36,9361
Non-polymers1,0173
Water9,206511
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.343, 75.437, 81.646
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-1,3-xylanase XYL4 / Beta-1 / 3-xylanase


Mass: 36936.336 Da / Num. of mol.: 1 / Fragment: UNP residues 23-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio (bacteria) / Strain: AX-4 / Gene: xyl4 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: D5MP61, endo-1,3-beta-xylanase
#2: Polysaccharide beta-D-xylopyranose-(1-3)-beta-D-xylopyranose-(1-3)-2-deoxy-2-fluoro-beta-D-xylopyranose


Type: oligosaccharide / Mass: 416.351 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a212h-1b_1-5_2*F][a212h-1b_1-5]/1-2-2/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][<C5O2F1>]{[(1+1)][b-D-Xylp]{[(3+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-3)-2-deoxy-2-fluoro-beta-D-xylopyranose


Type: oligosaccharide / Mass: 416.351 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a212h-1b_1-5_2*F][a212h-1b_1-5]/1-2-2/a3-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][<C5O2F1>]{[(1+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-DNX / 3,4-dinitrophenol


Mass: 184.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4N2O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE GLU212 ATTACKS AND BREAKS THE BOND BETWEEN BXF-DNX AND A NEW BOND BETWEEN BXF(A1001)-GLU212 IS ...THE GLU212 ATTACKS AND BREAKS THE BOND BETWEEN BXF-DNX AND A NEW BOND BETWEEN BXF(A1001)-GLU212 IS FORMED, AND THE ENZYME REACTION WAS STOPPED AT A GLYCOSYL-ENZYME INTERMEDIATE STATE.

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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: 2.18 Å3/Da / Density % sol: 43.63 % / Mosaicity: 0.174 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.0M sodium citrate, 0.1M MES, pH 6.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 101571 / Num. obs: 98695 / % possible obs: 97.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.044 / Χ2: 1.305 / Net I/σ(I): 14.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.2-1.227.20.25747491.047194.6
1.22-1.247.40.24247891.074195.1
1.24-1.277.40.22247621.09195.2
1.27-1.297.40.19748291.137195.4
1.29-1.327.40.18247891.147195.7
1.32-1.357.40.16548441.174196
1.35-1.397.40.15248281.208196.1
1.39-1.427.40.13248531.24196.7
1.42-1.467.40.11548941.279196.6
1.46-1.517.40.09848991.276196.9
1.51-1.577.40.08448841.321197.3
1.57-1.637.40.07449481.333197.5
1.63-1.77.40.06549741.348197.8
1.7-1.797.40.05749751.377198.2
1.79-1.97.30.05349991.569198.3
1.9-2.057.30.0550201.915198.8
2.05-2.267.20.04350911.867199.1
2.26-2.597.10.03351031.413199.2
2.59-3.267.10.02751831.189199.4
3.26-506.90.02452821.039197.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
KEK-PFBEAMLINE SOFTWAREdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ddx

2ddx


Resolution: 1.2→29.61 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.426 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.15607 4931 5 %RANDOM
Rwork0.14079 ---
obs0.14156 98433 96.9 %-
all-101571 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.28 Å2 / Biso mean: 12.5689 Å2 / Biso min: 4.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.2→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 67 511 3118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.022879
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4341.9473999
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0935386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06325146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95715415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.131513
X-RAY DIFFRACTIONr_chiral_restr0.2580.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0212307
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 331 -
Rwork0.171 6375 -
obs--94.25 %

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