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- PDB-7dfm: Crystal structure of glycoside hydrolase family 11 beta-xylanase ... -

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Basic information

Entry
Database: PDB / ID: 7dfm
TitleCrystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / glycoside hydrolase family 11
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, 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 / Twin arginine translocation (Tat) signal profile. ...Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesStreptomyces olivaceoviridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFujimoto, Z. / Kishine, N. / Kaneko, S.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2021
Title: Structure-based substrate specificity analysis of GH11 xylanase from Streptomyces olivaceoviridis E-86.
Authors: Fujimoto, Z. / Kishine, N. / Teramoto, K. / Tsutsui, S. / Kaneko, S.
History
DepositionNov 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: Endo-1,4-beta-xylanase
C: Endo-1,4-beta-xylanase
D: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,92926
Polymers90,1494
Non-polymers78022
Water2,450136
1
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7868
Polymers22,5371
Non-polymers2487
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area7980 Å2
MethodPISA
2
B: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6795
Polymers22,5371
Non-polymers1424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area7890 Å2
MethodPISA
3
C: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7507
Polymers22,5371
Non-polymers2136
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area8010 Å2
MethodPISA
4
D: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7156
Polymers22,5371
Non-polymers1775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area8120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.039, 135.039, 72.343
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Endo-1,4-beta-xylanase


Mass: 22537.367 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: GB LC578783
Source: (gene. exp.) Streptomyces olivaceoviridis (bacteria)
Strain: E-86 / Gene: soxB / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A7G1MBT0*PLUS, endo-1,4-beta-xylanase
#2: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.11 Å3/Da / Density % sol: 41.77 % / Description: needle
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 2.9 M sodium chloride, 0.1 M sodium citrate buffer pH 5.4

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. obs: 30040 / % possible obs: 100 % / Redundancy: 19.3 % / Rmerge(I) obs: 0.225 / Net I/σ(I): 10.8
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2952

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HIX

1hix


Resolution: 2.4→49.409 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.141 / SU B: 8.897 / SU ML: 0.199 / Average fsc free: 0.906 / Average fsc work: 0.9307 / Cross valid method: THROUGHOUT / ESU R: 0.518 / ESU R Free: 0.278
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2449 1571 5.236 %
Rwork0.1678 28432 -
all0.172 --
obs-30003 99.983 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.848 Å2
Baniso -1Baniso -2Baniso -3
1--0.013 Å2-0.006 Å20 Å2
2---0.013 Å20 Å2
3---0.041 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5986 0 22 136 6144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0126162
X-RAY DIFFRACTIONr_bond_other_d0.0010.0185010
X-RAY DIFFRACTIONr_angle_refined_deg1.8961.6518394
X-RAY DIFFRACTIONr_angle_other_deg1.3951.56911610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0875770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15322.25320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6315836
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1361528
X-RAY DIFFRACTIONr_chiral_restr0.0720.2770
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027194
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021514
X-RAY DIFFRACTIONr_nbd_refined0.1860.2989
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.24574
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22894
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.22987
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2197
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.110.212
X-RAY DIFFRACTIONr_nbd_other0.1590.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2240.28
X-RAY DIFFRACTIONr_mcbond_it2.6942.8383092
X-RAY DIFFRACTIONr_mcbond_other2.6842.8373091
X-RAY DIFFRACTIONr_mcangle_it3.8634.2483858
X-RAY DIFFRACTIONr_mcangle_other3.8634.253859
X-RAY DIFFRACTIONr_scbond_it3.0643.0333070
X-RAY DIFFRACTIONr_scbond_other3.0643.0353071
X-RAY DIFFRACTIONr_scangle_it4.3984.4494536
X-RAY DIFFRACTIONr_scangle_other4.3984.4514537
X-RAY DIFFRACTIONr_lrange_it5.8130.7946803
X-RAY DIFFRACTIONr_lrange_other5.8430.86801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.291040.2612087X-RAY DIFFRACTION100
2.462-2.530.3311310.2522009X-RAY DIFFRACTION100
2.53-2.6030.3451230.2331978X-RAY DIFFRACTION100
2.603-2.6830.3651060.2061898X-RAY DIFFRACTION100
2.683-2.7710.275990.1941854X-RAY DIFFRACTION100
2.771-2.8680.247820.1811827X-RAY DIFFRACTION100
2.868-2.9770.28810.181732X-RAY DIFFRACTION100
2.977-3.0980.2931060.1741683X-RAY DIFFRACTION100
3.098-3.2360.25820.1751611X-RAY DIFFRACTION100
3.236-3.3930.2481020.1641528X-RAY DIFFRACTION100
3.393-3.5770.25940.1571454X-RAY DIFFRACTION100
3.577-3.7940.224780.1411395X-RAY DIFFRACTION100
3.794-4.0550.227700.141312X-RAY DIFFRACTION100
4.055-4.380.167790.1151218X-RAY DIFFRACTION100
4.38-4.7970.169590.1171128X-RAY DIFFRACTION100
4.797-5.3620.187540.1461024X-RAY DIFFRACTION100
5.362-6.190.258400.178924X-RAY DIFFRACTION100
6.19-7.5750.23320.166792X-RAY DIFFRACTION100
7.575-10.6910.185350.139612X-RAY DIFFRACTION100
10.691-49.4090.269140.256367X-RAY DIFFRACTION98.7047

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