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- PDB-1f5j: CRYSTAL STRUCTURE OF XYNB, A HIGHLY THERMOSTABLE BETA-1,4-XYLANAS... -

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Basic information

Entry
Database: PDB / ID: 1f5j
TitleCRYSTAL STRUCTURE OF XYNB, A HIGHLY THERMOSTABLE BETA-1,4-XYLANASE FROM DICTYOGLOMUS THERMOPHILUM RT46B.1, AT 1.8 A RESOLUTION
ComponentsBETA-1,4-XYLANASE
KeywordsHYDROLASE / Xylanase / beta-barrel
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding
Similarity search - Function
Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / 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 ...Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / 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 / Galactose-binding-like domain superfamily / 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 speciesDictyoglomus thermophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsMcCarthy, A.A. / Baker, E.N.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Structure of XynB, a highly thermostable beta-1,4-xylanase from Dictyoglomus thermophilum Rt46B.1, at 1.8 A resolution.
Authors: McCarthy, A.A. / Morris, D.D. / Bergquist, P.L. / Baker, E.N.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallography & NMR system: A new software suite for macromolecular structure determination
Authors: Brunger, A.T. / Adams, P.D. / Clore, G.M. / Delano, W.L. / Gros, P. / Grosse-Kunstleve, R. / Jiang, J.-S. / Kuszewski, J. / Nilges, M. / Pannu, N.S. / Read, R.J. / Rice, L.M. / Simonson, T. / Warren, G.
History
DepositionJul 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: BETA-1,4-XYLANASE
B: BETA-1,4-XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8134
Polymers44,6212
Non-polymers1922
Water5,296294
1
A: BETA-1,4-XYLANASE


Theoretical massNumber of molelcules
Total (without water)22,3101
Polymers22,3101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BETA-1,4-XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5023
Polymers22,3101
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.290, 91.290, 44.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein BETA-1,4-XYLANASE


Mass: 22310.373 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyoglomus thermophilum (bacteria) / Strain: RT46B.1 / Plasmid: PJLA602 / Production host: Escherichia coli (E. coli) / References: UniProt: P77853, 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.: 294 / 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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.5-1.6 M ammonium sulphate, 0.2 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21.5-1.6 Mammonium sulfate1drop
30.2 MHEPES1drop
410 %glycerol1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 17, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 207114 / Num. obs: 34109 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 13
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 6 % / Rmerge(I) obs: 0.307 / % possible all: 97
Reflection
*PLUS
Num. measured all: 207114
Reflection shell
*PLUS
% possible obs: 97 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→19.86 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1922542.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3404 10 %RANDOM
Rwork0.185 ---
obs0.185 34109 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.18 Å2 / ksol: 0.417 e/Å3
Displacement parametersBiso mean: 13.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.97 Å20 Å20 Å2
2---2.97 Å20 Å2
3---5.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3174 0 10 295 3479
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it11.5
X-RAY DIFFRACTIONc_mcangle_it1.322
X-RAY DIFFRACTIONc_scbond_it1.632
X-RAY DIFFRACTIONc_scangle_it2.272.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.245 536 9.6 %
Rwork0.206 5030 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 13.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.245 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.206

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