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- PDB-1nof: THE FIRST CRYSTALLOGRAPHIC STRUCTURE OF A XYLANASE FROM GLYCOSYL ... -

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Basic information

Entry
Database: PDB / ID: 1nof
TitleTHE FIRST CRYSTALLOGRAPHIC STRUCTURE OF A XYLANASE FROM GLYCOSYL HYDROLASE FAMILY 5: IMPLICATIONS FOR CATALYSIS
Componentsxylanase
KeywordsHYDROLASE / XYLANASE / GLYCOHYDROLASE FAMILY 5 / CARBOHYDRATE-BINDING MODULE / CATALYTIC DOMAIN
Function / homology
Function and homology information


glucosylceramidase activity / sphingolipid metabolic process / xylan catabolic process
Similarity search - Function
Glycosyl hydrolase family 30, TIM-barrel domain / Glycosyl hydrolase family 30 TIM-barrel domain / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycosyl hydrolase family 30, TIM-barrel domain / Glycosyl hydrolase family 30 TIM-barrel domain / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Xylanase
Similarity search - Component
Biological speciesErwinia chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.42 Å
AuthorsLarson, S.B. / Day, J. / McPherson, A. / Barba De La Rosa, A.P. / Keen, N.T.
Citation
Journal: Biochemistry / Year: 2003
Title: First crystallographic structure of a xylanase from glycoside hydrolase family 5: implications for catalysis.
Authors: Larson, S.B. / Day, J. / Barba de la Rosa, A.P. / Keen, N.T. / McPherson, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallization of Xylanase from Erwinia chrysanthemi: Influence of Heat and Polymeric Substrate
Authors: Barba De La Rosa, A.P. / Day, J. / Larson, S.B. / Keen, N.T. / McPherson, A.
#2: Journal: Mol.Plant Microbe Interact. / Year: 1996
Title: Cloning and Characterization of a Xylanase Gene from Corn Strains of Erwinia chrysanthemi
Authors: Keen, N.T. / Boyd, C. / Henrissat, B.
History
DepositionJan 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2012Group: Derived calculations
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1312
Polymers42,0721
Non-polymers591
Water9,404522
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.368, 49.580, 91.009
Angle α, β, γ (deg.)90.00, 101.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein xylanase


Mass: 42072.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Gene: xynA / Plasmid: pNTK136 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q46961, endo-1,4-beta-xylanase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE WATER MOLECULES HAVE BEEN NUMBERED TO REFLECT THEIR STATE 1001-1292 FIRST HYDRATION SHELL, FULL ...THE WATER MOLECULES HAVE BEEN NUMBERED TO REFLECT THEIR STATE 1001-1292 FIRST HYDRATION SHELL, FULL OCCUPANCY 2001-2048 FIRST HYDRATION SHELL, HALF OCCUPANCY 3001-4503 FIRST HYDRATION SHELL, DISORDERED (CONFLICT WITH DISORDERED PROTEIN OR WATER) 5001-5028 SECOND HYDRATION SHELL, FULL OCCUPANCY 6001-6060 SECOND HYDRATION SHELL, HALF OCCUPANCY 7001-7502 SECOND HYDRATION SHELL, DISORDERED (CONFLICT WITH OTHER WATER)
Sequence detailsTHE ENZYME USED IN THIS CRYSTALLOGRAPHIC STUDY IS A CLONE PRODUCT EXPRESSED IN E. COLI. UPON ...THE ENZYME USED IN THIS CRYSTALLOGRAPHIC STUDY IS A CLONE PRODUCT EXPRESSED IN E. COLI. UPON SECRETION FROM THE BACTERIAL PERIPLASM, THE FIRST 30 RESIDUES ARE CLEAVED FROM THE ENZYME. THUS, THE MODEL CONTAINS ONLY RESIDUES 31 THROUGH 413.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.74 Å3/Da / Density % sol: 29.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 30% PEG 4000, 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE, pH 6.5, VAPOR DIFFUSION, temperature 291K
Crystal grow
*PLUS
Details: Keen, N.T., (1996) Mol. Plant-Microbe Interact., 9, 651.

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Mar 1, 1996
RadiationMonochromator: SUPPER GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.42→44.57 Å / Num. all: 58915 / Num. obs: 58915 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.51 % / Biso Wilson estimate: 12.67 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.17
Reflection shellResolution: 1.42→1.52 Å / Redundancy: 1.91 % / Rmerge(I) obs: 0.132 / Mean I/σ(I) obs: 4.02 / Num. unique all: 8061 / % possible all: 55.8
Reflection
*PLUS
Num. measured all: 206521 / Rmerge(I) obs: 0.0656
Reflection shell
*PLUS
% possible obs: 61.9 % / Mean I/σ(I) obs: 3.14

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Processing

Software
NameVersionClassification
SOLVEphasing
PHASESphasing
X-PLOR3.851model building
SHELXL-97refinement
SDMSDETECTOR SYSTEMdata reduction
SDMSdata scaling
X-PLORV. 3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 1.42→50 Å / Num. parameters: 30307 / Num. restraintsaints: 37937 / Cross valid method: FREE R THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.161 5972 10.1 %RANDOM
Rwork0.102 ---
all0.108 58915 --
obs0.108 58915 90.6 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeLuzzati coordinate error obs: 0.07 Å / Luzzati d res low obs: 2 Å / Num. disordered residues: 28 / Occupancy sum hydrogen: 2893.99 / Occupancy sum non hydrogen: 3389.15
Refinement stepCycle: LAST / Resolution: 1.42→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2963 0 4 522 3489
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.018
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.056
X-RAY DIFFRACTIONs_approx_iso_adps0.136
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 9999 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.029
X-RAY DIFFRACTIONs_chiral_restr0.06

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