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- PDB-1ukr: STRUCTURE OF ENDO-1,4-BETA-XYLANASE C -

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Basic information

Entry
Database: PDB / ID: 1ukr
TitleSTRUCTURE OF ENDO-1,4-BETA-XYLANASE C
ComponentsENDO-1,4-B-XYLANASE I
KeywordsHYDROLASE / XYLAN DEGRADATION / GLYCOSIDASE
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region
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 A
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKrengel, U. / Dijkstra, B.W.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Three-dimensional structure of Endo-1,4-beta-xylanase I from Aspergillus niger: molecular basis for its low pH optimum.
Authors: Krengel, U. / Dijkstra, B.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization and Preliminary Crystallographic Analysis of Endo-1,4-Beta-Xyalanase I from Aspergillus Niger
Authors: Krengel, U. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W.
History
DepositionAug 23, 1996Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDO-1,4-B-XYLANASE I
B: ENDO-1,4-B-XYLANASE I
C: ENDO-1,4-B-XYLANASE I
D: ENDO-1,4-B-XYLANASE I


Theoretical massNumber of molelcules
Total (without water)79,4244
Polymers79,4244
Non-polymers00
Water5,188288
1
A: ENDO-1,4-B-XYLANASE I


Theoretical massNumber of molelcules
Total (without water)19,8561
Polymers19,8561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ENDO-1,4-B-XYLANASE I


Theoretical massNumber of molelcules
Total (without water)19,8561
Polymers19,8561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ENDO-1,4-B-XYLANASE I


Theoretical massNumber of molelcules
Total (without water)19,8561
Polymers19,8561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ENDO-1,4-B-XYLANASE I


Theoretical massNumber of molelcules
Total (without water)19,8561
Polymers19,8561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.300, 85.300, 113.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ENDO-1,4-B-XYLANASE I / XYLANASE


Mass: 19855.941 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Production host: Escherichia coli (E. coli) / References: UniProt: P55329, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growMethod: vapor diffusion - sitting drop - macroseeding / pH: 4.7
Details: SITTING DROP SETUP USING SILICONIZED GLASS WELLS USING 15 MICROLITER DROPS AT ROOM TEMPERATURE AND MACROSEEDING. PROTEIN SOLUTION: 4.5 MG/ML IN 10 MM NA ACETATE PH 4.7. RESERVOIR SOLUTION: 1. ...Details: SITTING DROP SETUP USING SILICONIZED GLASS WELLS USING 15 MICROLITER DROPS AT ROOM TEMPERATURE AND MACROSEEDING. PROTEIN SOLUTION: 4.5 MG/ML IN 10 MM NA ACETATE PH 4.7. RESERVOIR SOLUTION: 1.5 ML 1.8 M NA2S2O3 (PH 8.0)., vapor diffusion - sitting drop - macroseeding
Temp details: room temp
Crystal grow
*PLUS
Temperature: 295, 277, 310 K / Method: vapor diffusion, hanging drop / Details: or sitting drop vapor diffusion or batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.5 mg/mlprotein1drop
210 mMsodium acetate1drop

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.35→38.06 Å / Num. obs: 33131 / % possible obs: 95.3 % / Redundancy: 4.6 % / Rsym value: 0.082
Reflection
*PLUS
Rmerge(I) obs: 0.082

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Processing

Software
NameVersionClassification
XDSdata scaling
BRUTEmodel building
X-PLOR3.1refinement
XDSdata reduction
BRUTEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TRICHODERMA HARZIANUM XYLANASE, PDB ENTRY 1XND.

1xnd


Resolution: 2.4→6 Å / σ(F): 0
Details: REFINEMENT INCLUDED NCS-RESTRAINTS AT PLACES WITHOUT CRYSTAL CONTACTS. ONLY IN THE FINAL REFINEMENT CYCLE ALL DATA WERE INCLUDED. IN THE EARLIER STAGES OF REFINEMENT, 10% OF THE DATA WERE ...Details: REFINEMENT INCLUDED NCS-RESTRAINTS AT PLACES WITHOUT CRYSTAL CONTACTS. ONLY IN THE FINAL REFINEMENT CYCLE ALL DATA WERE INCLUDED. IN THE EARLIER STAGES OF REFINEMENT, 10% OF THE DATA WERE TAKEN TO CALCULATE A FREE R-FACTOR (R=17.7 AND RFREE=21.9 %, RESPECTIVELY).
RfactorNum. reflection
Rwork0.179 -
obs0.179 28728
Displacement parametersBiso mean: 19.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5556 0 0 288 5844
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.295
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.882
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.882

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