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- PDB-1aq0: BARLEY 1,3-1,4-BETA-GLUCANASE IN MONOCLINIC SPACE GROUP -

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Basic information

Entry
Database: PDB / ID: 1aq0
TitleBARLEY 1,3-1,4-BETA-GLUCANASE IN MONOCLINIC SPACE GROUP
Components1,3-1,4-BETA-GLUCANASE
KeywordsHYDROLASE / GLYCOSIDASE / GLYCOPROTEIN / GLYCOSYLATED PROTEIN
Function / homologyGlycoside hydrolase family 17 / Glycoside hydrolase superfamily / Glycosyl hydrolases family 17 / Glycosyl hydrolases family 17 signature. / licheninase / licheninase activity / carbohydrate metabolic process / Lichenase-2
Function and homology information
Specimen sourceHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 2 Å resolution
AuthorsMueller, J.J. / Thomsen, K.K. / Heinemann, U.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: Crystal structure of barley 1,3-1,4-beta-glucanase at 2.0-A resolution and comparison with Bacillus 1,3-1,4-beta-glucanase.
Authors: Muller, J.J. / Thomsen, K.K. / Heinemann, U.
#1: Journal: Plant Physiol.Biochem. (Paris) / Year: 1995
Title: Analysis of Glycan Structures of Barley (1-3,1-4)-Beta-D Glucan 4-Glucanohydrolase Isoenzyme Eii
Authors: Harthill, J.E. / Thomsen, K.K.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of Barley (1-3,1-4)-Beta-Glucanase, Isoenzyme II
Authors: Keitel, T. / Thomsen, K.K. / Heinemann, U.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 5, 1997 / Release: Feb 11, 1998
RevisionDateData content typeGroupProviderType
1.0Feb 11, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1,3-1,4-BETA-GLUCANASE
B: 1,3-1,4-BETA-GLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2868
Polyers64,2832
Non-polymers1,0036
Water7,530418
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)49.580, 82.990, 77.560
Angle α, β, γ (deg.)90.00, 104.36, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

#1: Protein/peptide 1,3-1,4-BETA-GLUCANASE / 1 / 3-1 / 4-BETA-D-GLUCAN 4-GLUCANOHYDROLASE


Mass: 32141.320 Da / Num. of mol.: 2 / Details: ISOENZYME 2 / Source: (natural) Hordeum vulgare (barley) / Genus: Hordeum / References: UniProt: P12257, licheninase
#2: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 4 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Formula: C2H3O2 / Acetate
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Formula: H2O / Water

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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: 2.41 / Density percent sol: 25.2 %
Crystal growMethod: vapor diffusion / pH: 5.8
Details: PROTEIN SOLUTION: 20MM NAOAC/HOAC (PH 4.6), 2MM CACL2, C=60MG/ML. DROPLETS SIZE: 0.001 ML PROTEIN SOLUTION, 0.001 ML RESERVOIR SOLUTION; RESERVOIR SOLUTION: 100MM NAOAC/HOAC (PH 5.8), 20%(W/W) POLYETHYLENE GLYCOL 8000; VAPOUR DIFFUSION, FOUR DAYS, vapor diffusion
Crystal grow
*PLUS
Method: vapor diffusion / Details: Keitel, T., (1993) J.Mol.Biol., 232, 1003.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
130 mg/mlprotein1drop
260 mM1dropNaOAc
31 mM1dropCaCl2
410 %(w/w)PEG80001drop
5100 mM1reservoirNaOAc
620 %(w/w)PEG80001reservoir

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Data collection

DiffractionMean temperature: 294.2 kelvins
SourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Details: PINHOLE / Detector: IMAGE PLATE / Collection date: Oct 1, 1992
RadiationMonochromator: GRAPHITE(002) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 14.35 Å2 / D resolution high: 2 Å / D resolution low: 13.65 Å / Number obs: 40727 / Observed criterion sigma I: 2 / Rsym value: 0.081 / Percent possible obs: 99.21
Reflection shellHighest resolution: 2 Å / Lowest resolution: 2.09 Å / Percent possible all: 96.61
Reflection
*PLUS
Rmerge I obs: 0.081

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GHR
R Free selection details: RANDOM / Data cutoff high absF: 1 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / Sigma F: 2
Displacement parametersB iso mean: 14.2 Å2
Least-squares processR factor R free: 0.213 / R factor R free error: 0.0058 / R factor R work: 0.17 / R factor obs: 0.17 / Highest resolution: 2 Å / Lowest resolution: 13.6 Å / Number reflection R free: 1363 / Number reflection obs: 40727 / Percent reflection R free: 3 / Percent reflection obs: 99.3
Refine analyzeLuzzati coordinate error free: 0.2 Å / Luzzati coordinate error obs: 0.19 Å / Luzzati d res low obs: 13.6 Å
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 13.6 Å
Number of atoms included #LASTProtein: 4528 / Nucleic acid: 0 / Ligand: 64 / Solvent: 418 / Total: 5010
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.314
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.06
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.184
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
Refine LS restraints ncsNcs model details: RESTRAINTS
Refine LS shellHighest resolution: 2 Å / R factor R free: 0.1932 / R factor R free error: 0.015 / R factor R work: 0.2089 / Lowest resolution: 2.09 Å / Number reflection R free: 171 / Number reflection R work: 4760 / Total number of bins used: 8 / Percent reflection R free: 3 / Percent reflection obs: 96.61
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Least-squares process
*PLUS
R factor R work: 0.17 / R factor obs: 0.17
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.06
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.184

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