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- PDB-1bg4: XYLANASE FROM PENICILLIUM SIMPLICISSIMUM -

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Basic information

Entry
Database: PDB / ID: 1bg4
TitleXYLANASE FROM PENICILLIUM SIMPLICISSIMUM
ComponentsENDO-1,4-BETA-XYLANASEXylanase
KeywordsFAMILY 10 XYLANASE / PENICILLIUM SIMPLICISSIMUM / TIM-BARREL / GLYCOSYL HYDROLASE
Function / homologyGlycoside hydrolase family 10 domain / Glycoside hydrolase superfamily / Glycosyl hydrolases family 10, active site / Glycosyl hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process / extracellular region / Endo-1,4-beta-xylanase
Function and homology information
Specimen sourcePenicillium simplicissimum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.75 Å resolution
AuthorsSchmidt, A. / Kratky, C.
CitationJournal: Protein Sci. / Year: 1998
Title: Structure of the xylanase from Penicillium simplicissimum.
Authors: Schmidt, A. / Schlacher, A. / Steiner, W. / Schwab, H. / Kratky, C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 5, 1998 / Release: Aug 12, 1998
RevisionDateData content typeGroupProviderType
1.0Aug 12, 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: ENDO-1,4-BETA-XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,59316
Polyers32,5661
Non-polymers1,02715
Water5,693316
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)81.020, 81.020, 113.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP 31 2 1

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Components

#1: Protein/peptide ENDO-1,4-BETA-XYLANASE / Xylanase


Mass: 32566.473 Da / Num. of mol.: 1 / Source: (natural) Penicillium simplicissimum (fungus) / Details: PENICILLIUM SIMPLICISSIMUM (OUDEM.) THOM / Genus: Penicillium / Cellular location: SECRETEDSecretion / References: UniProt: P56588, endo-1,4-beta-xylanase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Formula: Na / Sodium
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Formula: C4H12NO3 / Tris / Comment: pH buffer *YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Formula: C3H8O3 / Glycerol
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 3.25 / Density percent sol: 62 %
Description: DATA WERE COLLECTED AT THE ELETTRA SYNCHROTRON LIGHT SOURCE, TRIESTE, ITALY
Crystal growTemp: 277 K / pH: 8.4
Details: PROTEIN WAS CRYSTALLIZED FROM 1.9M (NH4)2SO4, 0.1M TRISHCL PH 8.4 AT 4 C, temperature 277K
Crystal grow
*PLUS
Temp: 4 ℃ / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
11.9 Mammonium sulfate1reservoir
20.1 MTris-HCl1reservoir
33-6 mg/mlpyrazole1drop

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.85
DetectorType: MARRESEARCH / Details: TOROIDAL MIRROR / Detector: IMAGE PLATE AREA DETECTOR / Collection date: Jul 1, 1997
RadiationMonochromator: SI(111) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 11.6 Å2 / D resolution high: 1.75 Å / D resolution low: 1 Å / Number obs: 43712 / Observed criterion sigma I: -3 / Rsym value: 0.059 / NetI over sigmaI: 15 / Redundancy: 5 % / Percent possible obs: 100
Reflection shellHighest resolution: 1.75 Å / Lowest resolution: 1.79 Å / MeanI over sigI obs: 4 / Rsym value: 0.232 / Redundancy: 5 % / Percent possible all: 100
Reflection
*PLUS
Rmerge I obs: 0.059
Reflection shell
*PLUS
Percent possible obs: 100 / Rmerge I obs: 0.232

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XYZ
Details: PARAMETER/TOPOLOGY FILES FOR HET GROUPS EXCEPT WATER SELF-SETUP
R Free selection details: RANDOM / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: FREE R THROUGHOUT / Sigma F: 0
Displacement parametersB iso mean: 10 Å2
Least-squares processR factor R free: 0.229 / R factor R free error: 0.0034 / R factor R work: 0.2 / R factor obs: 0.2 / Highest resolution: 1.75 Å / Lowest resolution: 1 Å / Number reflection R free: 4462 / Number reflection obs: 43712 / Percent reflection R free: 1 / Percent reflection obs: 100
Refine hist #LASTHighest resolution: 1.75 Å / Lowest resolution: 1 Å
Number of atoms included #LASTProtein: 2298 / Nucleic acid: 0 / Ligand: 64 / Solvent: 316 / Total: 2678
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.5321.50
X-RAY DIFFRACTIONx_mcangle_it2.8442.0
X-RAY DIFFRACTIONx_scbond_it3.4412.0
X-RAY DIFFRACTIONx_scangle_it3.9232.5
Refine LS shellHighest resolution: 1.75 Å / R factor R free: 0.285 / R factor R free error: 0.011 / R factor R work: 0.268 / Lowest resolution: 1.83 Å / Number reflection R free: 548 / Number reflection R work: 4840 / Total number of bins used: 8 / Percent reflection R free: 1 / Percent reflection obs: 100
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.PYQTOPH19.SOL
X-RAY DIFFRACTION3PARAM19.SOLTOP.GLYC
X-RAY DIFFRACTION4PARAM.GLYTOP.PYQ
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS shell
*PLUS
R factor obs: 0.268

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