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- PDB-1b31: XYLANASE FROM PENICILLIUM SIMPLICISSIMUM, NATIVE WITH PEG200 AS C... -

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Basic information

Entry
Database: PDB / ID: 1b31
TitleXYLANASE FROM PENICILLIUM SIMPLICISSIMUM, NATIVE WITH PEG200 AS CRYOPROTECTANT
ComponentsPROTEIN (XYLANASE)
KeywordsFAMILY 10 XYLANASE / PENICILLIUM SIMPLICISSIMUM / GLYCOSYL HYDROLASE / SUBSTRATE BINDING
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
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesPenicillium simplicissimum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSchmidt, A. / Kratky, C.
Citation
Journal: Biochemistry / Year: 1999
Title: Xylan binding subsite mapping in the xylanase from Penicillium simplicissimum using xylooligosaccharides as cryo-protectant.
Authors: Schmidt, A. / Gubitz, G.M. / Kratky, C.
#1: Journal: Protein Sci. / Year: 1998
Title: Structure of the Xylanase from Penicillium Simplicissimum
Authors: Schmidt, A. / Schlacher, A. / Steiner, W. / Schwab, H. / Kratky, C.
History
DepositionDec 15, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 7, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: diffrn_source / entity_poly ...diffrn_source / entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can ..._diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (XYLANASE)


Theoretical massNumber of molelcules
Total (without water)32,5661
Polymers32,5661
Non-polymers00
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.188, 81.188, 113.042
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PROTEIN (XYLANASE)


Mass: 32566.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PENICILLIUM SIMPLICISSIMUM (OUDEM.) THOM. / Source: (natural) Penicillium simplicissimum (fungus) / Cellular location: SECRETED / References: UniProt: P56588, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 62 %
Crystal growpH: 8.4
Details: CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 1.9M (NH4)2SO4, 0.1M TRISHCL PH 8.4 AT 4 C
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13-6 mg/mlprotein1drop
21.9 Mammonium sulfate1reservoir
30.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9058
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9058 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. obs: 47863 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rsym value: 0.083 / Net I/σ(I): 3
Reflection shellResolution: 1.7→1.72 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1 / Rsym value: 0.398 / % possible all: 99.4
Reflection
*PLUS
Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 99.4 % / Rmerge(I) obs: 0.398

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BG4

1bg4


Resolution: 1.75→15 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: FREE R THROUGHOUT / σ(F): 0
Details: PARAMETER/TOPOLOGY FILES FOR HET GROUPS EXCEPT WATER SELF-SETUP
RfactorNum. reflection% reflectionSelection details
Rfree0.243 4485 10 %RANDOM
Rwork0.213 ---
obs-43914 99.8 %-
Refinement stepCycle: LAST / Resolution: 1.75→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2307 0 0 352 2659
LS refinement shellResolution: 1.75→1.83 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.297 534 10 %
Rwork0.274 4879 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.PYQTOPH19.SOL
X-RAY DIFFRACTION3PARAM19.SOLTOP.PYQ
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.274

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