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- PDB-1b3y: XYLANASE FROM PENICILLIUM SIMPLICISSIMUM, COMPLEX WITH XYLOTETRAOSE -

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Basic information

Entry
Database: PDB / ID: 1b3y
TitleXYLANASE FROM PENICILLIUM SIMPLICISSIMUM, COMPLEX WITH XYLOTETRAOSE
ComponentsPROTEIN (XYLANASE)
KeywordsFAMILY 10 XYLANASE / PENICILLIUM SIMPLICISSIMUM / GLYCOSYL HYDROLASE / SUBSTRATE BINDING
Function / homology
Function and homology information


endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / 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
4beta-beta-xylotriose / alpha-D-xylopyranose / : / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesPenicillium simplicissimum (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 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 6, 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: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (XYLANASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1313
Polymers32,5661
Non-polymers5642
Water4,576254
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.340, 81.340, 113.240
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: GenBank: AF070417, UniProt: P56588*PLUS, endo-1,4-beta-xylanase
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 414.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylotriose
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a212h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-XYS / alpha-D-xylopyranose / alpha-D-xylose / D-xylose / xylose / XYLOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-xylopyranoseCOMMON NAMEGMML 1.0
a-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsXYLOSE UNITS 557, 558 AND 559 BETA-1,4 LINKED

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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: 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: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→15 Å / Num. obs: 16297 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.116 / Net I/σ(I): 2
Reflection shellResolution: 2.45→2.5 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1 / Rsym value: 0.357 / % possible all: 95.6
Reflection
*PLUS
Rmerge(I) obs: 0.116
Reflection shell
*PLUS
% possible obs: 95.6 % / Rmerge(I) obs: 0.357

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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: 2.45→10 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
Rfree0.248 1633 10 %RANDOM
Rwork0.191 ---
obs-16086 99.6 %-
Refinement stepCycle: LAST / Resolution: 2.45→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 38 254 2596
LS refinement shellResolution: 2.45→2.54 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.335 223 10 %
Rwork0.239 1727 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.PYQTOPH19.SOL
X-RAY DIFFRACTION3PARAM19.SOLTOP.XYS_MONO
X-RAY DIFFRACTION4PARAM3.CHOTOP.PYQ
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.239

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