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- PDB-1xyf: ENDO-1,4-BETA-XYLANASE FROM STREPTOMYCES OLIVACEOVIRIDIS -

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Basic information

Entry
Database: PDB / ID: 1xyf
TitleENDO-1,4-BETA-XYLANASE FROM STREPTOMYCES OLIVACEOVIRIDIS
ComponentsENDO-1,4-BETA-XYLANASE
KeywordsHYDROLASE / Xylan degradation
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Ricin-type beta-trefoil lectin domain / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. ...Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Ricin-type beta-trefoil lectin domain / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces olivaceoviridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFujimoto, Z. / Mizuno, H. / Kuno, A. / Kusakabe, I.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of Streptomyces olivaceoviridis E-86 beta-xylanase containing xylan-binding domain.
Authors: Fujimoto, Z. / Kuno, A. / Kaneko, S. / Yoshida, S. / Kobayashi, H. / Kusakabe, I. / Mizuno, H.
#1: Journal: J.Biochem.(Tokyo) / Year: 1997
Title: Crystallization and Preliminary X-Ray Crystallographic Study of Streptomyces olivaceoviridis E-86 Xylanase
Authors: Fujimoto, Z. / Mizuno, H. / Kuno, A. / Yoshida, S. / Kobayashi, H. / Kusakabe, I.
History
DepositionMay 11, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDO-1,4-BETA-XYLANASE
B: ENDO-1,4-BETA-XYLANASE


Theoretical massNumber of molelcules
Total (without water)93,5822
Polymers93,5822
Non-polymers00
Water8,881493
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.770, 95.010, 141.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.424, -0.9053, 0.0249), (-0.9055, 0.4232, -0.0302), (-0.0168, -0.0354, -0.9992)
Vector: 77.1208, 52.3547, 148.37489)

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Components

#1: Protein ENDO-1,4-BETA-XYLANASE


Mass: 46791.223 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, XYLAN-BINDING DOMAIN / Source method: isolated from a natural source / Source: (natural) Streptomyces olivaceoviridis (bacteria) / Strain: E-86 / References: UniProt: Q7SI98, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58 %
Crystal growpH: 5.7
Details: 25% SATURATED AMMONIUM SULFATE, 2% MCILVAINE BUFFER PH 5.7
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
225 %satammonium sulfate1reservoir
30.1 Mcitric acid1reservoir
40.2 Msodium phosphate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorDate: Dec 1, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 80196 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 22.4
Reflection shellResolution: 1.9→1.971 Å / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 4.9 / % possible all: 77.7
Reflection
*PLUS
Num. measured all: 441579

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XAS, 2EXO

1xas

2exo


Resolution: 1.9→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3816 5.1 %RANDOM
Rwork0.197 ---
obs-75408 90 %-
Displacement parametersBiso mean: 21.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-6 Å
Luzzati sigma a0.39 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6470 0 0 493 6963
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.27
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.011.5
X-RAY DIFFRACTIONx_mcangle_it2.832
X-RAY DIFFRACTIONx_scbond_it3.462
X-RAY DIFFRACTIONx_scangle_it4.612.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 489 4.7 %
Rwork0.304 9865 -
obs--75.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19X.SOL
X-RAY DIFFRACTION3TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5.1 % / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.27
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Lowest resolution: 1.97 Å / Rfactor Rfree: 0.353 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.304 / Rfactor obs: 0.305

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