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- PDB-3mf9: Computationally designed endo-1,4-beta-xylanase -

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Basic information

Entry
Database: PDB / ID: 3mf9
TitleComputationally designed endo-1,4-beta-xylanase
ComponentsEndo-1,4-beta-xylanaseXylanase
KeywordsHYDROLASE / peptide binding / jelly-role / family 11 / thumb / Glycosidase / Xylan degradation
Function / homology
Function and homology information


polysaccharide binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 ...Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / CBM2/CBM3, carbohydrate-binding domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesThermopolyspora flexuosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMorin, A. / Harp, J.M.
CitationJournal: Protein Eng.Des.Sel. / Year: 2011
Title: Computational design of an endo-1,4-{beta}-xylanase ligand binding site.
Authors: Morin, A. / Kaufmann, K.W. / Fortenberry, C. / Harp, J.M. / Mizoue, L.S. / Meiler, J.
History
DepositionApr 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)21,6114
Polymers21,3231
Non-polymers2883
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.778, 63.778, 106.234
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 Endo-1,4-beta-xylanase / Xylanase


Mass: 21323.033 Da / Num. of mol.: 1 / Fragment: UNP residues 44-234 / Mutation: W21R,N47L,Y75R,E88S,Y90H,F134Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermopolyspora flexuosa (bacteria) / Gene: xyn11A / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8GMV7, endo-1,4-beta-xylanase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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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: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10mg.mL protein conc., 0.1 M NaCl, 1.125 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 3% Jeffamine M600 pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Mar 1, 2009
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→55.23 Å / Num. all: 26750 / Num. obs: 26745 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.744 Å

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
REFMAC5.5.0102refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→55.23 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.779 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.172 1417 5 %RANDOM
Rwork0.12802 ---
all0.13015 26750 --
obs0.13015 26745 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.363 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.13 Å2-0 Å2
2--0.27 Å2-0 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.7→55.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1507 0 15 202 1724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0211617
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.9072221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7245212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28622.59777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.59215231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2541512
X-RAY DIFFRACTIONr_chiral_restr0.2130.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021280
X-RAY DIFFRACTIONr_mcbond_it2.4691.5973
X-RAY DIFFRACTIONr_mcangle_it3.48721575
X-RAY DIFFRACTIONr_scbond_it5.3053644
X-RAY DIFFRACTIONr_scangle_it7.1964.5636
X-RAY DIFFRACTIONr_rigid_bond_restr3.2131617
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 108 -
Rwork0.181 1934 -
obs--100 %

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