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- PDB-2jem: Native family 12 xyloglucanase from Bacillus licheniformis -

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Basic information

Entry
Database: PDB / ID: 2jem
TitleNative family 12 xyloglucanase from Bacillus licheniformis
ComponentsENDO-BETA-1,4-GLUCANASE
KeywordsHYDROLASE / PLANT CELL WALL / GLYCOSIDASE / XYLOGLUCANASE / FAMILY 12
Function / homology
Function and homology information


cellulase / cellulase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBACILLUS LICHENIFORMIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsGloster, T.M. / Ibatullin, F.M. / Macauley, K. / Eklof, J.M. / Roberts, S. / Turkenburg, J.P. / Bjornvad, M.E. / Jorgensen, P.L. / Danielsen, S. / Johansen, K.S. ...Gloster, T.M. / Ibatullin, F.M. / Macauley, K. / Eklof, J.M. / Roberts, S. / Turkenburg, J.P. / Bjornvad, M.E. / Jorgensen, P.L. / Danielsen, S. / Johansen, K.S. / Borchert, T.V. / Wilson, K.S. / Brumer, H. / Davies, G.J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Characterization and Three-Dimensional Structures of Two Distinct Bacterial Xyloglucanases from Families Gh5 and Gh12.
Authors: Gloster, T.M. / Ibatullin, F.M. / Macauley, K. / Eklof, J.M. / Roberts, S. / Turkenburg, J.P. / Bjornvad, M.E. / Jorgensen, P.L. / Danielsen, S. / Johansen, K.S. / Borchert, T.V. / Wilson, K. ...Authors: Gloster, T.M. / Ibatullin, F.M. / Macauley, K. / Eklof, J.M. / Roberts, S. / Turkenburg, J.P. / Bjornvad, M.E. / Jorgensen, P.L. / Danielsen, S. / Johansen, K.S. / Borchert, T.V. / Wilson, K.S. / Brumer, H. / Davies, G.J.
History
DepositionJan 18, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,1842
Polymers58,1842
Non-polymers00
Water12,773709
1
A: ENDO-BETA-1,4-GLUCANASE


Theoretical massNumber of molelcules
Total (without water)29,0921
Polymers29,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ENDO-BETA-1,4-GLUCANASE


Theoretical massNumber of molelcules
Total (without water)29,0921
Polymers29,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.748, 78.133, 69.103
Angle α, β, γ (deg.)90.00, 109.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.989, -0.1362, 0.05756), (-0.1359, 0.6835, -0.7172), (0.05836, -0.7171, -0.6945)
Vector: 11.27, 18.66, 50.3)

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Components

#1: Protein ENDO-BETA-1,4-GLUCANASE / XYLOGLUCANASE


Mass: 29092.229 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS LICHENIFORMIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q7X4S4, cellulase, xyloglucan-specific endo-beta-1,4-glucanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 709 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 155 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 155 TO GLN

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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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.5
Details: 10% W/V PEG4000, 0.05 M MGCL2, 0.1 M BIS-TRIS, PH 6.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5472
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MULTILAYER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5472 Å / Relative weight: 1
ReflectionResolution: 1.78→20 Å / Num. obs: 44098 / % possible obs: 94.3 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 27.7
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.1 / % possible all: 81.5

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Processing

Software
NameVersionClassification
REFMAC5.3.0011refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NLR

1nlr


Resolution: 1.78→64.55 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.37 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1372 3.1 %RANDOM
Rwork0.155 ---
obs0.156 42703 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.07 Å2
2--0.77 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.78→64.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3694 0 0 709 4403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213989
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.361.8775498
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.085517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34224.794194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.01215590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.471159
X-RAY DIFFRACTIONr_chiral_restr0.1030.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023177
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.21895
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22736
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2540
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.265
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.771.52442
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.19623885
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.89331915
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6984.51587
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.83 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.353 84
Rwork0.25 2816

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