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- PDB-2uwa: Crystal structure of the Nasturtium seedling xyloglucanase isofor... -

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Basic information

Entry
Database: PDB / ID: 2uwa
TitleCrystal structure of the Nasturtium seedling xyloglucanase isoform NXG1
ComponentsCELLULASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / XYLOGLUCAN-ENDO-TRANSFERASE / GLYCOSIDASE / FAMILY GH16 / TROPAEOLUM MAJUS XYLOGLUCANASE
Function / homology
Function and homology information


xyloglucan:xyloglucosyl transferase / xyloglucan:xyloglucosyl transferase activity / xyloglucan metabolic process / cell wall biogenesis / apoplast / hydrolase activity, hydrolyzing O-glycosyl compounds / cell wall organization / metal ion binding
Similarity search - Function
Xyloglucan endo-transglycosylase, C-terminal / Xyloglucan endotransglucosylase/hydrolase / Xyloglucan endo-transglycosylase (XET) C-terminus / Beta-glucanase/XTH / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Xyloglucan endo-transglycosylase, C-terminal / Xyloglucan endotransglucosylase/hydrolase / Xyloglucan endo-transglycosylase (XET) C-terminus / Beta-glucanase/XTH / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Xyloglucan endotransglucosylase/hydrolase
Similarity search - Component
Biological speciesTROPAEOLUM MAJUS (nasturtium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBaumann, M.J. / Eklof, J. / Michel, G. / Kallasa, A. / Teeri, T.T. / Brumer, H. / Czjzek, M.
CitationJournal: Plant Cell / Year: 2007
Title: Structural Evidence for the Evolution of Xyloglucanase Activity from Xyloglucan Endo-Transglycosylases: Biological Implications for Cell Wall Metabolism.
Authors: Baumann, M.J. / Eklof, J. / Michel, G. / Kallasa, A. / Teeri, T.T. / Czjzek, M. / Brumer, H.
History
DepositionMar 19, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 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: CELLULASE
B: CELLULASE
C: CELLULASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1177
Polymers93,7483
Non-polymers3684
Water7,981443
1
A: CELLULASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4343
Polymers31,2491
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CELLULASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3422
Polymers31,2491
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: CELLULASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3422
Polymers31,2491
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)116.109, 116.109, 63.071
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 5 / Auth seq-ID: 1 - 271 / Label seq-ID: 4 - 274

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

NCS oper:
IDCodeMatrixVector
1given(0.91717, 0.39843, -0.00429), (0.39847, -0.91716, 0.00799), (-0.00712, -0.00562, -0.99996)-0.02098, 66.97905, -19.11879
2given(-0.86712, 0.49799, -0.0101), (-0.49809, -0.86685, 0.02197), (0.00219, 0.02408, 0.99971)-58.01492, 33.4462, -32.5147

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Components

#1: Protein CELLULASE / XYLOGLUCAN HYDROLASE


Mass: 31249.467 Da / Num. of mol.: 3 / Fragment: RESIDUES 25-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TROPAEOLUM MAJUS (nasturtium) / Tissue: SEEDLING / Plasmid: PPIC9-NXG1 / Production host: PICHIA PASTORIS (fungus)
References: UniProt: Q07524, xyloglucan-specific endo-beta-1,4-glucanase, cellulase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FIRST THREE RESIDUES (CHAIN K, RESIDUES AYV) ARE DUE TO THE CLONING CONSTRUCTION FOR ...THE FIRST THREE RESIDUES (CHAIN K, RESIDUES AYV) ARE DUE TO THE CLONING CONSTRUCTION FOR HETEROLOGOUS EXPRESSION

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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: 2.64 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 7.5
Details: THE SOLUTIONS FOR THE OPTIMIZED CONDITIONS OF NXG1 CONTAINED 15-20% OF POLYETHYLENE GLYCOL (PEG) 20000 AND 100 MM HEPES BUFFER AT PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→45 Å / Num. obs: 87640 / % possible obs: 99.4 % / Observed criterion σ(I): 0.5 / Redundancy: 4.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.4 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UN1

1un1


Resolution: 1.8→40.5 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.644 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2 4392 5 %RANDOM
Rwork0.176 ---
obs0.177 83243 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6639 0 24 443 7106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226887
X-RAY DIFFRACTIONr_bond_other_d0.0010.025727
X-RAY DIFFRACTIONr_angle_refined_deg1.251.9339395
X-RAY DIFFRACTIONr_angle_other_deg0.768313379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7885816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72223.879348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19415999
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8971533
X-RAY DIFFRACTIONr_chiral_restr0.080.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027776
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021509
X-RAY DIFFRACTIONr_nbd_refined0.2020.21275
X-RAY DIFFRACTIONr_nbd_other0.1860.25711
X-RAY DIFFRACTIONr_nbtor_refined0.1890.23330
X-RAY DIFFRACTIONr_nbtor_other0.0820.23702
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2442
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1050.236
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1830.2114
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6491.55251
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74826630
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.32633520
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9324.52765
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1583medium positional0.130.5
2B1583medium positional0.220.5
3C1583medium positional0.170.5
1A2483loose positional0.435
2B2483loose positional0.485
3C2483loose positional0.495
1A1583medium thermal0.632
2B1583medium thermal0.842
3C1583medium thermal0.492
1A2483loose thermal0.9410
2B2483loose thermal1.0710
3C2483loose thermal0.8210
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.279 355
Rwork0.237 6115

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