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- PDB-2uwc: Crystal structure of Nasturtium xyloglucan hydrolase isoform NXG2 -

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Basic information

Entry
Database: PDB / ID: 2uwc
TitleCrystal structure of Nasturtium xyloglucan hydrolase isoform NXG2
ComponentsCELLULASE
KeywordsHYDROLASE / TROPAEOLUM MAJUS / XYLOGLUCAN HYDROLASE / XYLOGLUCAN-ENDO-TRANSFERASE / GLYCOSIDASE / FAMILY GH16 / ISOFORM NXG2
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: 2.3 Å
AuthorsBaumann, M.J. / Eklof, J.M. / Michel, G. / Kallas, 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.M. / Michel, G. / Kallas, A.M. / Teeri, T.T. / Czjzek, M. / Brumer, H.
History
DepositionMar 20, 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 / 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
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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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

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Assembly

Deposited unit
A: CELLULASE
B: CELLULASE


Theoretical massNumber of molelcules
Total (without water)61,8322
Polymers61,8322
Non-polymers00
Water5,296294
1
A: CELLULASE


Theoretical massNumber of molelcules
Total (without water)30,9161
Polymers30,9161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CELLULASE


Theoretical massNumber of molelcules
Total (without water)30,9161
Polymers30,9161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)152.123, 152.123, 83.233
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROSERSERAA3 - 1893 - 189
21PROPROSERSERBB3 - 1893 - 189
12LYSLYSHISHISAA198 - 265198 - 265
22LYSLYSHISHISBB198 - 265198 - 265

NCS oper: (Code: given
Matrix: (0.49921, -0.86648, 0.00206), (-0.86648, -0.49921, -0.00067), (0.00161, -0.00145, -1)
Vector: 76.11953, 131.68204, -40.42295)

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Components

#1: Protein CELLULASE / XYLOGLUCAN HYDROLASE


Mass: 30916.084 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TROPAEOLUM MAJUS (nasturtium) / Tissue: SEEDLING / Plasmid: PPIC9-NXG2 / Production host: PICHIA PASTORIS (fungus)
References: UniProt: Q07524, xyloglucan-specific endo-beta-1,4-glucanase, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FIRST TWO RESIDUES ARE NOT DEFINED BY THE ELECTRON DENSITY

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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: 4.5 Å3/Da / Density % sol: 72.7 %
Crystal growpH: 8.5
Details: 2-3 M POTASSIUM ACETATE, 2% 2, 5-METHYLPENTANE-DIOL AND 100 MM TRIS BUFFER AT PH 8.5

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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: 2.3→45 Å / Num. obs: 47776 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.5 / % possible all: 99.1

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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: 2.3→31.31 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.172 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.196 2420 5.1 %RANDOM
Rwork0.167 ---
obs0.168 45345 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.4 Å20 Å2
2--0.79 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.3→31.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4299 0 0 294 4593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224445
X-RAY DIFFRACTIONr_bond_other_d0.0010.023700
X-RAY DIFFRACTIONr_angle_refined_deg2.1031.9296065
X-RAY DIFFRACTIONr_angle_other_deg1.05338639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2465527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39223.75224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.05815648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8081522
X-RAY DIFFRACTIONr_chiral_restr0.1460.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025015
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02983
X-RAY DIFFRACTIONr_nbd_refined0.2360.2803
X-RAY DIFFRACTIONr_nbd_other0.2070.23716
X-RAY DIFFRACTIONr_nbtor_refined0.1980.22073
X-RAY DIFFRACTIONr_nbtor_other0.0970.22557
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2278
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2591.53284
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65224290
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.732245
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.864.51775
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

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1491medium positional0.080.5
2348loose positional0.35
1491medium thermal0.442
2348loose thermal0.7410
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 163
Rwork0.24 3334

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