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- PDB-2uwb: Crystal structure of the Nasturtium seedling mutant xyloglucanase... -

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Basic information

Entry
Database: PDB / ID: 2uwb
TitleCrystal structure of the Nasturtium seedling mutant xyloglucanase isoform NXG1-delta-YNIIG
ComponentsCELLULASE
KeywordsHYDROLASE / XYLOGLUCAN-ENDO-TRANSFERASE / GLYCOSIDE HYDROLASE / LOOP MUTANT NXG1- YNIIG / 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: 2 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 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

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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)60,9092
Polymers60,9092
Non-polymers00
Water4,234235
1
A: CELLULASE


Theoretical massNumber of molelcules
Total (without water)30,4551
Polymers30,4551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CELLULASE


Theoretical massNumber of molelcules
Total (without water)30,4551
Polymers30,4551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)153.894, 153.894, 83.819
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:

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 - 266 / Label seq-ID: 2 - 267

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

NCS oper: (Code: given
Matrix: (0.49997, 0.86604, 0.00025), (0.86604, -0.49997, -4.0E-5), (9.0E-5, 0.00024, -1)
Vector: -76.95838, 133.28055, 41.4879)

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Components

#1: Protein CELLULASE / XYLOGLUCAN HYDROLASE


Mass: 30454.574 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-145,151-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TROPAEOLUM MAJUS (nasturtium) / Tissue: SEEDLING / Plasmid: PPIC9-NXG1-DELTAYNIIG / 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.: 235 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FIRST RESIDUE (CHAIN K, RESIDUE V) IS DUE TO THE CLONING CONSTRUCTION FOR HETEROLOGOUS ...THE FIRST RESIDUE (CHAIN K, RESIDUE V) IS DUE TO THE CLONING CONSTRUCTION FOR HETEROLOGOUS EXPRESSION. THE RESIDUES IN THE LOOP Y122-G126 HAVE BEEN DELETED.

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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: 4.62 Å3/Da / Density % sol: 73.4 % / Description: NONE
Crystal growpH: 6.5
Details: 1.4 M SODIUM ACETATE AND 100 MM SODIUM-CACODYLATE BUFFER AT PH 6.5

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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: Dec 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→45 Å / Num. obs: 76393 / % possible obs: 100 % / Observed criterion σ(I): 0.5 / Redundancy: 10.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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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 2UWA

2uwa


Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.866 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 3844 5 %RANDOM
Rwork0.193 ---
obs0.194 72537 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0.31 Å20 Å2
2---0.63 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4312 0 0 235 4547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224460
X-RAY DIFFRACTIONr_bond_other_d0.0010.023702
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9326088
X-RAY DIFFRACTIONr_angle_other_deg0.87538654
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5125530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89823.894226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3215652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0361522
X-RAY DIFFRACTIONr_chiral_restr0.1080.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02976
X-RAY DIFFRACTIONr_nbd_refined0.1950.2777
X-RAY DIFFRACTIONr_nbd_other0.1920.23589
X-RAY DIFFRACTIONr_nbtor_refined0.190.22090
X-RAY DIFFRACTIONr_nbtor_other0.0880.22350
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0680.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1231.53391
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34724312
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.06732261
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9524.51776
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
1554medium positional0.040.5
2435loose positional0.175
1554medium thermal0.192
2435loose thermal0.3710
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 286
Rwork0.246 5338

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