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- PDB-1umz: Xyloglucan endotransglycosylase in complex with the xyloglucan no... -

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Basic information

Entry
Database: PDB / ID: 1umz
TitleXyloglucan endotransglycosylase in complex with the xyloglucan nonasaccharide XLLG.
ComponentsXYLOGLUCAN ENDOTRANSGLYCOSYLASE
KeywordsTRANSFERASE / GLYCOSIDE HYDROLASE / XET / XTH / XEH / TRANSGLYCOSYLATION / XYLOGLUCAN / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


xyloglucan:xyloglucosyl transferase / xyloglucan:xyloglucosyl transferase activity / xyloglucan metabolic process / cell wall biogenesis / apoplast / polysaccharide binding / hydrolase activity, hydrolyzing O-glycosyl compounds / cell wall organization / cytoplasm
Similarity search - Function
Xyloglucan endo-transglycosylase, C-terminal / Xyloglucan endotransglucosylase/hydrolase / Xyloglucan endo-transglycosylase (XET) C-terminus / Beta-glucanase/XTH / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 ...Xyloglucan endo-transglycosylase, C-terminal / Xyloglucan endotransglucosylase/hydrolase / Xyloglucan endo-transglycosylase (XET) C-terminus / Beta-glucanase/XTH / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / 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 protein 34
Similarity search - Component
Biological speciesPOPULUS TREMULA (European aspen)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJohansson, P. / Brumer, H. / Kallas, A.M. / Henriksson, H. / Denman, S.E. / Teeri, T.T. / Jones, T.A.
CitationJournal: Plant Cell / Year: 2004
Title: Crystal Structures of a Poplar Xyloglucan Endotransglycosylase Reveal Details of Transglycosylation Acceptor Binding
Authors: Johansson, P. / Brumer, H. / Baumann, M.J. / Kallas, A.M. / Henriksson, H. / Denman, S.E. / Teeri, T.T. / Jones, T.A.
History
DepositionSep 3, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XYLOGLUCAN ENDOTRANSGLYCOSYLASE
B: XYLOGLUCAN ENDOTRANSGLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0986
Polymers65,0632
Non-polymers3,0354
Water4,414245
1
A: XYLOGLUCAN ENDOTRANSGLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0493
Polymers32,5321
Non-polymers1,5172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: XYLOGLUCAN ENDOTRANSGLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0493
Polymers32,5321
Non-polymers1,5172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)188.162, 188.162, 45.896
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8446, 0.5335, 0.0456), (-0.5286, 0.8443, -0.0875), (-0.0852, 0.0498, 0.9951)
Vector: -1.2948, 1.2361, 10.3606)

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Components

#1: Protein XYLOGLUCAN ENDOTRANSGLYCOSYLASE


Mass: 32531.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) POPULUS TREMULA (European aspen) / Production host: PICHIA PASTORIS (fungus)
References: UniProt: Q8GZD5, xyloglucan:xyloglucosyl transferase
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 930.808 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpb1-4[DGalpb1-2DXylpa1-6]DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5][a212h-1a_1-5][a2112h-1b_1-5]/1-1-1-2-2-3/a4-b1_b4-c1_b6-e1_c6-d1_e2-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{[(2+1)][b-D-Galp]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 4 Å3/Da / Density % sol: 68 %
Crystal growpH: 7
Details: 10 MG ML-1 PROTEIN SOLUTION 1:1 WITH 1.0 M NAOAC AND 0.2 M IMIDAZOLE PH 6.5
Crystal grow
*PLUS
Temperature: 293 K / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
21.0 M1reservoirNaOAc
30.2 Mimidazole1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2002 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 83886 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 3.61 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 15.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2 / % possible all: 71.7
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 29 Å / Redundancy: 3.61 % / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 71.7 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UN1

1un1


Resolution: 1.8→28.99 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 4215 5 %RANDOM
Rwork0.201 ---
obs0.203 79649 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.91 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4417 0 202 245 4864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214769
X-RAY DIFFRACTIONr_bond_other_d00.023955
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.9616489
X-RAY DIFFRACTIONr_angle_other_deg4.16339145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9295529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025163
X-RAY DIFFRACTIONr_gen_planes_other0.010.021092
X-RAY DIFFRACTIONr_nbd_refined0.2210.2831
X-RAY DIFFRACTIONr_nbd_other0.2880.24437
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1210.22290
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0381.52639
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.93524246
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.47832130
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9184.52242
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.302 230
Rwork0.272 4400
Refinement
*PLUS
Lowest resolution: 29 Å / Rfactor Rfree: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.56

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