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- PDB-3vlb: Crystal structure of xeg-edgp -

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Basic information

Entry
Database: PDB / ID: 3vlb
TitleCrystal structure of xeg-edgp
Components
  • EDGP
  • Xyloglucan-specific endo-beta-1,4-glucanase A
KeywordsPLANT PROTEIN/HYDROLASE / cell-wall / PLANT PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


xyloglucan-specific endo-beta-1,4-glucanase / xyloglucan-specific endo-beta-1,4-glucanase activity / cellulase activity / polysaccharide catabolic process / cell wall organization / aspartic-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Xylanase inhibitor, C-terminal / Xylanase inhibitor I-like / Xylanase inhibitor C-terminal / Xylanase inhibitor, N-terminal / Xylanase inhibitor N-terminal / Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / Aspartic peptidase A1 family ...Xylanase inhibitor, C-terminal / Xylanase inhibitor I-like / Xylanase inhibitor C-terminal / Xylanase inhibitor, N-terminal / Xylanase inhibitor N-terminal / Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Concanavalin A-like lectin/glucanase domain superfamily / Aspartic peptidase domain superfamily / Jelly Rolls / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Xyloglucan-specific endo-beta-1,4-glucanase A / EDGP
Similarity search - Component
Biological speciesDaucus carota (carrot)
Aspergillus aculeatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsYoshizawa, T. / Shimizu, T. / Hirano, H. / Sato, M. / Hashimoto, H.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis for inhibition of xyloglucan-specific endo-beta-1,4-glucanase (XEG) by XEG-protein inhibitor
Authors: Yoshizawa, T. / Shimizu, T. / Hirano, H. / Sato, M. / Hashimoto, H.
History
DepositionNov 30, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EDGP
B: Xyloglucan-specific endo-beta-1,4-glucanase A
C: EDGP
D: Xyloglucan-specific endo-beta-1,4-glucanase A


Theoretical massNumber of molelcules
Total (without water)134,0734
Polymers134,0734
Non-polymers00
Water95553
1
A: EDGP
B: Xyloglucan-specific endo-beta-1,4-glucanase A


Theoretical massNumber of molelcules
Total (without water)67,0362
Polymers67,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-8 kcal/mol
Surface area24470 Å2
MethodPISA
2
C: EDGP
D: Xyloglucan-specific endo-beta-1,4-glucanase A


Theoretical massNumber of molelcules
Total (without water)67,0362
Polymers67,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-8 kcal/mol
Surface area24550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)249.043, 51.691, 143.235
Angle α, β, γ (deg.)90.00, 122.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein EDGP


Mass: 43660.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Daucus carota (carrot) / Gene: EDGP1 / Cell (production host): carrot callus cell / Production host: Daucus carota (carrot) / References: UniProt: Q05929
#2: Protein Xyloglucan-specific endo-beta-1,4-glucanase A / Xyloglucanase A / Xyloglucanendohydrolase A


Mass: 23376.160 Da / Num. of mol.: 2 / Fragment: UNP residues 21-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus aculeatus (mold) / Gene: xgeA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O94218, xyloglucan-specific endo-beta-1,4-glucanase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.91 Å3/Da / Density % sol: 57.72 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 40308

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VL8, 3VLA

3vl8

3vla


Resolution: 2.7→10 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.841 / SU B: 38.454 / SU ML: 0.368 / Cross valid method: THROUGHOUT / ESU R: 2.924 / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34075 1994 5 %RANDOM
Rwork0.25743 ---
obs0.26167 37706 91.96 %-
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: 52.327 Å2
Baniso -1Baniso -2Baniso -3
1--3.28 Å20 Å2-2.36 Å2
2--4.89 Å20 Å2
3----4.12 Å2
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9232 0 0 53 9285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.029427
X-RAY DIFFRACTIONr_bond_other_d00.026017
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.94612888
X-RAY DIFFRACTIONr_angle_other_deg4.0283.00414726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.30351236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3924.571350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.467151414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1991534
X-RAY DIFFRACTIONr_chiral_restr0.0830.21542
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110610
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021904
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.474 123 -
Rwork0.376 2305 -
obs--82.19 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4410.26740.09511.06510.23813.3771-0.008-0.2416-0.0324-0.04430.03310.1540.2939-0.4015-0.0250.0854-0.06340.01140.10640.00940.1247-25.186-4.3027-1.2008
22.55850.8140.62122.186-0.41892.92830.07340.26670.0983-0.0268-0.03540.07950.0650.0609-0.0380.11620.01440.01980.0401-0.00290.0423-15.24334.482-34.5675
32.8155-0.4515-0.69010.94930.0321.64170.14560.37960.2968-0.11230.01820.1123-0.07820.0545-0.16370.10050.01460.00020.08810.06740.099726.0916-17.0904-82.7941
43.47240.0020.71692.2905-1.04823.0270.1072-0.15920.1664-0.08840.0020.10250.047-0.3019-0.10920.06330.01020.02030.0452-0.00760.07210.4212-25.8477-59.414
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 412
2X-RAY DIFFRACTION2B7 - 224
3X-RAY DIFFRACTION3C5 - 412
4X-RAY DIFFRACTION4D7 - 224

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