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- PDB-3a0f: The crystal structure of Geotrichum sp. M128 xyloglucanase -

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Basic information

Entry
Database: PDB / ID: 3a0f
TitleThe crystal structure of Geotrichum sp. M128 xyloglucanase
ComponentsXyloglucanase
KeywordsHYDROLASE / BETA-PROPELLER
Function / homology
Function and homology information


xyloglucan metabolic process / hydrolase activity, acting on glycosyl bonds / polysaccharide catabolic process
Similarity search - Function
BNR-Asp box repeat / : / BNR repeat / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesGeotrichum sp. M128 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYaoi, K. / Kondo, H. / Hiyoshi, A. / Noro, N. / Sugimoto, H. / Tsuda, S. / Miyazaki, K.
CitationJournal: Febs J. / Year: 2009
Title: The crystal structure of a xyloglucan-specific endo-beta-1,4-glucanase from Geotrichum sp. M128 xyloglucanase reveals a key amino acid residue for substrate specificity
Authors: Yaoi, K. / Kondo, H. / Hiyoshi, A. / Noro, N. / Sugimoto, H. / Tsuda, S. / Miyazaki, K.
History
DepositionMar 16, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 1.3Oct 16, 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: Xyloglucanase


Theoretical massNumber of molelcules
Total (without water)81,5571
Polymers81,5571
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.192, 135.192, 119.895
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Xyloglucanase / xyloglucan-specific endo-beta-1 / 4-glucanase


Mass: 81557.078 Da / Num. of mol.: 1 / Fragment: residues in UNP 21-776
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geotrichum sp. M128 (yeast) / Gene: XEG / Plasmid: pET14-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3) RP
References: UniProt: Q764N8, xyloglucan-specific endo-beta-1,4-glucanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.92 Å3/Da / Density % sol: 68.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1M MES, 6% PEG 8000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 43425 / Num. obs: 43425 / % possible obs: 98.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 19.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 8.6 / Num. unique all: 4042 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SQJ

1sqj


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.847 / SU B: 8.154 / SU ML: 0.19 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27582 2139 4.9 %RANDOM
Rwork0.23633 ---
obs0.23829 41246 98.52 %-
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: 32.283 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.1 Å20 Å2
2--0.19 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5676 0 0 107 5783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225845
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.9297993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8445752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38624.008247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.09815820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0641528
X-RAY DIFFRACTIONr_chiral_restr0.130.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024596
X-RAY DIFFRACTIONr_nbd_refined0.2220.22667
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23889
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2314
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.28
X-RAY DIFFRACTIONr_mcbond_it0.6731.53796
X-RAY DIFFRACTIONr_mcangle_it1.12125930
X-RAY DIFFRACTIONr_scbond_it1.6832475
X-RAY DIFFRACTIONr_scangle_it2.4234.52063
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 144 -
Rwork0.251 2738 -
obs--91.38 %

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