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- PDB-1sqj: Crystal Structure Analysis of Oligoxyloglucan reducing-end-specif... -

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Basic information

Entry
Database: PDB / ID: 1sqj
TitleCrystal Structure Analysis of Oligoxyloglucan reducing-end-specific cellobiohydrolase (OXG-RCBH)
Componentsoligoxyloglucan reducing-end-specific cellobiohydrolase
KeywordsHYDROLASE / BETA-PROPELLER
Function / homology
Function and homology information


oligoxyloglucan reducing-end-specific cellobiohydrolase / oligoxyloglucan reducing-end-specific cellobiohydrolase activity / xyloglucan metabolic process / cellulose 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
Oligoxyloglucan reducing end-specific cellobiohydrolase
Similarity search - Component
Biological speciesGeotrichum sp. M128 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsYaoi, K. / Kondo, H. / Noro, N. / Suzuki, M. / Tsuda, S. / Mitsuishi, Y.
Citation
Journal: Structure / Year: 2004
Title: Tandem Repeat of a Seven-Bladed beta-Propeller Domain in Oligoxyloglucan Reducing-End-Specific Cellobiohydrolase
Authors: Yaoi, K. / Kondo, H. / Noro, N. / Suzuki, M. / Tsuda, S. / Mitsuishi, Y.
#1: Journal: J.BIOL.CHEM. / Year: 2002
Title: Purification, characterization, cloning, and expression of a novel xyloglucan-specific glycosidase, oligoxyloglucan reducing end-specific cellobiohydrolase
Authors: Yaoi, K. / Mitsuishi, Y.
#2: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003
Title: Crystallization and preliminary X-ray crystallographic study on a xyloglucan-specific exo-beta-glycosidase, oligoxyloglucan reducing-end specific cellobiohydrolase
Authors: Yaoi, K. / Kondo, H. / Suzuki, M. / Noro, N. / Tsuda, S. / Mitsuishi, Y.
History
DepositionMar 19, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: oligoxyloglucan reducing-end-specific cellobiohydrolase
B: oligoxyloglucan reducing-end-specific cellobiohydrolase


Theoretical massNumber of molelcules
Total (without water)169,9492
Polymers169,9492
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.077, 146.051, 212.711
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein oligoxyloglucan reducing-end-specific cellobiohydrolase / OXG-RCBH


Mass: 84974.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geotrichum sp. M128 (yeast) / Plasmid: pET29a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)RP
References: UniProt: Q8J0D2, oligoxyloglucan reducing-end-specific cellobiohydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.8
Details: PEG 3000, PEG 400, pH 5.8, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.978, 0.9792, 0.9794, 0.9500
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2002 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
20.97921
30.97941
40.951
ReflectionResolution: 2.2→40 Å / Num. all: 294393 / Num. obs: 294393 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3 / % possible all: 70.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.901 / SU B: 6.611 / SU ML: 0.166 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.301 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 4300 5.1 %RANDOM
Rwork0.21676 ---
all0.21877 80654 --
obs0.21877 80654 87.22 %-
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: 36.686 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å20 Å2
2--1.26 Å20 Å2
3----3.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11709 0 0 63 11772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02112078
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.92316515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.34151535
X-RAY DIFFRACTIONr_chiral_restr0.1040.21721
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029589
X-RAY DIFFRACTIONr_nbd_refined0.210.25320
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2425
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.25
X-RAY DIFFRACTIONr_mcbond_it0.6181.57633
X-RAY DIFFRACTIONr_mcangle_it1.124212238
X-RAY DIFFRACTIONr_scbond_it1.81434445
X-RAY DIFFRACTIONr_scangle_it2.7764.54277
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.32 228
Rwork0.261 4282
obs-4658

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