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- PDB-7n6h: The crystal structure of the GH30 subfamily 10 enzyme, AcXbh30A f... -

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Basic information

Entry
Database: PDB / ID: 7n6h
TitleThe crystal structure of the GH30 subfamily 10 enzyme, AcXbh30A from Acetivibrio clariflavus
ComponentsAcXbh30A
KeywordsHYDROLASE / GH30
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Endo-beta-1,6-galactanase/Exo-beta-1,6-galactobiohydrolase / Endo-beta-1,6-galactanase-like / O-Glycosyl hydrolase family 30 / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily ...Endo-beta-1,6-galactanase/Exo-beta-1,6-galactobiohydrolase / Endo-beta-1,6-galactanase-like / O-Glycosyl hydrolase family 30 / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / O-glycosyl hydrolase
Similarity search - Component
Biological speciesAcetivibrio clariflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsTan, K. / St John, F.J.
CitationJournal: Febs Lett. / Year: 2022
Title: The first crystal structure of a xylobiose-bound xylobiohydrolase with high functional specificity from the bacterial glycoside hydrolase family 30, subfamily 10.
Authors: St John, F.J. / Crooks, C. / Kim, Y. / Tan, K. / Joachimiak, A.
History
DepositionJun 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AcXbh30A
B: AcXbh30A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,14928
Polymers100,1572
Non-polymers99326
Water12,917717
1
A: AcXbh30A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,72818
Polymers50,0781
Non-polymers65017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AcXbh30A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,42110
Polymers50,0781
Non-polymers3439
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.868, 108.018, 66.836
Angle α, β, γ (deg.)90.00, 90.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AcXbh30A


Mass: 50078.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio clariflavus (bacteria) / Gene: Clocl_1795 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: G8LU16
#2: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 717 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: 0.1M Sodium Acetate, 25% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2020
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.28→41.2 Å / Num. obs: 211708 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.064 / Rrim(I) all: 0.128 / Χ2: 2.012 / Net I/σ(I): 20
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 8265 / CC1/2: 0.326 / CC star: 0.701 / Rpim(I) all: 0.642 / Rrim(I) all: 1.215 / Χ2: 0.694 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M5Z

6m5z


Resolution: 1.28→41.18 Å / Cross valid method: FREE R-VALUE / σ(F): 16.7 / Phase error: 27.99 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2542 10864 5.14 %
Rwork0.2015 --
obs0.2098 211560 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.28→41.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6875 0 35 717 7627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0017096
X-RAY DIFFRACTIONf_angle_d0.3929656
X-RAY DIFFRACTIONf_dihedral_angle_d12.1192513
X-RAY DIFFRACTIONf_chiral_restr0.0611037
X-RAY DIFFRACTIONf_plane_restr0.0031244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.30.34724180.29468669X-RAY DIFFRACTION79
1.3-1.320.32385180.29069835X-RAY DIFFRACTION90
1.32-1.350.33635400.28459989X-RAY DIFFRACTION92
1.35-1.370.3035230.28210186X-RAY DIFFRACTION93
1.37-1.40.31895300.279110169X-RAY DIFFRACTION93
1.4-1.440.31135990.277310115X-RAY DIFFRACTION92
1.44-1.470.3215530.265810113X-RAY DIFFRACTION92
1.47-1.510.28975160.263710148X-RAY DIFFRACTION93
1.51-1.560.29735400.254410007X-RAY DIFFRACTION91
1.56-1.610.30275560.25210240X-RAY DIFFRACTION93
1.61-1.670.2985600.245710265X-RAY DIFFRACTION93
1.67-1.730.29575640.241810182X-RAY DIFFRACTION93
1.73-1.810.28925530.233610226X-RAY DIFFRACTION93
1.81-1.910.28775130.22510057X-RAY DIFFRACTION91
1.91-2.030.25064990.213510241X-RAY DIFFRACTION93
2.03-2.180.24535400.202610257X-RAY DIFFRACTION93
2.18-2.40.25485190.19210201X-RAY DIFFRACTION93
2.4-2.750.2564920.182610024X-RAY DIFFRACTION91
2.75-3.460.24384970.172910109X-RAY DIFFRACTION92
3.46-41.180.19434990.16599998X-RAY DIFFRACTION90

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