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- PDB-8uwt: A X-ray Crystallographic Structure Model of a Glycoside Hydrolase... -

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Basic information

Entry
Database: PDB / ID: 8uwt
TitleA X-ray Crystallographic Structure Model of a Glycoside Hydrolase (GH) Family 39 (GH39)-like Enzyme Encoded within a Xylan Utilization Locus of the pSOL1 Megaplasmid of Clostridium acetobutylicum
ComponentsPossible beta-xylosidase diverged, family 5/39 of glycosyl hydrolases and alpha-amylase C (Greek key) C-terminal domain
KeywordsHYDROLASE / Glycoside Hydrolase Family 39 / Clostridium acetobutylicum / pSOL1 / Xylan
Function / homologyGlycoside hydrolase superfamily / hydrolase activity / FORMIC ACID / TRIETHYLENE GLYCOL / Possible beta-xylosidase diverged, family 5/39 of glycosyl hydrolases and alpha-amylase C (Greek key) C-terminal domain
Function and homology information
Biological speciesClostridium acetobutylicum ATCC 824 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSt John, F.J. / Fujimoto, Z.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)L17552 Japan
CitationJournal: To Be Published
Title: A X-ray Crystallographic Structure Model of a Glycoside Hydrolase (GH) Family 39 (GH39)-like Enzyme Encoded within a Xylan Utilization Locus of the pSOL1 Megaplasmid of Clostridium acetobutylicum
Authors: St John, F.J. / Fujimoto, Z.
History
DepositionNov 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Possible beta-xylosidase diverged, family 5/39 of glycosyl hydrolases and alpha-amylase C (Greek key) C-terminal domain
B: Possible beta-xylosidase diverged, family 5/39 of glycosyl hydrolases and alpha-amylase C (Greek key) C-terminal domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,89539
Polymers90,8562
Non-polymers2,03937
Water15,709872
1
A: Possible beta-xylosidase diverged, family 5/39 of glycosyl hydrolases and alpha-amylase C (Greek key) C-terminal domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,25618
Polymers45,4281
Non-polymers82817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Possible beta-xylosidase diverged, family 5/39 of glycosyl hydrolases and alpha-amylase C (Greek key) C-terminal domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,63921
Polymers45,4281
Non-polymers1,21120
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.407, 88.245, 106.593
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Possible beta-xylosidase diverged, family 5/39 of glycosyl hydrolases and alpha-amylase C (Greek key) C-terminal domain


Mass: 45427.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Mega plasmid pSOL1
Source: (gene. exp.) Clostridium acetobutylicum ATCC 824 (bacteria)
Gene: CA_P0117 / Details (production host): pET27 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q97TI4

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Non-polymers , 6 types, 909 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 872 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 1.95 Å3/Da / Density % sol: 36.98 %
Description: Thin 2D plates no more than a few microns thick growing as a rosette
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Hampton Research PEGRx HT: Condition 80 (G8): 0.2 M Sodium Formate, 0.1 M BICINE pH 8.5, 20% PEG5000 MME. This condition was extensively refined and the crystal which generated the data for ...Details: Hampton Research PEGRx HT: Condition 80 (G8): 0.2 M Sodium Formate, 0.1 M BICINE pH 8.5, 20% PEG5000 MME. This condition was extensively refined and the crystal which generated the data for this deposit consisted of the same, but had pH adjusted to 8.3.

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 12, 2018 / Details: Rhodium coated silicon single crystal
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→100 Å / Num. obs: 96886 / % possible obs: 94.3 % / Redundancy: 11 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.047 / Rrim(I) all: 0.162 / Χ2: 0.955 / Net I/σ(I): 4.7 / Num. measured all: 1062381
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.55-1.613.81.5361670.2770.6580.7511.720.83360.6
1.61-1.675.71.35487850.0720.3680.5511.4721.00286.7
1.67-1.758.81.22897130.5110.8230.4211.3030.90595.5
1.75-1.8411.41.004101640.7990.9420.3071.0510.90199.6
1.84-1.95120.704101510.9170.9780.2110.7360.94100
1.95-2.112.30.427102640.9610.990.1260.4460.985100
2.1-2.3213.30.282102460.9820.9950.080.2941.036100
2.32-2.6512.90.183103030.9920.9980.0530.191.067100
2.65-3.3412.70.105103690.9970.9990.030.1091.015100
3.34-100130.059107240.99910.0170.0610.77499.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→35.89 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.089 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17987 4294 5.2 %RANDOM
Rwork0.14238 ---
obs0.14429 78644 80.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.324 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0 Å2-0 Å2
2---0.25 Å20 Å2
3---0.56 Å2
Refinement stepCycle: 1 / Resolution: 1.55→35.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6250 0 130 872 7252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0126735
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175897
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.6419137
X-RAY DIFFRACTIONr_angle_other_deg1.4581.57913732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9975849
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59623.029350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.399151037
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6891535
X-RAY DIFFRACTIONr_chiral_restr0.080.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027791
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021490
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_it1.3041.6173312
X-RAY DIFFRACTIONr_mcbond_other1.3041.6173313
X-RAY DIFFRACTIONr_mcangle_it1.9192.424174
X-RAY DIFFRACTIONr_mcangle_other1.922.4214175
X-RAY DIFFRACTIONr_scbond_it2.1961.8933423
X-RAY DIFFRACTIONr_scbond_other2.0581.8483358
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1932.7054959
X-RAY DIFFRACTIONr_long_range_B_refined5.72620.938125
X-RAY DIFFRACTIONr_long_range_B_other5.57620.2317927
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.553→1.594 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 26 -
Rwork0.31 562 -
obs--7.77 %

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