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- PDB-8ah3: DG04279 glycoside hydrolase family 172 -

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Basic information

Entry
Database: PDB / ID: 8ah3
TitleDG04279 glycoside hydrolase family 172
ComponentsDG02479 GH127
KeywordsHYDROLASE / arabinogalactan / glycoside hydrolase family 172 / GH172 / arabinofuranosidase / hexamer
Function / homologyProtein of unknown function DUF2961 / Protein of unknown function (DUF2961) / metal ion binding / DUF2961 domain-containing protein
Function and homology information
Biological speciesDysgonomonas gadei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsAl-Jourani, O. / Lowe, E.C. / Basle, A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011186/1 United Kingdom
Royal SocietyRG/R2/202228 United Kingdom
CitationJournal: To Be Published
Title: Mining the human gut microbiome identifies mycobacterial D-arabinan degrading enzymes
Authors: Al-Jourani, O. / Benedict, S. / Ross, J. / Layton, A. / van der Peet, P. / Bailey, N.P. / Heunis, T. / Marando, V. / Manion, J. / Mensitieri, F. / Abellon-Ruiz, J. / Oram, S.L. / Parsons, L. ...Authors: Al-Jourani, O. / Benedict, S. / Ross, J. / Layton, A. / van der Peet, P. / Bailey, N.P. / Heunis, T. / Marando, V. / Manion, J. / Mensitieri, F. / Abellon-Ruiz, J. / Oram, S.L. / Parsons, L. / Cartmel, A. / Wright, G.S.A. / Basle, A. / Trost, M. / Kiessling, L.L. / Henrissat, B. / Munoz-Munoz, J. / Lovering, A. / Hirt, R.P. / Williams, S.J. / Lowe, E.C. / Moynihan, P.J.
History
DepositionJul 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DG02479 GH127
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5085
Polymers43,3471
Non-polymers1604
Water3,747208
1
A: DG02479 GH127
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)261,04630
Polymers260,0846
Non-polymers96224
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
crystal symmetry operation17_434x-y-2/3,-y-4/3,-z-1/31
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
Buried area47220 Å2
ΔGint-446 kcal/mol
Surface area66750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.150, 89.150, 289.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-503-

CA

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Components

#1: Protein DG02479 GH127


Mass: 43347.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dysgonomonas gadei (bacteria) / Gene: HMPREF9455_02479 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F5IZG2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.55 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM MOPS/HEPES pH 7.5, 20 mM 1,6-Hexanediol; 20 mM 1-Butanol 20 mM 1,2-Propanediol; 20 mM 2-Propanol; 20 mM 1,4-Butanediol; 20 mM 1,3-Propanedioalcohol, 20 % Etylene Glycol and 10 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.4→68.112 Å / Num. obs: 87401 / % possible obs: 99.9 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.036 / Rrim(I) all: 0.086 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID
7.67-68.119.3874010.9991
1.4-1.426.642370.4121

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Processing

Software
NameVersionClassification
XDSdata scaling
xia2data scaling
pointlessdata scaling
Aimlessdata scaling
PHASERphasing
Cootmodel building
BUCCANEERmodel building
MolProbitymodel building
REFMAC5refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KQ7

4kq7


Resolution: 1.4→68.112 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.4 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.052
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1839 4427 5.065 %
Rwork0.1622 82973 -
all0.163 --
obs-87400 99.921 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.541 Å2
Baniso -1Baniso -2Baniso -3
1-0.865 Å20.432 Å20 Å2
2--0.865 Å20 Å2
3----2.805 Å2
Refinement stepCycle: LAST / Resolution: 1.4→68.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3043 0 4 208 3255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123147
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162676
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.6444286
X-RAY DIFFRACTIONr_angle_other_deg0.6061.5516260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6855374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.5471019
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06210477
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.71210165
X-RAY DIFFRACTIONr_chiral_restr0.0940.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023641
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02679
X-RAY DIFFRACTIONr_nbd_refined0.2080.2496
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.22456
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21506
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21560
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2155
X-RAY DIFFRACTIONr_metal_ion_refined0.0870.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3030.251
X-RAY DIFFRACTIONr_nbd_other0.1970.2158
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1150.225
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0920.28
X-RAY DIFFRACTIONr_mcbond_it2.0492.4631499
X-RAY DIFFRACTIONr_mcbond_other2.0092.4631499
X-RAY DIFFRACTIONr_mcangle_it2.4973.6881872
X-RAY DIFFRACTIONr_mcangle_other2.4983.6891873
X-RAY DIFFRACTIONr_scbond_it3.1622.7291648
X-RAY DIFFRACTIONr_scbond_other3.1612.731649
X-RAY DIFFRACTIONr_scangle_it4.5843.9722414
X-RAY DIFFRACTIONr_scangle_other4.5843.9732415
X-RAY DIFFRACTIONr_lrange_it5.22336.6473545
X-RAY DIFFRACTIONr_lrange_other5.17435.3543512
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.4-1.4360.4083340.39660270.39764120.8550.85599.20460.384
1.436-1.4760.3533070.35559420.35562500.8790.87799.9840.332
1.476-1.5180.3163150.31157490.31260680.8920.89599.93410.285
1.518-1.5650.2762680.27556270.27558950.930.9261000.246
1.565-1.6160.2543320.2453740.24157090.9450.94699.94740.208
1.616-1.6730.2293030.21252440.21355490.9580.96199.9640.181
1.673-1.7360.2142940.19350690.19453630.9680.9711000.16
1.736-1.8070.1912420.16949030.1751470.9740.97899.96110.14
1.807-1.8870.1682440.15447070.15449520.9790.98399.97980.128
1.887-1.9790.1652340.14244910.14347250.9810.9861000.123
1.979-2.0860.172260.14243080.14345340.9810.9871000.128
2.086-2.2130.1712030.14540490.14642520.980.9861000.133
2.213-2.3660.1782020.13438250.13640270.9810.9891000.127
2.366-2.5550.1591950.12335800.12537750.9850.9911000.12
2.555-2.7980.1561730.12533000.12734730.9850.991000.128
2.798-3.1280.161500.13729950.13831450.9860.9891000.146
3.128-3.610.1551510.14926540.14928050.9850.9871000.164
3.61-4.4190.1651100.14922810.1523910.9850.9881000.178
4.419-6.2360.192890.15117860.15318760.9860.9999.94670.188
6.236-68.1120.154550.17410620.17211190.9830.98499.82130.219

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