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- PDB-9gpc: The crystal structure of ManDH5 E303Q mutant at 1.4 Angstroms Res... -

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Basic information

Entry
Database: PDB / ID: 9gpc
TitleThe crystal structure of ManDH5 E303Q mutant at 1.4 Angstroms Resolution - a beta-D-Mannanase of GH5 family from Dictyoglomus thermophilium
ComponentsDUF5060 domain-containing protein
KeywordsHYDROLASE / Glycoside-Hydrolase / Mannanase / Thermostable protein / EQ mutant
Function / homologyMannan endo-1,4-beta-mannosidase-like / mannan endo-1,4-beta-mannosidase activity / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / Immunoglobulin-like fold / extracellular region / DUF5060 domain-containing protein
Function and homology information
Biological speciesDictyoglomus thermophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSivron, Y. / Romano, A. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: The crystal structure of ManDH5 E303Q mutant at 1.4 Angstroms Resolution - a beta-D-Mannanase of GH5 family from Dictyoglomus thermophilium
Authors: Sivron, Y. / Romano, A. / Shoham, Y. / Shoham, G.
History
DepositionSep 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF5060 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4992
Polymers67,4071
Non-polymers921
Water8,935496
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint0 kcal/mol
Surface area21950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.499, 99.128, 154.563
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1159-

HOH

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Components

#1: Protein DUF5060 domain-containing protein


Mass: 67407.398 Da / Num. of mol.: 1 / Mutation: E303Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyoglomus thermophilum (bacteria) / Strain: SpSt-81 / Gene: ENW00_02810 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
Variant (production host): F- ompT hsdSB (rB- mB-) dcm gal LambdaDE3
References: UniProt: A0A7C3MIF0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O
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: 2.86 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M MMT buffer pH 7.0, 28% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2019
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→83.44 Å / Num. obs: 143534 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 10.99 Å2 / CC1/2: 0.999 / Net I/σ(I): 14
Reflection shellResolution: 1.4→1.42 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7037 / CC1/2: 0.731

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.17.1_3660refinement
xia2CCP4i2 7.0.078data scaling
Coot8,9, Wincoot 9model building
PHASER1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ManDH5 Native structure

Resolution: 1.4→83.44 Å / SU ML: 0.1165 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.5924
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1688 7409 5.16 %
Rwork0.1471 136085 -
obs0.1482 143494 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.21 Å2
Refinement stepCycle: LAST / Resolution: 1.4→83.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4719 0 6 496 5221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00994899
X-RAY DIFFRACTIONf_angle_d1.14836650
X-RAY DIFFRACTIONf_chiral_restr0.0883667
X-RAY DIFFRACTIONf_plane_restr0.0085844
X-RAY DIFFRACTIONf_dihedral_angle_d15.5355640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.2372350.21244550X-RAY DIFFRACTION99.98
1.42-1.430.25482140.20334516X-RAY DIFFRACTION99.98
1.43-1.450.24112450.19434479X-RAY DIFFRACTION99.96
1.45-1.470.22212410.18514502X-RAY DIFFRACTION99.98
1.47-1.490.21742570.16854497X-RAY DIFFRACTION99.96
1.49-1.510.20032480.17164462X-RAY DIFFRACTION100
1.51-1.530.21172440.1664544X-RAY DIFFRACTION99.98
1.53-1.550.20252480.16224494X-RAY DIFFRACTION99.98
1.55-1.580.18372420.15764493X-RAY DIFFRACTION99.92
1.58-1.60.20692450.15234522X-RAY DIFFRACTION99.9
1.6-1.630.17972310.14544504X-RAY DIFFRACTION99.94
1.63-1.660.17132430.13584540X-RAY DIFFRACTION99.96
1.66-1.690.16842430.13284510X-RAY DIFFRACTION99.98
1.69-1.730.15592470.13434512X-RAY DIFFRACTION100
1.73-1.760.17042410.12684527X-RAY DIFFRACTION100
1.76-1.80.15382430.12984513X-RAY DIFFRACTION100
1.8-1.850.17952750.12694511X-RAY DIFFRACTION99.96
1.85-1.90.15282710.12484456X-RAY DIFFRACTION99.96
1.9-1.960.14282600.12844554X-RAY DIFFRACTION99.94
1.96-2.020.15852370.1314517X-RAY DIFFRACTION99.96
2.02-2.090.1472550.13254506X-RAY DIFFRACTION99.96
2.09-2.180.15072540.12754548X-RAY DIFFRACTION99.98
2.18-2.270.15832300.12814567X-RAY DIFFRACTION99.94
2.27-2.390.15492710.1334541X-RAY DIFFRACTION99.96
2.39-2.540.17122600.13924545X-RAY DIFFRACTION99.94
2.54-2.740.16852620.1444543X-RAY DIFFRACTION99.96
2.74-3.020.16962380.15224585X-RAY DIFFRACTION99.79
3.02-3.450.17392670.16064593X-RAY DIFFRACTION99.69
3.45-4.350.15542380.14644633X-RAY DIFFRACTION99.53
4.35-83.440.17082240.16824821X-RAY DIFFRACTION99.51

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