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- PDB-9gmj: The crystal structure of ManDH5 Selenomethionine derivative at 1.... -

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Basic information

Entry
Database: PDB / ID: 9gmj
TitleThe crystal structure of ManDH5 Selenomethionine derivative at 1.6 Angstroms resolution - a beta-D-Mannanase of GH5 family from Dictyoglomus thermophilium
ComponentsDUF5060 domain-containing protein
KeywordsHYDROLASE / Glycoside-Hydrolase / Mannanase / Thermostable protein
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 / SAD / Resolution: 1.6 Å
AuthorsSivron, Y. / Romano, A. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: The crystal structure of ManDH5 Selenomethionine derivative at 1.6 Angstroms Resolution - a beta-D-Mannanase of GH5 family from Dictyoglomus thermophilium
Authors: Sivron, Y. / Romano, A. / Shoham, Y. / Shoham, G.
History
DepositionAug 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 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)67,9043
Polymers67,6901
Non-polymers2142
Water7,566420
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.207, 99.274, 153.724
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

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Components

#1: Protein DUF5060 domain-containing protein


Mass: 67689.758 Da / Num. of mol.: 1
Mutation: Selenomethionine replacing all Metionine residues; According to the phase solution (performed using Crank 2), only 6 out of 7 MET residues were substituted by MSE. The first in the sequence appears to be MET.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyoglomus thermophilum (bacteria) / Strain: SpSt-81 / Gene: ENW00_02810 / Plasmid: bacterial plasmid / Details (production host): 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: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.84 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 32% PEG 1500, 0.1 M MMT buffer pH 7.0

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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: 0.986 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.986 Å / Relative weight: 1
ReflectionResolution: 1.6→83.4 Å / Num. obs: 95883 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 19.27 Å2 / CC1/2: 0.999 / Net I/σ(I): 22
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 3.6 / Num. unique obs: 4677 / CC1/2: 0.874 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
xia2data scaling
CRANK2phasing
BUCCANEERmodel building
PHENIX1.14-3228refinement
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→83.4 Å / SU ML: 0.186 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.2011 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1903 9334 5.03 %
Rwork0.177 176354 -
obs0.1776 95871 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.21 Å2
Refinement stepCycle: LAST / Resolution: 1.6→83.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 14 420 5142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00654902
X-RAY DIFFRACTIONf_angle_d0.91176655
X-RAY DIFFRACTIONf_chiral_restr0.0586668
X-RAY DIFFRACTIONf_plane_restr0.0056841
X-RAY DIFFRACTIONf_dihedral_angle_d4.8873985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.28852850.2665858X-RAY DIFFRACTION99.98
1.62-1.640.25013420.24865911X-RAY DIFFRACTION100
1.64-1.660.25522910.23155844X-RAY DIFFRACTION100
1.66-1.680.2373390.245850X-RAY DIFFRACTION99.97
1.68-1.70.26842960.22975883X-RAY DIFFRACTION99.97
1.7-1.720.25433410.23165842X-RAY DIFFRACTION99.98
1.72-1.750.23663370.21845894X-RAY DIFFRACTION99.97
1.75-1.770.22563230.21125866X-RAY DIFFRACTION99.87
1.77-1.80.22793730.20465792X-RAY DIFFRACTION99.89
1.8-1.830.20913050.19065888X-RAY DIFFRACTION99.94
1.83-1.860.19712940.17325885X-RAY DIFFRACTION99.95
1.86-1.90.17922690.17635865X-RAY DIFFRACTION99.98
1.9-1.930.21763000.17435946X-RAY DIFFRACTION99.98
1.93-1.970.20093020.17455870X-RAY DIFFRACTION99.97
1.97-2.020.19353470.17945836X-RAY DIFFRACTION100
2.02-2.060.19813090.17655937X-RAY DIFFRACTION99.97
2.06-2.110.1842870.17395885X-RAY DIFFRACTION100
2.11-2.170.19673020.1735848X-RAY DIFFRACTION100
2.17-2.240.19533250.17685888X-RAY DIFFRACTION100
2.24-2.310.21033490.17245821X-RAY DIFFRACTION100
2.31-2.390.20292690.17935942X-RAY DIFFRACTION100
2.39-2.490.1982870.17965931X-RAY DIFFRACTION99.97
2.49-2.60.21323130.17655861X-RAY DIFFRACTION100
2.6-2.740.18042900.17835886X-RAY DIFFRACTION100
2.74-2.910.18992970.18335901X-RAY DIFFRACTION100
2.91-3.130.18943070.17855897X-RAY DIFFRACTION100
3.13-3.450.17842980.17395904X-RAY DIFFRACTION100
3.45-3.950.1663100.15975893X-RAY DIFFRACTION100
3.95-4.970.15673210.14695867X-RAY DIFFRACTION100

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