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- PDB-9hhj: ManDH5 E303Q in complex with mannotetraose after co-crystalliztio... -

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Basic information

Entry
Database: PDB / ID: 9hhj
TitleManDH5 E303Q in complex with mannotetraose after co-crystalliztion with mannotetraose 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 / homology
Function and homology information


mannan endo-1,4-beta-mannosidase activity / extracellular region
Similarity search - Function
Mannan endo-1,4-beta-mannosidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
beta-D-mannopyranose / D-MALATE / TRIETHYLENE GLYCOL / DUF5060 domain-containing protein
Similarity search - Component
Biological speciesDictyoglomus thermophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsSivron, Y. / Romano, A. / Shoham, Y. / Shoham, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: ManDH5 E303Q in complex with mannotetraose after co-crystalliztion with mannotetraose 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
DepositionNov 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF5060 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1679
Polymers67,4071
Non-polymers1,7608
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint32 kcal/mol
Surface area21750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.942, 99.482, 153.448
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1147-

HOH

21A-1159-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a1122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 381 molecules

#4: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.84 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MMT buffer, pH 7.15, 27% PEG 1500, 0.01% Na-azide, 12.5mM Mannohexaose (drop ratio of 1:125 enzyme:substrate).

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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: 0.976 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: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.83→83.5 Å / Num. obs: 64042 / % possible obs: 99.8 % / Redundancy: 13.4 % / Biso Wilson estimate: 22.79 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.6
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 53734 / CC1/2: 0.715 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
xia27.0.078data scaling
PHASER1.17.1_3660phasing
Coot8,9, Wincootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native ManDH5

Resolution: 1.83→51.17 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2021 6288 5.09 %
Rwork0.1726 --
obs0.174 3247 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→51.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4735 0 118 375 5228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075010
X-RAY DIFFRACTIONf_angle_d0.8796780
X-RAY DIFFRACTIONf_dihedral_angle_d13.715705
X-RAY DIFFRACTIONf_chiral_restr0.057691
X-RAY DIFFRACTIONf_plane_restr0.005844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.850.33312210.30543839X-RAY DIFFRACTION99
1.85-1.870.30892040.26863962X-RAY DIFFRACTION99
1.87-1.90.26122310.26233822X-RAY DIFFRACTION100
1.9-1.920.27162500.24923874X-RAY DIFFRACTION99
1.92-1.940.24681970.23653949X-RAY DIFFRACTION100
1.94-1.970.25241940.23083846X-RAY DIFFRACTION100
1.97-20.26782030.23083889X-RAY DIFFRACTION99
2-2.030.29022400.22483879X-RAY DIFFRACTION99
2.03-2.060.23612360.21143938X-RAY DIFFRACTION100
2.06-2.090.28032240.20613809X-RAY DIFFRACTION100
2.09-2.130.24692230.19823896X-RAY DIFFRACTION100
2.13-2.170.23672430.19893869X-RAY DIFFRACTION100
2.17-2.210.21441720.17743935X-RAY DIFFRACTION100
2.21-2.260.21092020.18233982X-RAY DIFFRACTION100
2.26-2.310.22271720.17393893X-RAY DIFFRACTION100
2.31-2.360.23021880.17533935X-RAY DIFFRACTION100
2.36-2.420.18522130.17033947X-RAY DIFFRACTION100
2.42-2.480.21382020.1713895X-RAY DIFFRACTION100
2.48-2.560.2032000.17023938X-RAY DIFFRACTION100
2.56-2.640.21842360.16233914X-RAY DIFFRACTION100
2.64-2.730.21292210.16653859X-RAY DIFFRACTION100
2.73-2.840.21082000.16683910X-RAY DIFFRACTION100
2.84-2.970.22032050.16713941X-RAY DIFFRACTION100
2.97-3.130.16061840.16563966X-RAY DIFFRACTION100
3.13-3.330.18132360.15973893X-RAY DIFFRACTION100
3.33-3.580.18371800.15453934X-RAY DIFFRACTION100
3.58-3.940.13791780.13693958X-RAY DIFFRACTION100
3.94-4.510.13512370.1343886X-RAY DIFFRACTION100
4.51-5.680.18751780.1473948X-RAY DIFFRACTION100
5.68-51.170.19622180.17283924X-RAY DIFFRACTION100

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