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- PDB-9gpg: Complex of ManDH5 native enzyme with Mannobiose after co crystall... -

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Basic information

Entry
Database: PDB / ID: 9gpg
TitleComplex of ManDH5 native enzyme with Mannobiose after co crystallization with Mannopentaose at 1.7 angstroms resolution- a beta-D-Mannanase of GH5 family from Dictyoglomus thermophilium
ComponentsDUF5060 domain-containing protein
KeywordsHYDROLASE / Glycoside-Hydrolase / Mannanase / Thermostable protein / Mannobiose
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 / 4beta-beta-mannobiose / beta-D-mannopyranose / DUF5060 domain-containing protein
Function and homology information
Biological speciesDictyoglomus thermophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSivron, Y. / Romano, A. / Shoham, Y. / Shoham, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Complex of ManDH5 native enzyme with Mannobiose after co crystallization with Mannopentaose at 1.7 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

Downloads & links

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Assembly

Deposited unit
A: DUF5060 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0534
Polymers67,4081
Non-polymers6453
Water10,106561
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint11 kcal/mol
Surface area21870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.528, 99.359, 153.728
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein DUF5060 domain-containing protein


Mass: 67408.383 Da / Num. of mol.: 1
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: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-mannobiose
DescriptorTypeProgram
DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][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
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / Source method: isolated from a natural source / Formula: H2O
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: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MMT buffer pH 7.15, 28% PEG 1500, 12.5 mM Mannopentaose (drop ratio of 1:244 enzyme:substrate)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.7→68.9 Å / Num. obs: 79520 / % possible obs: 98.9 % / Redundancy: 12.4 % / Biso Wilson estimate: 13.87 Å2 / CC1/2: 0.999 / Net I/σ(I): 20.06
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 3622 / CC1/2: 0.898 / % possible all: 89.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DIALSV1-9-2data reduction
xia27.0.078data scaling
PHASER1.17.1_3660phasing
Coot8,9, Wincootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native ManDH5

Resolution: 1.7→51.29 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1831 3997 5.03 %
Rwork0.166 --
obs0.1669 79464 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→51.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4735 0 43 561 5339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084951
X-RAY DIFFRACTIONf_angle_d0.9876721
X-RAY DIFFRACTIONf_dihedral_angle_d13.782649
X-RAY DIFFRACTIONf_chiral_restr0.061682
X-RAY DIFFRACTIONf_plane_restr0.006844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.2821230.22472217X-RAY DIFFRACTION84
1.72-1.740.23961310.20582295X-RAY DIFFRACTION89
1.74-1.760.2161270.20282455X-RAY DIFFRACTION94
1.76-1.790.28971450.20032549X-RAY DIFFRACTION98
1.79-1.810.24291240.1962664X-RAY DIFFRACTION100
1.81-1.840.1991390.18652581X-RAY DIFFRACTION100
1.84-1.860.21451430.17782586X-RAY DIFFRACTION100
1.86-1.890.2171350.16882607X-RAY DIFFRACTION100
1.89-1.920.18711340.17472605X-RAY DIFFRACTION100
1.92-1.960.2141280.17552637X-RAY DIFFRACTION100
1.96-1.990.18951430.17572612X-RAY DIFFRACTION100
1.99-2.030.19841430.17982616X-RAY DIFFRACTION100
2.03-2.070.2071530.17112586X-RAY DIFFRACTION100
2.07-2.120.19471460.16842603X-RAY DIFFRACTION100
2.12-2.170.17561470.16732608X-RAY DIFFRACTION100
2.17-2.220.18241240.16482635X-RAY DIFFRACTION100
2.22-2.280.19921390.17042622X-RAY DIFFRACTION100
2.28-2.350.18141650.17122609X-RAY DIFFRACTION100
2.35-2.420.17481350.17222635X-RAY DIFFRACTION100
2.42-2.510.22971250.17912648X-RAY DIFFRACTION100
2.51-2.610.17421340.17162629X-RAY DIFFRACTION100
2.61-2.730.191230.1762657X-RAY DIFFRACTION100
2.73-2.870.20291370.16872651X-RAY DIFFRACTION100
2.87-3.050.19311360.17682633X-RAY DIFFRACTION100
3.05-3.290.18551300.172678X-RAY DIFFRACTION100
3.29-3.620.18731420.16142654X-RAY DIFFRACTION100
3.62-4.140.14011490.14082698X-RAY DIFFRACTION100
4.14-5.220.13791520.12942677X-RAY DIFFRACTION100
5.22-51.290.15261450.16042820X-RAY DIFFRACTION100

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