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- PDB-9gpf: ManDH5 E303Q in complex with mannopentaose after co-crystalliztio... -

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Basic information

Entry
Database: PDB / ID: 9gpf
TitleManDH5 E303Q in complex with mannopentaose after co-crystalliztion with mannopentaose 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 / beta-cellopentaose / 4beta-beta-mannobiose / DUF5060 domain-containing protein
Function and homology information
Biological speciesDictyoglomus thermophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 mannopentaose after co-crystalliztion with mannopentaose 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
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)68,8556
Polymers67,4071
Non-polymers1,4475
Water10,323573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint17 kcal/mol
Surface area22070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.568, 98.902, 153.246
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: 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: 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: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D- ...beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellopentaose
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a1122h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 573 / 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: 2.8 Å3/Da / Density meas: 56.2 Mg/m3 / Density % sol: 53.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MMT buffer, pH 7.0, 28% PEG 1500, 0.01% Na-azide, 24.2mM Mannopentaose (drop ratio of 1:245 for protein:sugar)

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→83.1 Å / Num. obs: 94609 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 1 / Net I/σ(I): 28
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 5.6 / Num. unique obs: 4656 / CC1/2: 0.964 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3228refinement
XDSdata reduction
xia2CCP4 7.8.078data scaling
PHASER1.14_3228phasing
Coot8,9, Wincootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native ManDH5

Resolution: 1.6→76.623 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1744 4844 5.12 %
Rwork0.1594 --
obs0.1601 94599 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→76.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4735 0 97 573 5405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065010
X-RAY DIFFRACTIONf_angle_d0.8986802
X-RAY DIFFRACTIONf_dihedral_angle_d6.6714077
X-RAY DIFFRACTIONf_chiral_restr0.057702
X-RAY DIFFRACTIONf_plane_restr0.006842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.23721520.19342936X-RAY DIFFRACTION100
1.6182-1.63720.21281720.18722988X-RAY DIFFRACTION100
1.6372-1.65720.19931820.18392951X-RAY DIFFRACTION100
1.6572-1.67820.21441550.18112948X-RAY DIFFRACTION100
1.6782-1.70030.22531700.18032945X-RAY DIFFRACTION100
1.7003-1.72360.19841560.17332979X-RAY DIFFRACTION100
1.7236-1.74820.17691670.16372952X-RAY DIFFRACTION100
1.7482-1.77430.22041550.1673008X-RAY DIFFRACTION100
1.7743-1.8020.20391360.16982996X-RAY DIFFRACTION100
1.802-1.83160.19221460.16652958X-RAY DIFFRACTION100
1.8316-1.86310.17661710.16022969X-RAY DIFFRACTION100
1.8631-1.8970.19451860.16272935X-RAY DIFFRACTION100
1.897-1.93350.19591630.15552969X-RAY DIFFRACTION100
1.9335-1.9730.18961640.16072977X-RAY DIFFRACTION100
1.973-2.01590.18651600.16112979X-RAY DIFFRACTION100
2.0159-2.06280.18531620.15892948X-RAY DIFFRACTION100
2.0628-2.11440.16971590.1582986X-RAY DIFFRACTION100
2.1144-2.17150.16391690.1542978X-RAY DIFFRACTION100
2.1715-2.23540.17641680.1582987X-RAY DIFFRACTION100
2.2354-2.30760.18321740.15622982X-RAY DIFFRACTION100
2.3076-2.39010.19291730.16182956X-RAY DIFFRACTION100
2.3901-2.48580.1751700.16652982X-RAY DIFFRACTION100
2.4858-2.59890.19471590.15953010X-RAY DIFFRACTION100
2.5989-2.73590.19411320.1663026X-RAY DIFFRACTION100
2.7359-2.90740.1741470.16153028X-RAY DIFFRACTION100
2.9074-3.13180.1871710.15533007X-RAY DIFFRACTION100
3.1318-3.4470.15061390.15223046X-RAY DIFFRACTION100
3.447-3.94580.141630.14323062X-RAY DIFFRACTION100
3.9458-4.97120.13851710.13753060X-RAY DIFFRACTION100
4.9712-76.60.16351520.17873207X-RAY DIFFRACTION100

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