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- PDB-9gpa: ManDH5- a beta-D-Mannanase of GH5 family from Dictyoglomus thermo... -

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Basic information

Entry
Database: PDB / ID: 9gpa
TitleManDH5- 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 / D-MALATE / TRIETHYLENE GLYCOL / DUF5060 domain-containing protein
Function and homology information
Biological speciesDictyoglomus thermophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSivron, Y. / Romano, A. / Shoham, Y. / Shoham, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: ManDH5- 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)69,17411
Polymers67,4081
Non-polymers1,76610
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint34 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.648, 99.256, 153.284
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

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 7 types, 423 molecules

#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: 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
#6: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.81 Å3/Da / Density % sol: 0.563 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M MMT buffer (pH 7.0),30% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 31, 2018 / Details: Focusing optics- Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.5→49.63 Å / Num. obs: 1151036 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 14.9 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.6
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 67102 / CC1/2: 0.918 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSCCP4i2 7.0.078data scaling
PHENIX1.14.3228_000refinement
PHASER1.14.3228_000phasing
Coot0.8-0.9model building
xia2CCP4i2 7.0.078data reduction
CootWincoot 0.8.9.2model building
xia2CCP4i2 7.0.078data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Semet derivative

Resolution: 1.5→49.63 Å / SU ML: 0.1359 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.9229 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1609 5961 5.18 %
Rwork0.1442 109135 -
obs0.1451 115096 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.81 Å2
Refinement stepCycle: LAST / Resolution: 1.5→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4690 0 118 413 5221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084983
X-RAY DIFFRACTIONf_angle_d1.07156731
X-RAY DIFFRACTIONf_chiral_restr0.0632669
X-RAY DIFFRACTIONf_plane_restr0.008844
X-RAY DIFFRACTIONf_dihedral_angle_d6.97923998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.21951980.20433609X-RAY DIFFRACTION99.95
1.52-1.530.22532120.18883635X-RAY DIFFRACTION99.84
1.53-1.550.24071990.16813573X-RAY DIFFRACTION99.92
1.55-1.570.19361850.15393589X-RAY DIFFRACTION99.84
1.57-1.590.17722170.15293606X-RAY DIFFRACTION99.95
1.59-1.620.18291940.15273592X-RAY DIFFRACTION99.97
1.62-1.640.22132040.1573611X-RAY DIFFRACTION99.95
1.64-1.660.18672030.15273598X-RAY DIFFRACTION99.95
1.66-1.690.19892020.15163629X-RAY DIFFRACTION99.95
1.69-1.720.17661780.14623621X-RAY DIFFRACTION99.95
1.72-1.750.19731760.14263624X-RAY DIFFRACTION99.89
1.75-1.780.18152140.14253600X-RAY DIFFRACTION99.9
1.78-1.810.20082340.14513574X-RAY DIFFRACTION99.97
1.81-1.850.17881780.13633625X-RAY DIFFRACTION99.97
1.85-1.890.16422000.12813602X-RAY DIFFRACTION100
1.89-1.930.15462140.12133647X-RAY DIFFRACTION99.9
1.93-1.980.16421660.12443651X-RAY DIFFRACTION99.97
1.98-2.040.15162020.13083599X-RAY DIFFRACTION99.95
2.04-2.10.15281790.13093682X-RAY DIFFRACTION99.95
2.1-2.160.15372110.12673597X-RAY DIFFRACTION99.95
2.16-2.240.14412040.12193622X-RAY DIFFRACTION99.97
2.24-2.330.13641830.12693652X-RAY DIFFRACTION99.97
2.33-2.440.15621960.12923653X-RAY DIFFRACTION99.9
2.44-2.560.15312060.14763649X-RAY DIFFRACTION99.92
2.56-2.730.15012070.14283641X-RAY DIFFRACTION100
2.73-2.940.15362010.14533668X-RAY DIFFRACTION99.95
2.94-3.230.16722140.15493666X-RAY DIFFRACTION99.97
3.23-3.70.16471780.1523713X-RAY DIFFRACTION100
3.7-4.660.13532370.13493693X-RAY DIFFRACTION100

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