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- PDB-9gpd: ManDH5 E303Q mutant in complex with mannotriose a beta-D-Mannanas... -

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Basic information

Entry
Database: PDB / ID: 9gpd
TitleManDH5 E303Q mutant in complex with mannotriose 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 / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSivron, Y. / Romano, A. / Shoham, Y. / Shoham, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: ManDH5 E303Q mutant in complex with mannotriose, 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)67,9122
Polymers67,4071
Non-polymers5041
Water12,322684
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint8 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.785, 99.114, 153.841
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-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1M MMT buffer pH 7.0, 27% PEG 1500, 0.01% Na-azide Protein solution (in tris) was mixed with mannotetraose solution (in tris), final conentrations: 0.22mM protein, 15mM M3

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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: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.35→83.3 Å / Num. obs: 159142 / % possible obs: 99.7 % / Redundancy: 13.3 % / Biso Wilson estimate: 10.99 Å2 / CC1/2: 1 / Net I/σ(I): 22.1
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 7778 / CC1/2: 0.894 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.14_3228refinement
XDSdata reduction
xia2CCP4i2 7.0.078data scaling
PHASER1.14_3228phasing
Coot8, 9, Wincootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native ManDH5

Resolution: 1.35→83.3 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1674 7938 4.99 %
Rwork0.1558 --
obs0.1564 159134 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→83.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4706 0 34 684 5424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094961
X-RAY DIFFRACTIONf_angle_d1.1256750
X-RAY DIFFRACTIONf_dihedral_angle_d7.4992904
X-RAY DIFFRACTIONf_chiral_restr0.086688
X-RAY DIFFRACTIONf_plane_restr0.008853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36530.24822530.2094959X-RAY DIFFRACTION99
1.3653-1.38140.21732500.20344979X-RAY DIFFRACTION99
1.3814-1.39830.22462840.20434935X-RAY DIFFRACTION99
1.3983-1.4160.21742390.19435023X-RAY DIFFRACTION99
1.416-1.43460.1962360.18654993X-RAY DIFFRACTION99
1.4346-1.45420.18592320.18135027X-RAY DIFFRACTION99
1.4542-1.4750.19862430.17615011X-RAY DIFFRACTION99
1.475-1.4970.19532770.17594981X-RAY DIFFRACTION99
1.497-1.52040.19622230.17855013X-RAY DIFFRACTION99
1.5204-1.54540.17592430.17215004X-RAY DIFFRACTION100
1.5454-1.5720.17942510.17075014X-RAY DIFFRACTION100
1.572-1.60060.19492960.1654969X-RAY DIFFRACTION100
1.6006-1.63140.17592750.16214981X-RAY DIFFRACTION100
1.6314-1.66470.16372540.15155060X-RAY DIFFRACTION100
1.6647-1.70090.18152790.15744980X-RAY DIFFRACTION100
1.7009-1.74050.18472480.1555068X-RAY DIFFRACTION100
1.7405-1.7840.16322620.15565042X-RAY DIFFRACTION100
1.784-1.83220.16632480.15715060X-RAY DIFFRACTION100
1.8322-1.88610.17432900.1575003X-RAY DIFFRACTION100
1.8861-1.9470.15922960.14935037X-RAY DIFFRACTION100
1.947-2.01660.15722830.14915014X-RAY DIFFRACTION100
2.0166-2.09740.14322420.14735091X-RAY DIFFRACTION100
2.0974-2.19280.15492760.14555052X-RAY DIFFRACTION100
2.1928-2.30850.14622710.14275048X-RAY DIFFRACTION100
2.3085-2.45310.15593090.14345061X-RAY DIFFRACTION100
2.4531-2.64250.16242740.14615071X-RAY DIFFRACTION100
2.6425-2.90840.16362670.15085103X-RAY DIFFRACTION100
2.9084-3.32930.17382610.15675143X-RAY DIFFRACTION100
3.3293-4.19460.16663020.14815123X-RAY DIFFRACTION100
4.1946-77.04560.15652740.15715351X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 20.2857 Å / Origin y: 13.9622 Å / Origin z: 40.7253 Å
111213212223313233
T0.0809 Å2-0 Å2-0.0011 Å2-0.097 Å20.0007 Å2--0.1006 Å2
L0.2452 °20.1811 °20.0445 °2-0.4767 °20.0107 °2--0.3315 °2
S-0.0095 Å °-0.0252 Å °-0.0029 Å °0.0099 Å °-0.0066 Å °-0.0384 Å °-0.0117 Å °0.0041 Å °-0.0013 Å °
Refinement TLS groupSelection details: all

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