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- PDB-8ip1: Escherichia coli OpgD mutant-D388N with beta-1,2-glucan -

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Basic information

Entry
Database: PDB / ID: 8ip1
TitleEscherichia coli OpgD mutant-D388N with beta-1,2-glucan
ComponentsGlucans biosynthesis protein D
KeywordsHYDROLASE / Beta-1 / 2-glucanase
Function / homology
Function and homology information


beta-glucan biosynthetic process / glucan biosynthetic process / catalytic activity / outer membrane-bounded periplasmic space / carbohydrate binding
Similarity search - Function
Glucan biosynthesis, MdoD / Glucan biosynthesis, periplasmic, MdoG C-terminal / Glucan biosynthesis protein MdoG/MdoD / Periplasmic glucan biosynthesis protein, MdoG / Glycoside hydrolase-type carbohydrate-binding / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Galactose mutarotase-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Glucans biosynthesis protein D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsMotouchi, S. / Nakajima, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Commun Biol / Year: 2023
Title: Identification of enzymatic functions of osmo-regulated periplasmic glucan biosynthesis proteins from Escherichia coli reveals a novel glycoside hydrolase family.
Authors: Motouchi, S. / Kobayashi, K. / Nakai, H. / Nakajima, M.
History
DepositionMar 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 17, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucans biosynthesis protein D
B: Glucans biosynthesis protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,0907
Polymers127,8002
Non-polymers4,2905
Water10,196566
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14280 Å2
ΔGint84 kcal/mol
Surface area39660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.092, 87.099, 110.853
Angle α, β, γ (deg.)90.000, 101.132, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glucans biosynthesis protein D


Mass: 63899.949 Da / Num. of mol.: 2 / Mutation: D388N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: opgD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40120

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D- ...beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1801.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,11,10/[a2122h-1b_1-5]/1-1-1-1-1-1-1-1-1-1-1/a2-b1_b2-c1_c2-d1_d2-e1_e2-f1_f2-g1_g2-h1_h2-i1_i2-j1_j2-k1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{}}}}}}}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D- ...beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 2125.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,13,12/[a2122h-1b_1-5]/1-1-1-1-1-1-1-1-1-1-1-1-1/a2-b1_b2-c1_c2-d1_d2-e1_e2-f1_f2-g1_g2-h1_h2-i1_i2-j1_j2-k1_k2-l1_l2-m1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{}}}}}}}}}}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 569 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MMT (pH 4.0), PEG1500, Beta-1,2-glucan

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→47.74 Å / Num. obs: 66585 / % possible obs: 99.3 % / Redundancy: 6.5 % / CC1/2: 0.996 / Net I/σ(I): 12.8
Reflection shellResolution: 2.06→2.11 Å / Num. unique obs: 4130 / CC1/2: 0.697

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→47.74 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.198 / WRfactor Rwork: 0.155 / Average fsc free: 0.9129 / Average fsc work: 0.9237 / Cross valid method: FREE R-VALUE / ESU R: 0.211 / ESU R Free: 0.177
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.224 3252 4.886 %
Rwork0.1751 63310 -
all0.178 --
obs-66562 99.212 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.845 Å2
Baniso -1Baniso -2Baniso -3
1--1.061 Å20 Å2-1.133 Å2
2--2.574 Å2-0 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.06→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8157 0 290 566 9013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138714
X-RAY DIFFRACTIONr_bond_other_d0.0340.0157899
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.711856
X-RAY DIFFRACTIONr_angle_other_deg3.1381.62518145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.46651001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.7921.36500
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.956151337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.371568
X-RAY DIFFRACTIONr_chiral_restr0.0730.21166
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029611
X-RAY DIFFRACTIONr_gen_planes_other0.010.022149
X-RAY DIFFRACTIONr_nbd_refined0.1980.21425
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.27644
X-RAY DIFFRACTIONr_nbtor_refined0.1720.24110
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1270.24098
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2637
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0950.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.110.219
X-RAY DIFFRACTIONr_nbd_other0.2640.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1470.222
X-RAY DIFFRACTIONr_mcbond_it1.4932.2824016
X-RAY DIFFRACTIONr_mcbond_other1.4912.2814015
X-RAY DIFFRACTIONr_mcangle_it2.1923.4155013
X-RAY DIFFRACTIONr_mcangle_other2.1923.4165014
X-RAY DIFFRACTIONr_scbond_it2.0242.4814698
X-RAY DIFFRACTIONr_scbond_other2.0242.4824699
X-RAY DIFFRACTIONr_scangle_it3.1593.6326843
X-RAY DIFFRACTIONr_scangle_other3.1593.6326844
X-RAY DIFFRACTIONr_lrange_it4.32126.1159534
X-RAY DIFFRACTIONr_lrange_other4.33726.1139535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.1140.2892110.2574341X-RAY DIFFRACTION92.7654
2.114-2.1710.2762120.2274579X-RAY DIFFRACTION98.8854
2.171-2.2340.262450.2054449X-RAY DIFFRACTION99.8086
2.234-2.3030.2572010.1884319X-RAY DIFFRACTION99.9116
2.303-2.3790.2522160.1844194X-RAY DIFFRACTION99.932
2.379-2.4620.2492090.1864028X-RAY DIFFRACTION99.9057
2.462-2.5550.2341980.1723966X-RAY DIFFRACTION99.928
2.555-2.6590.2242040.1743721X-RAY DIFFRACTION99.8474
2.659-2.7770.2211960.1733631X-RAY DIFFRACTION99.9739
2.777-2.9130.2241890.1693456X-RAY DIFFRACTION99.9452
2.913-3.070.2161480.1723307X-RAY DIFFRACTION99.8266
3.07-3.2560.241830.1823070X-RAY DIFFRACTION99.9386
3.256-3.4810.2491570.1832949X-RAY DIFFRACTION99.8393
3.481-3.7590.2271580.1742693X-RAY DIFFRACTION99.8949
3.759-4.1180.1851350.1552520X-RAY DIFFRACTION99.6248
4.118-4.6030.1821190.1352275X-RAY DIFFRACTION99.75
4.603-5.3140.155850.1342032X-RAY DIFFRACTION99.7644
5.314-6.5040.2541020.1771709X-RAY DIFFRACTION99.6698
6.504-9.1810.169490.1621346X-RAY DIFFRACTION99.9284
9.181-47.740.175350.193726X-RAY DIFFRACTION94.5342

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