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- PDB-8ip2: Escherichia coli OpgG mutant-D361N with beta-1,2-glucan -

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Basic information

Entry
Database: PDB / ID: 8ip2
TitleEscherichia coli OpgG mutant-D361N with beta-1,2-glucan
ComponentsGlucans biosynthesis protein G
KeywordsHYDROLASE / Beta-1 / 2-glucanase
Function / homology
Function and homology information


beta-glucan biosynthetic process / catalytic activity / outer membrane-bounded periplasmic space / carbohydrate binding
Similarity search - Function
Glucan biosynthesis protein G / Glucan biosynthesis, periplasmic, MdoG C-terminal / Glucan biosynthesis protein MdoG/MdoD / Periplasmic glucan biosynthesis protein, MdoG / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Glucans biosynthesis protein G
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsMotouchi, S. / Nakajima, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Novel glycoside hydrolase family enzymes from Escherichia coli associating with osmo-regulated periplasmic glucan synthesis
Authors: Motouchi, S. / Nakajima, M.
History
DepositionMar 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucans biosynthesis protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6652
Polymers59,0521
Non-polymers2,6121
Water2,198122
1
A: Glucans biosynthesis protein G
hetero molecules

A: Glucans biosynthesis protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,3294
Polymers118,1052
Non-polymers5,2252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area14990 Å2
ΔGint137 kcal/mol
Surface area37540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.821, 80.970, 213.225
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-625-

HOH

21A-719-

HOH

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Components

#1: Protein Glucans biosynthesis protein G


Mass: 59052.453 Da / Num. of mol.: 1 / Mutation: D361N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: opgG / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P33136
#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-(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: 2612.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,16,15/[a2122h-1b_1-5]/1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1/a2-b1_b2-c1_c2-d1_d2-e1_e2-f1_f2-g1_g2-h1_h2-i1_i2-j1_j2-k1_k2-l1_l2-m1_m2-n1_n2-o1_o2-p1WURCSPDB2Glycan 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]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{}}}}}}}}}}}}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MMT (pH 5.0), PEG400

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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: Jul 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→48.34 Å / Num. obs: 50021 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 17.2
Reflection shellResolution: 1.81→1.85 Å / Num. unique obs: 2971 / CC1/2: 0.891

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→48.34 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: FREE R-VALUE / ESU R: 0.248 / ESU R Free: 0.138
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.254 2535 5.074 %
Rwork0.2134 47424 -
all0.215 --
obs-49959 99.876 %
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: 41.948 Å2
Baniso -1Baniso -2Baniso -3
1--0.123 Å2-0 Å20 Å2
2---0.075 Å2-0 Å2
3---0.198 Å2
Refinement stepCycle: LAST / Resolution: 1.81→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3819 0 177 122 4118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0134111
X-RAY DIFFRACTIONr_bond_other_d0.0340.0153825
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.7235605
X-RAY DIFFRACTIONr_angle_other_deg3.3791.6468806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4575475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45222.477214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0815650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2511525
X-RAY DIFFRACTIONr_chiral_restr0.0980.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024453
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02933
X-RAY DIFFRACTIONr_nbd_refined0.2010.2632
X-RAY DIFFRACTIONr_symmetry_nbd_other0.230.23618
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21952
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1150.22034
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2187
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0250.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1420.29
X-RAY DIFFRACTIONr_nbd_other0.2390.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.211
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0020.21
X-RAY DIFFRACTIONr_mcbond_it0.284.3521909
X-RAY DIFFRACTIONr_mcbond_other0.2944.351908
X-RAY DIFFRACTIONr_mcangle_it0.4916.5112381
X-RAY DIFFRACTIONr_mcangle_other0.4986.5142382
X-RAY DIFFRACTIONr_scbond_it0.2864.5192202
X-RAY DIFFRACTIONr_scbond_other0.2864.522203
X-RAY DIFFRACTIONr_scangle_it0.4826.6533224
X-RAY DIFFRACTIONr_scangle_other0.4826.6543225
X-RAY DIFFRACTIONr_lrange_it0.72148.5414277
X-RAY DIFFRACTIONr_lrange_other0.72364.6394261
X-RAY DIFFRACTIONr_rigid_bond_restr13.05737862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.8570.351960.3693435X-RAY DIFFRACTION99.9449
1.857-1.9080.3891550.3443450X-RAY DIFFRACTION99.9723
1.908-1.9630.3581810.3123277X-RAY DIFFRACTION100
1.963-2.0230.31670.2963175X-RAY DIFFRACTION99.7612
2.023-2.090.2951810.2763075X-RAY DIFFRACTION99.9079
2.09-2.1630.3161710.2522973X-RAY DIFFRACTION99.8729
2.163-2.2440.3251550.2472925X-RAY DIFFRACTION99.9027
2.244-2.3360.3291490.2432793X-RAY DIFFRACTION99.9321
2.336-2.4390.2691240.2112709X-RAY DIFFRACTION99.8942
2.439-2.5580.271180.2212570X-RAY DIFFRACTION100
2.558-2.6960.2361360.2162460X-RAY DIFFRACTION99.923
2.696-2.8590.2561090.2082327X-RAY DIFFRACTION99.918
2.859-3.0550.2641140.2232172X-RAY DIFFRACTION99.9126
3.055-3.2990.2811130.2172030X-RAY DIFFRACTION99.8602
3.299-3.6120.216980.2021883X-RAY DIFFRACTION99.6479
3.612-4.0360.2271150.1791695X-RAY DIFFRACTION99.6696
4.036-4.6550.206660.1521555X-RAY DIFFRACTION99.6312
4.655-5.6880.204650.1661312X-RAY DIFFRACTION99.855
5.688-7.9890.226760.186998X-RAY DIFFRACTION100
7.989-48.340.209460.19610X-RAY DIFFRACTION99.5448

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