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- PDB-8iox: Escherichia coli OpgD mutant-D388N -

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Basic information

Entry
Database: PDB / ID: 8iox
TitleEscherichia coli OpgD mutant-D388N
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 / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Glycoside hydrolase-type carbohydrate-binding / 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
Glucans biosynthesis protein D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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 1.3Oct 16, 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
C: Glucans biosynthesis protein D
D: Glucans biosynthesis protein D
E: Glucans biosynthesis protein D
F: Glucans biosynthesis protein D
G: Glucans biosynthesis protein D
H: Glucans biosynthesis protein D
I: Glucans biosynthesis protein D
J: Glucans biosynthesis protein D
K: Glucans biosynthesis protein D
L: Glucans biosynthesis protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)770,22222
Polymers766,79912
Non-polymers3,42310
Water11,998666
1
A: Glucans biosynthesis protein D
B: Glucans biosynthesis protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,1423
Polymers127,8002
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Glucans biosynthesis protein D
D: Glucans biosynthesis protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4844
Polymers127,8002
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Glucans biosynthesis protein D
F: Glucans biosynthesis protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4844
Polymers127,8002
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
G: Glucans biosynthesis protein D
H: Glucans biosynthesis protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4844
Polymers127,8002
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
I: Glucans biosynthesis protein D
J: Glucans biosynthesis protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4844
Polymers127,8002
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
K: Glucans biosynthesis protein D
L: Glucans biosynthesis protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,1423
Polymers127,8002
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)226.750, 392.760, 324.648
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

#1: Protein
Glucans biosynthesis protein D


Mass: 63899.949 Da / Num. of mol.: 12 / Mutation: D388N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: opgD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40120
#2: Polysaccharide
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 10 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 4.71 Å3/Da / Density % sol: 73.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG2000MME, TMAO, tris-HCl (pH 8.5)

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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: 2.95→49.143 Å / Num. obs: 301232 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.208 / Net I/σ(I): 13
Reflection shellResolution: 2.95→3 Å / Num. unique obs: 14824 / CC1/2: 0.869

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→49.143 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.889 / Cross valid method: FREE R-VALUE / ESU R: 0.471 / ESU R Free: 0.296
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2322 14722 4.887 %
Rwork0.1937 286509 -
all0.196 --
obs-301231 99.939 %
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: 34.688 Å2
Baniso -1Baniso -2Baniso -3
1--1.584 Å2-0 Å20 Å2
2---0.932 Å2-0 Å2
3---2.516 Å2
Refinement stepCycle: LAST / Resolution: 2.95→49.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms50952 0 230 666 51848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01352752
X-RAY DIFFRACTIONr_bond_other_d0.0350.01547372
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.65671630
X-RAY DIFFRACTIONr_angle_other_deg2.3321.586109084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.23956276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.72221.5333132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.449158340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.01415408
X-RAY DIFFRACTIONr_chiral_restr0.0650.26628
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0260252
X-RAY DIFFRACTIONr_gen_planes_other0.0090.0213332
X-RAY DIFFRACTIONr_nbd_refined0.210.28696
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2320.245962
X-RAY DIFFRACTIONr_nbtor_refined0.1810.224574
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.225218
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.21231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.110.236
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2660.216
X-RAY DIFFRACTIONr_nbd_other0.2480.2104
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.211
X-RAY DIFFRACTIONr_mcbond_it2.7333.53125140
X-RAY DIFFRACTIONr_mcbond_other2.7333.5325139
X-RAY DIFFRACTIONr_mcangle_it4.3365.29531404
X-RAY DIFFRACTIONr_mcangle_other4.3375.29531405
X-RAY DIFFRACTIONr_scbond_it3.1493.80527612
X-RAY DIFFRACTIONr_scbond_other3.1493.80527613
X-RAY DIFFRACTIONr_scangle_it5.0285.58440226
X-RAY DIFFRACTIONr_scangle_other5.0285.58440227
X-RAY DIFFRACTIONr_lrange_it7.18139.10655629
X-RAY DIFFRACTIONr_lrange_other7.18239.10655612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.0270.35110750.28821076X-RAY DIFFRACTION100
3.027-3.110.30411420.26520478X-RAY DIFFRACTION100
3.11-3.20.2689960.23919971X-RAY DIFFRACTION100
3.2-3.2980.2659790.22819448X-RAY DIFFRACTION99.9951
3.298-3.4060.2919610.22718767X-RAY DIFFRACTION100
3.406-3.5260.2478460.21318326X-RAY DIFFRACTION100
3.526-3.6590.2488700.20917686X-RAY DIFFRACTION100
3.659-3.8080.2529180.20116877X-RAY DIFFRACTION100
3.808-3.9780.2218260.18616252X-RAY DIFFRACTION100
3.978-4.1720.2018160.16415516X-RAY DIFFRACTION100
4.172-4.3970.1847330.1514868X-RAY DIFFRACTION100
4.397-4.6640.1747460.14413972X-RAY DIFFRACTION100
4.664-4.9860.1766170.13813240X-RAY DIFFRACTION100
4.986-5.3850.1936150.1512346X-RAY DIFFRACTION100
5.385-5.8990.2186050.18211288X-RAY DIFFRACTION100
5.899-6.5950.2425580.18910268X-RAY DIFFRACTION100
6.595-7.6150.2125390.1939052X-RAY DIFFRACTION100
7.615-9.3250.2233910.197734X-RAY DIFFRACTION100
9.325-13.1820.2063250.1796052X-RAY DIFFRACTION100
13.182-49.090.2711640.2773292X-RAY DIFFRACTION94.9973

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