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- PDB-8x18: Xanthomonas campestris pv. campestris OpgD mutant-D379N with beta... -

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Basic information

Entry
Database: PDB / ID: 8x18
TitleXanthomonas campestris pv. campestris OpgD mutant-D379N with beta-1,2-glucan
ComponentsGlucans biosynthesis protein D
KeywordsTRANSFERASE / transglycosylase
Function / homology
Function and homology information


beta-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 / 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 speciesXanthomonas campestris pv. campestris str. ATCC 33913 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMotouchi, S. / Nakajima, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJSP2151 Japan
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Discovery of Anomer-Inverting Transglycosylase: Cyclic Glucohexadecaose-Producing Enzyme from Xanthomonas , a Phytopathogen.
Authors: Motouchi, S. / Komba, S. / Nakai, H. / Nakajima, M.
History
DepositionNov 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 28, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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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)129,56213
Polymers121,7992
Non-polymers7,76311
Water9,746541
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-11 kcal/mol
Surface area40730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.878, 171.878, 128.691
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glucans biosynthesis protein D


Mass: 60899.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris str. ATCC 33913 (bacteria)
Strain: ATCC 33913 / Gene: opgD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8P3C6

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Sugars , 3 types, 3 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-(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: 3585.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,22,21/[a2122h-1b_1-5]/1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1/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-p1_p2-q1_q2-r1_r2-s1_s2-t1_t2-u1_u2-v1WURCSPDB2Glycan 1.1.0
#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


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
#4: 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


Type: oligosaccharide / Mass: 1639.423 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,10,9/[a2122h-1b_1-5]/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-j1WURCSPDB2Glycan 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]{}}}}}}}}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 549 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.89 Å3/Da / Density % sol: 74.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Bis-Tris HCl (pH5.5), Ammonium sulfate, glycerol, 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: Jun 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→48.723 Å / Num. obs: 102253 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 0.996 / Net I/σ(I): 11.6
Reflection shellResolution: 2.25→2.29 Å / Num. unique obs: 5064 / CC1/2: 0.83

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→48.723 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: FREE R-VALUE / ESU R: 0.152 / ESU R Free: 0.123
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1761 5213 5.1 %
Rwork0.1726 96994 -
all0.173 --
obs-102207 99.987 %
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: 31.145 Å2
Baniso -1Baniso -2Baniso -3
1--0.632 Å2-0.316 Å2-0 Å2
2---0.632 Å20 Å2
3---2.049 Å2
Refinement stepCycle: LAST / Resolution: 2.25→48.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7947 0 524 541 9012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0128713
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167845
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.66611832
X-RAY DIFFRACTIONr_angle_other_deg0.8371.57418168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9775990
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.316565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57101259
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.1410411
X-RAY DIFFRACTIONr_chiral_restr0.0650.21299
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029822
X-RAY DIFFRACTIONr_gen_planes_other0.0120.022070
X-RAY DIFFRACTIONr_nbd_refined0.4090.21505
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2290.27148
X-RAY DIFFRACTIONr_nbtor_refined0.1840.24086
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.24532
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2516
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0440.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2350.26
X-RAY DIFFRACTIONr_nbd_other0.1970.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1240.214
X-RAY DIFFRACTIONr_mcbond_it3.0423.0253972
X-RAY DIFFRACTIONr_mcbond_other3.0423.0253972
X-RAY DIFFRACTIONr_mcangle_it4.3775.4174958
X-RAY DIFFRACTIONr_mcangle_other4.3775.4174959
X-RAY DIFFRACTIONr_scbond_it4.2973.5244741
X-RAY DIFFRACTIONr_scbond_other4.2973.5244742
X-RAY DIFFRACTIONr_scangle_it6.376.2286874
X-RAY DIFFRACTIONr_scangle_other6.3696.2276875
X-RAY DIFFRACTIONr_lrange_it7.94230.5729458
X-RAY DIFFRACTIONr_lrange_other7.95130.4579374
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc workWRfactor Rwork
2.25-2.3080.2274090.21771270.21875360.9680.970.19
2.308-2.3710.233690.22269300.22272990.9670.9690.192
2.371-2.440.2263810.21267820.21271630.9690.9720.182
2.44-2.5150.2193360.19765760.19869120.9730.9760.169
2.515-2.5970.1943820.1963190.1967010.9780.9780.16
2.597-2.6880.1863260.18161880.18165140.9790.980.153
2.688-2.7890.1643090.18259660.18162750.9830.980.154
2.789-2.9030.172990.17657390.17660380.9820.9810.151
2.903-3.0310.173200.16854840.16858040.9820.9830.145
3.031-3.1790.1623030.16552230.16555260.9850.9840.148
3.179-3.350.172690.16850220.16952910.9820.9840.155
3.35-3.5520.1842370.16747470.16849840.9830.9860.157
3.552-3.7960.1772250.16844600.16946850.9850.9860.161
3.796-4.0980.1581860.14442010.14543870.9850.9890.139
4.098-4.4860.1342170.1338170.1340340.9890.990.128
4.486-5.010.1371970.13734620.13736590.9890.990.137
5.01-5.7750.1551460.16730940.16732400.9880.9860.165
5.775-7.0480.2061420.20626100.20627520.980.9790.2
7.048-9.8650.191990.1920610.1921600.9830.9790.193
9.865-48.7230.226610.22211860.22212470.9680.9690.236

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