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- PDB-9fj8: Teth514_1788 1,2-beta-oligomannan phosphorylase in complex with m... -

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Basic information

Entry
Database: PDB / ID: 9fj8
TitleTeth514_1788 1,2-beta-oligomannan phosphorylase in complex with mannotetraose
Components1,2-beta-oligomannan phosphorylase
KeywordsCYTOSOLIC PROTEIN / phosphorylase / carbohydrate / enzyme / mannose
Function / homology1,2-beta-oligomannan phosphorylase / Mannoside phosphorylase / beta-1,4-mannooligosaccharide phosphorylase / GDP-mannose biosynthetic process / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / glycosyltransferase activity / 1,2-beta-oligomannan phosphorylase
Function and homology information
Biological speciesThermoanaerobacter sp. X514 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCioci, G. / Durand, J. / Potocki-Veronese, G. / Ladeveze, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Teth514_1788 1,2-beta-oligomannan phosphorylase in complex with mannotetraose
Authors: Cioci, G. / Durand, J. / Potocki-Veronese, G. / Ladeveze, S.
History
DepositionMay 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1,2-beta-oligomannan phosphorylase
B: 1,2-beta-oligomannan phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,65413
Polymers69,8562
Non-polymers1,79811
Water10,395577
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint5 kcal/mol
Surface area23280 Å2
Unit cell
Length a, b, c (Å)137.338, 137.338, 168.951
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 297 / Label seq-ID: 2 - 297

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 1,2-beta-oligomannan phosphorylase / 1 / 2-beta-oligomannan:phosphate alpha-D-mannosyltransferase


Mass: 34927.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter sp. X514 (bacteria) / Gene: Teth514_1788 / Production host: Escherichia coli (E. coli)
References: UniProt: B0K2C2, 1,2-beta-oligomannan phosphorylase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-2DManpb1-2DManpb1-2DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a1122h-1b_1-5]/1-1-1-1/a2-b1_b2-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(2+1)][b-D-Manp]{[(2+1)][b-D-Manp]{[(2+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-2DManpb1-2DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1b_1-5]/1-1-1/a2-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(2+1)][b-D-Manp]{[(2+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 586 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / 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: 6.73 Å3/Da / Density % sol: 81.72 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop
Details: 1.4M Ammonium Sulphate 0.2M NaCl 0.1M Na Cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 82187 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.107 / Net I/σ(I): 5.2
Reflection shellResolution: 2.3→2.42 Å / Rmerge(I) obs: 0.56 / Num. unique obs: 11887 / CC1/2: 0.925

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.675 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.181 / WRfactor Rwork: 0.167 / SU B: 3.057 / SU ML: 0.073 / Average fsc free: 0.9765 / Average fsc work: 0.9804 / Cross valid method: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.115
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1844 4054 4.936 %
Rwork0.1693 78082 -
all0.17 --
obs-82136 99.95 %
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: 34.006 Å2
Baniso -1Baniso -2Baniso -3
1-0.645 Å20.323 Å20 Å2
2--0.645 Å2-0 Å2
3----2.094 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4807 0 117 577 5501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125046
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164765
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.8366835
X-RAY DIFFRACTIONr_angle_other_deg0.4251.77811017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2815593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.147530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55610854
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.87110232
X-RAY DIFFRACTIONr_chiral_restr0.0520.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025777
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021123
X-RAY DIFFRACTIONr_nbd_refined0.1760.2666
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.24292
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22301
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22452
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2429
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0340.29
X-RAY DIFFRACTIONr_nbd_other0.1160.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.090.217
X-RAY DIFFRACTIONr_mcbond_it1.073.6232378
X-RAY DIFFRACTIONr_mcbond_other1.0693.6232378
X-RAY DIFFRACTIONr_mcangle_it1.8486.5092969
X-RAY DIFFRACTIONr_mcangle_other1.8486.512970
X-RAY DIFFRACTIONr_scbond_it1.4793.8332668
X-RAY DIFFRACTIONr_scbond_other1.4793.8342661
X-RAY DIFFRACTIONr_scangle_it2.5956.9693866
X-RAY DIFFRACTIONr_scangle_other2.5996.9723855
X-RAY DIFFRACTIONr_lrange_it4.44635.425416
X-RAY DIFFRACTIONr_lrange_other4.05634.4295258
X-RAY DIFFRACTIONr_ncsr_local_group_10.0520.0510018
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.051570.05011
12AX-RAY DIFFRACTIONLocal ncs0.051570.05011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.3-2.360.2733130.23956960.2460090.9570.9681000.216
2.36-2.4240.252990.22655540.22758540.9660.97199.98290.203
2.424-2.4940.2242880.21854250.21857130.9710.9731000.196
2.494-2.5710.2392540.20752590.20855130.9670.9741000.188
2.571-2.6550.1882510.18851460.18853970.9790.9781000.173
2.655-2.7480.22650.18649120.18751770.9760.9791000.174
2.748-2.8510.2052730.17547310.17650050.9770.98199.980.163
2.851-2.9670.1882450.17445950.17448430.9770.98299.9380.165
2.967-3.0980.1992260.1744060.17146340.9740.98399.95680.164
3.098-3.2490.1782230.17942340.17944610.9810.98299.91030.176
3.249-3.4240.21920.18640360.18742320.9810.98399.90550.186
3.424-3.6310.1821710.17838470.17940190.9860.98699.97510.179
3.631-3.880.1781890.16435820.16437730.9830.98699.9470.167
3.88-4.1880.1481860.14233550.14235430.9870.98899.94360.147
4.188-4.5850.1361790.12630860.12732670.9880.9999.93880.133
4.585-5.120.1541390.12928290.1329700.990.99299.93270.136
5.12-5.9010.1751300.14824990.14926300.9840.9999.9620.154
5.901-7.2010.1911020.16421510.16522530.9820.9871000.168
7.201-10.0740.181890.16217050.16317940.9830.9851000.169
10.074-48.6750.205400.18710340.18710760.9780.97499.81410.198

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