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

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Basic information

Entry
Database: PDB / ID: 9gqs
TitleTeth514_1788 1,2-beta-oligomannan phosphorylase in complex with mannose (+1) and phosphate
Components1,2-beta-oligomannan phosphorylase
KeywordsCARBOHYDRATE / phosphorylase
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 / alpha-D-mannopyranose / PHOSPHATE ION / 1,2-beta-oligomannan phosphorylase
Function and homology information
Biological speciesThermoanaerobacter sp. X514 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCioci, G. / Durand, J. / Veronese-Potocki, G. / Ladeveze, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Teth514_1788 1,2-beta-oligomannan phosphorylase in complex with mannose (-1) and phosphate
Authors: Cioci, G. / Durand, J. / Veronese-Potocki, G. / Ladeveze, S.
History
DepositionSep 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,09316
Polymers69,8562
Non-polymers1,23714
Water11,746652
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.269, 137.269, 169.384
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
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 2 - 298 / Label seq-ID: 2 - 298

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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

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Components

#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
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium cacodylate trihydrate pH 6.5, 1.0 M Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 64153 / % possible obs: 99.8 % / Redundancy: 5.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.112 / Net I/σ(I): 6.4
Reflection shellResolution: 2.5→2.64 Å / Num. unique obs: 9258 / CC1/2: 0.757

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→44.972 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.594 / SU ML: 0.093 / Cross valid method: FREE R-VALUE / ESU R: 0.145 / ESU R Free: 0.132
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1721 3113 4.856 %
Rwork0.1505 60991 -
all0.152 --
obs-64104 99.763 %
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: 34.922 Å2
Baniso -1Baniso -2Baniso -3
1-0.017 Å20.009 Å20 Å2
2--0.017 Å2-0 Å2
3----0.056 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4807 0 76 652 5535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0124998
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164735
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.8336760
X-RAY DIFFRACTIONr_angle_other_deg0.4681.7810930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5175592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.76530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96610855
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.47610233
X-RAY DIFFRACTIONr_chiral_restr0.0620.2716
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025776
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021124
X-RAY DIFFRACTIONr_nbd_refined0.1810.2765
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.24481
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22300
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22540
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2413
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1230.215
X-RAY DIFFRACTIONr_nbd_other0.1790.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.130.210
X-RAY DIFFRACTIONr_mcbond_it23.5532374
X-RAY DIFFRACTIONr_mcbond_other23.5532374
X-RAY DIFFRACTIONr_mcangle_it3.0936.3772964
X-RAY DIFFRACTIONr_mcangle_other3.0936.3782965
X-RAY DIFFRACTIONr_scbond_it3.9044.0362624
X-RAY DIFFRACTIONr_scbond_other3.9034.0362625
X-RAY DIFFRACTIONr_scangle_it6.4457.1663796
X-RAY DIFFRACTIONr_scangle_other6.4447.1663797
X-RAY DIFFRACTIONr_lrange_it8.23137.1285487
X-RAY DIFFRACTIONr_lrange_other8.2337.1275488
X-RAY DIFFRACTIONr_ncsr_local_group_10.0570.0510105
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.057230.05011
12AX-RAY DIFFRACTIONLocal ncs0.057230.05011
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
2.5-2.5650.2682040.2544800.2546870.9530.96199.9360.229
2.565-2.6350.2331950.23343640.23345670.9650.96799.82480.209
2.635-2.7110.282210.25141960.25244360.9540.96499.57170.224
2.711-2.7940.2551950.21541140.21743320.9640.97399.46910.189
2.794-2.8850.2282130.19439290.19641640.9660.97799.47170.168
2.885-2.9860.2242040.18438710.18640830.9710.9899.80410.157
2.986-3.0980.2121900.16636750.16839040.9710.98399.0010.144
3.098-3.2240.1741640.1636050.16137710.9810.98499.9470.141
3.224-3.3670.1741610.16134680.16136300.9820.98699.97250.147
3.367-3.530.181800.16333160.16434970.9830.98799.97140.152
3.53-3.720.1671600.15231380.15332980.9850.9891000.141
3.72-3.9440.161680.13829780.13931460.9850.9911000.128
3.944-4.2140.1321450.11228040.11329490.9910.9931000.104
4.214-4.5480.1251570.09726380.09927950.9910.9951000.09
4.548-4.9770.0991450.07823900.07925350.9940.9961000.073
4.977-5.5560.119930.10422310.10423240.9930.9941000.096
5.556-6.3990.1581260.12219340.12420600.9870.9931000.114
6.399-7.7980.129790.12317070.12317860.9920.9921000.115
7.798-10.8660.156560.12813580.12914140.9880.991000.122
10.866-44.9720.21570.2327950.238620.9750.95998.83990.237

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