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- PDB-7qsg: Methylmannose polysaccharide mannosyltransferase from M. hassiacum -

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Basic information

Entry
Database: PDB / ID: 7qsg
TitleMethylmannose polysaccharide mannosyltransferase from M. hassiacum
ComponentsD-inositol 3-phosphate glycosyltransferase
KeywordsTRANSFERASE / Methylmannose polysaccharide / mannosyltransferase / Mycobacterium hassiacum.
Function / homologyD-inositol-3-phosphate glycosyltransferase / D-inositol-3-phosphate glycosyltransferase activity / cellular biosynthetic process / : / Glycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / D-inositol 3-phosphate glycosyltransferase
Function and homology information
Biological speciesMycolicibacterium hassiacum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsManso, J.A. / Ripoll-Rozada, J. / Pereira, P.J.B.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BTM-TEC/29221/2017 Portugal
CitationJournal: Commun Biol / Year: 2023
Title: Self-recycling and partially conservative replication of mycobacterial methylmannose polysaccharides.
Authors: Maranha, A. / Costa, M. / Ripoll-Rozada, J. / Manso, J.A. / Miranda, V. / Mendes, V.M. / Manadas, B. / Macedo-Ribeiro, S. / Ventura, M.R. / Pereira, P.J.B. / Empadinhas, N.
History
DepositionJan 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: 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.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-inositol 3-phosphate glycosyltransferase
B: D-inositol 3-phosphate glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)96,5682
Polymers96,5682
Non-polymers00
Water00
1
A: D-inositol 3-phosphate glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)48,2841
Polymers48,2841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-inositol 3-phosphate glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)48,2841
Polymers48,2841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.261, 77.400, 101.210
Angle α, β, γ (deg.)90.000, 106.490, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein D-inositol 3-phosphate glycosyltransferase / Glycosyl transferases group 1 family protein


Mass: 48284.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium hassiacum (bacteria) / Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: mshA_2, C731_4166, MHAS_04402 / Production host: Escherichia coli (E. coli)
References: UniProt: K5BE02, D-inositol-3-phosphate glycosyltransferase

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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: 2.65 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Na-HEPES pH 7.5, 0.2 M sodium acetate, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.75→66.59 Å / Num. obs: 26401 / % possible obs: 99.62 % / Redundancy: 1.9 % / Biso Wilson estimate: 85.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03388 / Rpim(I) all: 0.03388 / Rrim(I) all: 0.04792 / Net I/σ(I): 9.97
Reflection shellResolution: 2.75→2.848 Å / Rmerge(I) obs: 0.5767 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 2609 / CC1/2: 0.649 / Rpim(I) all: 0.5767 / Rrim(I) all: 0.8156

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
PHENIX1.19_4092refinement
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N9W

4n9w


Resolution: 2.75→66.59 Å / SU ML: 0.463 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.3009
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2867 1325 5.03 %
Rwork0.2694 25043 -
obs0.2702 26368 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.6 Å2
Refinement stepCycle: LAST / Resolution: 2.75→66.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4801 0 0 0 4801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00194877
X-RAY DIFFRACTIONf_angle_d0.46776669
X-RAY DIFFRACTIONf_chiral_restr0.0405822
X-RAY DIFFRACTIONf_plane_restr0.0044876
X-RAY DIFFRACTIONf_dihedral_angle_d10.44041655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.860.38751390.37752748X-RAY DIFFRACTION99.07
2.86-2.990.42711500.33522762X-RAY DIFFRACTION99.45
2.99-3.150.31251590.30532747X-RAY DIFFRACTION99.62
3.15-3.350.40121330.30832774X-RAY DIFFRACTION99.76
3.35-3.60.34111340.30172801X-RAY DIFFRACTION99.73
3.6-3.970.28771620.2632762X-RAY DIFFRACTION99.86
3.97-4.540.28631430.23792795X-RAY DIFFRACTION99.93
4.54-5.720.26811450.26192796X-RAY DIFFRACTION99.76
5.72-66.590.24451600.25662858X-RAY DIFFRACTION99.44
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.953971158510.08039206223853.357341720713.88998607561-1.215947990694.65317955893-0.135139579131-0.187033129829-0.291558084316-0.1120952118060.07708146933130.588178687080.570998721864-1.127969037890.08416281296560.651916805247-0.09717239773790.003707382993070.642932527019-0.04125929782820.567048950111-39.2267281927-4.3384703343439.0183414528
23.02099484053-0.700309172911-0.3676015065962.598616842032.143232894947.32644741989-0.2390469182720.695310673605-0.2260083452290.0278146928770.1089126116230.0418118328130.2881115709620.3604852607530.1625834315870.501437734018-0.1105441894850.05803838293860.537431013319-0.01111485330110.515671307374-14.8473715088-9.644906972626.4962927772
37.11496435253-1.58663066789-2.684501020688.534049120120.3317732641145.146660041391.383307866121.01974070961.04893596142-1.9981112457-0.600748966228-0.308068389594-0.0450006677019-0.136074278518-0.5518647871481.213522129620.3168886833190.001636895589650.6951588093330.04563976559991.33350070174-26.78236110338.581562992129.9736963294
42.23996027074-0.158887155447-0.1976287066077.169971433871.768728707770.6312334901010.2439722005670.0535436546764-0.414751665258-0.2696590472430.469328432663-0.553311606837-0.8525202488490.274046304222-0.7009236378580.8909368646740.1339031520780.02497081462020.8552772573290.4407828433311.64234110235-19.061980887931.609619044127.4166317325
50.989944810328-0.466511720917-0.3030254488961.25117933344-0.5581821848721.48593788128-0.0734873002113-0.339832256860.3169198008890.981053287928-0.0576827158908-1.39081765532-0.376613494723-0.1311183455020.9781842000660.990253363673-0.116926640017-0.5986408276740.6248135329830.5384540598761.86205949598-23.646831996718.430854278827.1070493037
62.04603065168-0.6075508691461.311305996493.5356163281-1.111825306855.58063264602-0.181319766987-0.02466989381260.5367555000260.5162273205340.0467319621239-0.953200280478-0.765327466042-0.613395051890.3635051467750.6706242621330.22200463688-0.08430813325440.7241960465990.1995042508630.827478883716-42.726729982727.044231921715.959735787
74.88377601493-1.65030259903-0.224088618544.965474068543.202097553048.146352216280.4589680050691.31436607079-0.0641494146163-0.779615091545-0.722908740789-0.588984208149-0.497423449562-0.468824659269-0.2834583421990.8536217945080.4747768174320.1311789143140.8926734221520.3018949067650.634498370539-43.813335245830.28633234981.50148390164
82.496657500560.354729902222-0.581764642665.594813193541.599072725452.335444841850.2017529936780.2304442862130.2062572512690.39508731102-0.381955981319-1.13844125668-0.8985848552370.3387103623210.163051199680.8989407473210.238650081816-0.04494729084720.9675718566370.222503266430.884263794856-43.256117826830.89973564118.78834883811
93.3428464818-1.612599236660.4554785261246.48486257911.768772392075.2976614245-0.284423215658-0.466954683316-0.08634404853560.970072851808-0.1682253367130.198375678435-0.234680314356-2.166194458340.353579414780.6548980015580.145656227165-0.01861149282861.235768294870.244748875730.668126922885-49.207000121922.181884855119.341515963
100.688750707960.341712949606-0.9191309182362.77676188002-0.1830415725171.26037660679-0.454352567178-0.381633893295-0.06428028683381.04940425909-0.111724377915-0.77706593343-0.4025636716290.1275446859620.02082928688672.440585411160.372113146769-1.17430091450.797158442970.248566864511.4668836761-31.409116354830.382904054438.6912913331
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -2 through 205 )AA-2 - 2051 - 184
22chain 'A' and (resid 206 through 408 )AA206 - 408185 - 379
33chain 'B' and (resid 0 through 45 )BB0 - 451 - 40
44chain 'B' and (resid 46 through 147 )BB46 - 14741 - 74
55chain 'B' and (resid 148 through 199 )BB148 - 19975 - 100
66chain 'B' and (resid 200 through 253 )BB200 - 253101 - 152
77chain 'B' and (resid 254 through 273 )BB254 - 273153 - 172
88chain 'B' and (resid 274 through 316 )BB274 - 316173 - 215
99chain 'B' and (resid 317 through 389 )BB317 - 389216 - 288
1010chain 'B' and (resid 390 through 405 )BB390 - 405289 - 304

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