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- PDB-7qoq: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphogl... -

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Basic information

Entry
Database: PDB / ID: 7qoq
TitleCrystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 8.5 in complex with UMP and Magnesium
ComponentsGlucosyl-3-phosphoglycerate synthase
KeywordsTRANSFERASE / Glucose / UDP-glucose / thermostable / GTA-fold
Function / homologyglucosyl-3-phosphoglycerate synthase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / glycosyltransferase activity / Nucleotide-diphospho-sugar transferases / URIDINE-5'-MONOPHOSPHATE / Glucosyl-3-phosphoglycerate synthase
Function and homology information
Biological speciesMycolicibacterium hassiacum DSM 44199 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsSilva, A. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S. / Costa, D.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BTM-TEC/29221/2017 (POCI-01-0145-FEDER-029221). Portugal
CitationJournal: To Be Published
Title: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 8.5 in complex with UMP and Magnesium
Authors: Silva, A. / Nunes-Costa, D. / Empadinhas, N. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
History
DepositionDec 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
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: Glucosyl-3-phosphoglycerate synthase
B: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0839
Polymers70,3022
Non-polymers7817
Water10,052558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Alarico S, Nunes-Costa D, Silva A, Costa M, Macedo-Ribeiro S, Empadinhas N. A genuine mycobacterial thermophile: Mycobacterium hassiacum growth, survival and GpgS stability ...Evidence: gel filtration, Alarico S, Nunes-Costa D, Silva A, Costa M, Macedo-Ribeiro S, Empadinhas N. A genuine mycobacterial thermophile: Mycobacterium hassiacum growth, survival and GpgS stability at near-pasteurization temperatures. Microbiology (Reading). 2020;166(5):474-483. doi:10.1099/mic.0.000898
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-60 kcal/mol
Surface area24150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.076, 90.377, 96.007
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Glucosyl-3-phosphoglycerate synthase /


Mass: 35151.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The C-terminal KLAAALEHHHHHH sequence corresponds to a linker followed by an hexahistidine tag used for protein purification.
Source: (gene. exp.) Mycolicibacterium hassiacum DSM 44199 (bacteria)
Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: gpgS, C731_3243, MHAS_02845 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: K5B7Z4, glucosyl-3-phosphoglycerate synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-U / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Type: RNA linking / Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 558 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5; 0.2 M MgCl2; 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87261 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87261 Å / Relative weight: 1
ReflectionResolution: 1.93→48.29 Å / Num. obs: 46655 / % possible obs: 98.1 % / Redundancy: 5.1 % / Biso Wilson estimate: 19.89 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.094 / Rrim(I) all: 0.217 / Net I/σ(I): 7.9
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.106 / Mean I/σ(I) obs: 0.441 / Num. unique obs: 5966 / CC1/2: 0.441 / Rpim(I) all: 0.573 / Rrim(I) all: 1.251 / % possible all: 87.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PVL

7pvl


Resolution: 1.93→48 Å / SU ML: 0.2499 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.8712
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2276 2348 5.05 %
Rwork0.1756 44125 -
obs0.1782 46473 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.99 Å2
Refinement stepCycle: LAST / Resolution: 1.93→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4447 0 47 558 5052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074582
X-RAY DIFFRACTIONf_angle_d0.79416264
X-RAY DIFFRACTIONf_chiral_restr0.052757
X-RAY DIFFRACTIONf_plane_restr0.0105804
X-RAY DIFFRACTIONf_dihedral_angle_d11.82351659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.970.3955960.34861747X-RAY DIFFRACTION67.46
1.97-2.010.33551720.27612568X-RAY DIFFRACTION99.85
2.01-2.060.27031160.22992649X-RAY DIFFRACTION99.96
2.06-2.110.24921550.21822588X-RAY DIFFRACTION99.93
2.11-2.160.2691480.19812613X-RAY DIFFRACTION99.96
2.16-2.230.25661440.19812599X-RAY DIFFRACTION99.96
2.23-2.30.29181210.19452656X-RAY DIFFRACTION100
2.3-2.380.25391200.192638X-RAY DIFFRACTION99.93
2.38-2.480.25051450.18022588X-RAY DIFFRACTION99.85
2.48-2.590.26261390.17372664X-RAY DIFFRACTION99.86
2.59-2.730.21741410.16992631X-RAY DIFFRACTION99.93
2.73-2.90.20431380.16392630X-RAY DIFFRACTION99.82
2.9-3.120.20051410.16212670X-RAY DIFFRACTION99.86
3.12-3.430.20271380.15422648X-RAY DIFFRACTION99.93
3.44-3.930.1721440.14412692X-RAY DIFFRACTION100
3.93-4.950.18721480.13252699X-RAY DIFFRACTION99.96
4.95-480.23531420.18472845X-RAY DIFFRACTION99.7
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)
14.774849860181.34403019482.625449322184.918215538391.360042428056.720235041920.219098032163-0.140867824548-0.2246267803570.110142173786-0.2040691605030.5092824224330.551602247396-0.680564148217-0.04395672894170.165255049455-0.03563010471220.01160931024560.172601600617-0.02768911026780.20465188190214.7389450771-31.246049238-27.8574793133
20.5906451286950.08704113982790.1207280303513.481760848160.5963964798670.9422622458760.0286281620988-0.100618296004-0.03424549826380.21331930717-0.0460236326614-0.03623292376390.0536093228359-0.05667121301820.01183250487630.125843740944-0.00523138083571-0.005531291201780.1400502574240.01071472314570.089011803532824.4641298262-13.7164621874-5.68281721801
31.274287755750.4054650013910.4747982857211.112412841880.4403871549891.64854141211-0.04848983092330.0146401039190.137699804940.00558695907075-0.005880676180150.0761490071048-0.142081917255-0.07069381189260.03598217192080.138745872833-0.00741767369999-0.01491214179430.1039545004360.0005133307799010.13202903744324.5053821805-1.90411641923-10.7736257982
44.26288170423-0.185976333454-0.7874255021262.08050242747-0.04246199815973.83221780333-0.0209186347709-0.00443951432328-0.09707829248790.120166559884-0.02789586116470.02032879236460.201893189366-0.1275383310510.05240815696920.125085774557-0.0296027212219-0.01732393234020.08067403003610.002893164724840.12781918386422.160496138-21.1963112279-13.925954474
51.51722071580.3979731402510.1116853139953.07528974172-1.163190450654.89006758616-0.115027867228-0.200661939409-0.04464041208440.2442928701960.1754121618460.2709180063820.160820149933-0.329747375575-0.05094055849720.1108365041970.0170600129489-0.009037551196120.1532445755530.01351631119540.1308668343116.97001744113-14.8587214671-26.0131588759
60.780876299450.4201848070860.6330538367641.459608565860.5607751798172.49126943219-0.0156397598785-0.006840925425130.024310804258-0.0299672436880.03772167502230.0350950532135-0.1708164094090.00247337641231-0.02468063978750.112805454391-0.00444554348820.004002805804120.1072616406480.001703247733250.12938264060122.0094430671-13.5722633648-24.6820427903
70.990243502124-0.5166051738060.5219714342661.96293462022-0.8223774842550.4540223835960.084743438091-0.153021674614-0.06508647621870.184970127558-0.05059330834910.293120741458-0.470842345322-0.405498911567-0.0139227247790.1974138400790.04669259405210.03043821881410.22980461746-0.02456764576170.16926717564312.5567508963-17.1489421533-16.0857838223
89.38588779399-4.85979083055-6.318124502956.556261455533.22987286547.12129345571-0.0859741347531-0.3863432938420.3050521647190.2137308366240.170468274297-0.0249382538048-0.0622168110738-0.00889926349821-0.05942279319630.1519873079690.000589772169342-0.05991994547110.1269921702140.009445641833270.10412864335911.2799822319-4.15288472718-28.541768684
93.87572137386-0.962447064798-1.106262405166.177679171210.8710309912434.521605694920.0490267068244-0.4595959266460.7731204279760.08653553754770.06305234734190.00871461416352-0.356972593132-0.3397675799-0.3044705271980.2327083141030.0393275184177-0.04255289715720.262836784556-0.08482694392310.3044147956589.394883933243.4413638682-34.0518729346
100.8293535367381.474186381671.389717496982.830727238312.454982312292.329065098390.07842380721080.268872461735-0.0888555422079-0.03878085471720.22282715682-0.6274800922010.03520980531640.174513639114-0.3375266022330.174375582704-0.09141453107440.02205300087190.3233941307330.02329688220330.26875139819434.2843384179-10.4757731969-29.1607097833
110.85512124794-0.4523844215950.04501841900371.928327941260.957688752941.185400585930.0407522806244-0.0553103639232-0.001682749605850.158160109466-0.128218566990.2276639694560.116980138819-0.2045615011720.04508563344970.132962871748-0.01717972162910.03131348231370.172038201514-0.02344820560350.149621351626-19.2817930007-8.53863839121-43.9681064416
123.71000428875-0.123848844550.2026537631532.177951801110.7567428127232.817937347290.0373752018480.04247161730870.3052305192760.028583227562-0.07226160518250.181362287714-0.360155016275-0.07891708487390.06893196708240.1106138734760.00506228398930.01514628828140.0798712528906-0.007130991703140.188777433812-15.29874287553.06075545834-43.807160359
131.919188749830.1937826077240.5817355758721.465925399720.3857897505531.14097387863-0.0251172280551-0.102948275344-0.009813379004270.130051858020.07237568105770.01797160877390.0398779895439-0.0279545664632-0.06693082871180.1350005881140.004527954118080.005431823435410.1198012932270.0003047667244570.128239959855-3.53998775059-4.44656300196-42.0004055622
140.582901848444-0.6425060940380.6893415605321.92953343177-0.262971672452.130804459990.0306880439641-0.317708774326-0.3611030843830.318217471441-0.1396240674020.217670961504-0.314351707330.0237815674463-0.03898596981610.127478912856-0.02847081662690.06278168927160.2063936857280.01399489958960.235864027501-10.9909597767-1.30858707365-34.6742983822
152.175573536670.2845906008281.914328059460.1485069738410.3788566274412.447707300190.000641035553111-0.00389233881506-0.02357687279740.05756816500220.0298437521404-0.0212177142906-0.005693540940920.01847130258810.001956508099650.1384138474390.00526283812205-0.0001477564576740.112642655793-0.01578823257330.155563492269-1.8241084727-14.674938092-46.512914599
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 21 )AA6 - 211 - 16
22chain 'A' and (resid 22 through 77 )AA22 - 7717 - 72
33chain 'A' and (resid 78 through 140 )AA78 - 14073 - 135
44chain 'A' and (resid 141 through 163 )AA141 - 163136 - 158
55chain 'A' and (resid 164 through 192 )AA164 - 192159 - 175
66chain 'A' and (resid 193 through 237 )AA193 - 237176 - 220
77chain 'A' and (resid 238 through 256 )AA238 - 256221 - 239
88chain 'A' and (resid 257 through 274 )AA257 - 274240 - 257
99chain 'A' and (resid 275 through 302 )AA275 - 302258 - 277
1010chain 'A' and (resid 303 through 327 )AA303 - 327278 - 302
1111chain 'B' and (resid 10 through 140 )BF10 - 1401 - 131
1212chain 'B' and (resid 141 through 163 )BF141 - 163132 - 154
1313chain 'B' and (resid 164 through 237 )BF164 - 237155 - 217
1414chain 'B' and (resid 238 through 256 )BF238 - 256218 - 236
1515chain 'B' and (resid 257 through 324 )BF257 - 324237 - 291

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