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- PDB-7xpu: crystal structure of MtdL-S228A-His soaked GDP-Fucp and Mn -

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Basic information

Entry
Database: PDB / ID: 7xpu
Titlecrystal structure of MtdL-S228A-His soaked GDP-Fucp and Mn
ComponentsTransglycosylse
KeywordsTRANSFERASE
Function / homologySTELLO-like / Reversibly glycosylated polypeptide family / Reversibly glycosylated polypeptide / metal ion binding / GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE / : / Transglycosylse
Function and homology information
Biological speciesMarinactinospora thermotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLi, F.D. / He, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structures of the NDP-pyranose mutase belonging to glycosyltransferase family 75 reveal residues important for Mn 2+ coordination and substrate binding.
Authors: Du, X. / Chu, X. / Liu, N. / Jia, X. / Peng, H. / Xiao, Y. / Liu, L. / Yu, H. / Li, F. / He, C.
History
DepositionMay 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

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Assembly

Deposited unit
A: Transglycosylse
B: Transglycosylse
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1057
Polymers87,7242
Non-polymers1,3815
Water11,061614
1
A: Transglycosylse
B: Transglycosylse
hetero molecules

A: Transglycosylse
B: Transglycosylse
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,20914
Polymers175,4484
Non-polymers2,76110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area7900 Å2
ΔGint-57 kcal/mol
Surface area49950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.189, 162.548, 115.662
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-680-

HOH

21B-699-

HOH

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Components

#1: Protein Transglycosylse


Mass: 43862.031 Da / Num. of mol.: 2 / Mutation: S228A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinactinospora thermotolerans (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: G8HX37
#2: Chemical ChemComp-GFB / GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE


Mass: 589.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N5O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M Tris, pH 7.5, 20% (w/v) PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→47.64 Å / Num. obs: 46848 / % possible obs: 99.3 % / Redundancy: 9.3 % / Biso Wilson estimate: 26.92 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.054 / Rrim(I) all: 0.167 / Net I/σ(I): 9.9 / Num. measured all: 435511 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.279.20.993722340340.9160.341.0492.399.2
9.07-47.647.70.03556547320.9990.0130.03729.196.8

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Processing

Software
NameVersionClassification
PHENIX1.11refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XPR

7xpr


Resolution: 2.2→47.12 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2798 2174 4.66 %
Rwork0.2376 44486 -
obs0.2397 46660 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.47 Å2 / Biso mean: 31.5892 Å2 / Biso min: 14.28 Å2
Refinement stepCycle: final / Resolution: 2.2→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5788 0 84 614 6486
Biso mean--30.7 37.09 -
Num. residues----742
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.250.36131390.2922730286999
2.25-2.30.35081400.28732734287499
2.3-2.360.34171320.27162760289299
2.36-2.420.30941300.2552765289599
2.42-2.490.33321140.25882813292799
2.49-2.570.32331130.26182778289199
2.57-2.670.28691160.24262764288099
2.67-2.770.31421090.25052781289098
2.77-2.90.34531240.25132771289598
2.9-3.050.2991830.245127462929100
3.05-3.240.28981710.23632748291999
3.24-3.490.29281320.22822789292199
3.49-3.840.2454980.21212821291999
3.84-4.40.22091640.208728092973100
4.4-5.540.27611390.22072810294998
5.54-47.120.23281700.23862867303797
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)
13.4029-0.0845-0.43123.04750.35793.27520.00380.641-0.0278-0.6271-0.09440.0838-0.07910.08230.05210.39610.0229-0.00790.3514-0.04790.2014-31.2947-22.64150.0316
21.0658-0.3419-0.12941.3125-0.09990.9140.00340.0708-0.0614-0.0431-0.0024-0.17390.08010.0352-0.00820.2610.02840.01560.2204-0.02820.2777-25.2308-21.430821.3985
32.5534-2.1395-0.9125.10731.32291.9559-0.09010.0188-0.30910.27780.08620.26170.28620.01520.00460.2157-0.0454-0.01180.20640.03670.2302-41.4272-27.892728.5566
43.4020.3570.65132.24020.42152.3911-0.1192-0.48150.10710.3394-0.03250.0815-0.043-0.00610.12750.28210.0027-0.00170.23510.00630.1472-31.275315.600457.746
50.1226-0.05690.45030.9252-0.32961.67040.0508-0.22480.17050.1766-0.008-0.1004-0.1520.037-0.03870.1989-0.02720.02660.1503-0.00890.2996-27.523720.61145.6064
61.30990.17730.30712.0310.14540.34320.0090.06010.0006-0.02920.0605-0.2839-0.03750.0582-0.06290.1889-0.0170.02750.189-0.01570.2037-24.419312.251333.0656
72.30792.24520.96793.82631.22913.5586-0.0465-0.01840.0452-0.22950.06050.0065-0.2448-0.1065-0.00830.22020.05940.01080.22020.04130.2629-41.494220.848729.2722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 75 )A4 - 75
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 317 )A76 - 317
3X-RAY DIFFRACTION3chain 'A' and (resid 318 through 374 )A318 - 374
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 75 )B4 - 75
5X-RAY DIFFRACTION5chain 'B' and (resid 76 through 138 )B76 - 138
6X-RAY DIFFRACTION6chain 'B' and (resid 139 through 317 )B139 - 317
7X-RAY DIFFRACTION7chain 'B' and (resid 318 through 374 )B318 - 374

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