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- PDB-7xpv: crysteal structure of MtdL-S228A-His soaked with GDP-Fucf and Mn -

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Basic information

Entry
Database: PDB / ID: 7xpv
Titlecrysteal structure of MtdL-S228A-His soaked with GDP-Fucf and Mn
ComponentsTransglycosylse
KeywordsTRANSFERASE
Function / homologySTELLO-like / Reversibly glycosylated polypeptide family / Reversibly glycosylated polypeptide / metal ion binding / Chem-GRJ / : / Transglycosylse
Function and homology information
Biological speciesMarinactinospora thermotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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)89,0136
Polymers87,7242
Non-polymers1,2894
Water4,143230
1
A: Transglycosylse
B: Transglycosylse
hetero molecules

A: Transglycosylse
B: Transglycosylse
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,02512
Polymers175,4484
Non-polymers2,5778
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area7690 Å2
ΔGint-62 kcal/mol
Surface area50000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.135, 162.670, 114.927
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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: Marinactinospora thermotolerans (bacteria) / References: UniProt: G8HX37
#2: Chemical ChemComp-GRJ / [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{S},3~{S},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[(1~{S})-1-oxidanylethyl]oxolan-2-yl] hydrogen phosphate


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.61 Å3/Da / Density % sol: 52.95 %
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: 2.4→46.93 Å / Num. obs: 36272 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 39.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.045 / Rrim(I) all: 0.163 / Net I/σ(I): 12.1 / Num. measured all: 478202
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
2.4-2.4913.71.3875164837590.90.3861.442.299.9
8.98-46.9311.30.034869177210.010.03638.398.9

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XPR

7xpr


Resolution: 2.4→46.93 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2928 1823 5.05 %
Rwork0.2576 34266 -
obs0.2594 36089 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.8 Å2 / Biso mean: 46.1317 Å2 / Biso min: 22.36 Å2
Refinement stepCycle: final / Resolution: 2.4→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5776 0 78 230 6084
Biso mean--48.91 45.03 -
Num. residues----742
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.460.35621500.328325652715100
2.46-2.540.38321470.31492590273799
2.54-2.620.29841180.297526452763100
2.62-2.710.30911450.286926342779100
2.71-2.820.36961320.28832574270699
2.82-2.950.34031430.300326262769100
2.95-3.110.27281260.27232617274399
3.11-3.30.32081350.27192637277299
3.3-3.550.33821550.257426242779100
3.55-3.910.25371300.236626472777100
3.91-4.480.26071430.218826542797100
4.48-5.640.2721350.230527032838100
5.64-46.930.25911640.25152750291499
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)
15.3516-0.50342.163.57840.15384.7630.0218-0.71290.08830.6025-0.09280.37280.194-0.01450.05730.632-0.06160.03290.4642-0.03760.390415.240323.1203-2.7096
22.570.19070.00351.88830.02261.12780.0213-0.03370.14230.00760.0072-0.3552-0.03740.0983-0.02320.4753-0.06070.01330.2416-0.03090.400426.776121.9722-22.0347
32.65940.13531.09752.91310.70881.3181-0.01450.02670.0136-0.1590.08290.0026-0.14880.0545-0.07670.4127-0.03080.07690.2710.0090.358213.609422.4255-26.3519
42.60451.0731-0.80961.3864-0.18822.8803-0.29970.56550.0611-0.71370.3398-0.06590.0581-0.0729-0.14050.5848-0.02690.08910.3670.01670.264320.8656-14.61-57.8077
51.3772-0.783-0.33811.3372-0.33442.30220.09660.4516-0.33-0.3766-0.0773-0.31330.2151-0.0695-0.04560.42680.03130.01520.2145-0.04950.457419.1104-20.6072-47.9639
62.2740.62430.33077.2221-1.36573.9352-0.1723-0.4210.28570.05080.0532-0.8459-0.0830.21640.07850.4996-0.0133-0.06540.2016-0.07560.434730.8319-8.429-28.2747
72.59050.4678-0.64872.0880.34261.00520.035-0.0429-0.0810.15680.0577-0.32190.0660.0918-0.09910.45260.05040.01110.2222-0.03110.35524.9222-14.7044-35.1247
80.9285-1.50690.12528.65780.72262.5079-0.0277-0.0579-0.00870.18970.139-0.10310.26520.0237-0.08490.1568-0.04410.01590.24080.00070.218915.4077-11.8549-27.0303
93.2136-0.3608-1.24125.21970.9634.7764-0.0912-0.1127-0.00980.63210.0475-0.10050.7103-0.17910.01620.3185-0.01610.00790.19930.05130.32056.9231-20.1303-29.4671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 99 )A4 - 99
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 273 )A100 - 273
3X-RAY DIFFRACTION3chain 'A' and (resid 274 through 374 )A274 - 374
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 56 )B4 - 56
5X-RAY DIFFRACTION5chain 'B' and (resid 57 through 138 )B57 - 138
6X-RAY DIFFRACTION6chain 'B' and (resid 139 through 167 )B139 - 167
7X-RAY DIFFRACTION7chain 'B' and (resid 168 through 293 )B168 - 293
8X-RAY DIFFRACTION8chain 'B' and (resid 294 through 324 )B294 - 324
9X-RAY DIFFRACTION9chain 'B' and (resid 325 through 374 )B325 - 374

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