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- PDB-7xpr: Crystal structrue of SeMet-MtdL:GDP -

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Basic information

Entry
Database: PDB / ID: 7xpr
TitleCrystal structrue of SeMet-MtdL:GDP
ComponentsTransglycosylse
KeywordsTRANSFERASE
Function / homologySTELLO-like / Reversibly glycosylated polypeptide family / Reversibly glycosylated polypeptide / metal ion binding / GUANOSINE-5'-DIPHOSPHATE / Transglycosylse
Function and homology information
Biological speciesMarinactinospora thermotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transglycosylse
B: Transglycosylse
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1274
Polymers84,2402
Non-polymers8862
Water7,530418
1
A: Transglycosylse
hetero molecules

A: Transglycosylse
hetero molecules

B: Transglycosylse
hetero molecules

B: Transglycosylse
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,2538
Polymers168,4814
Non-polymers1,7734
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
crystal symmetry operation3_445x-1/2,y-1/2,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area9730 Å2
ΔGint-51 kcal/mol
Surface area51860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.213, 97.483, 57.923
Angle α, β, γ (deg.)90.000, 97.320, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transglycosylse


Mass: 42120.164 Da / Num. of mol.: 2
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-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 1.0 M lithium chloride, 0.1 M citric acid, pH 5.0, 10% (w/v) PEG6000

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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 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→83.373 Å / Num. all: 51416 / Num. obs: 51416 / % possible obs: 98.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 33.11 Å2 / Rpim(I) all: 0.051 / Rrim(I) all: 0.136 / Rsym value: 0.112 / Net I/av σ(I): 5.7 / Net I/σ(I): 10.8 / Num. measured all: 353130
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.1-2.216.50.8250.94818374070.380.9820.8252.298.2
2.21-2.357.10.6271.25066470970.2690.730.6273.298.8
2.35-2.517.10.4011.94747266900.1750.4720.4014.599
2.51-2.716.90.2632.94290862300.1190.3140.2636.399
2.71-2.976.70.1674.53815156710.0770.2020.1679.198.5
2.97-3.327.20.1116.53726152060.050.1340.11113.999.5
3.32-3.836.90.0729.23179846220.0330.0880.07220.299.5
3.83-4.76.60.05411.32559738640.0260.0670.05425.598.6
4.7-6.646.90.051112082530360.0250.0670.05126.899.6
6.64-19.776.40.04510.91027115930.0230.0590.04529.693.6

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Processing

Software
NameVersionClassification
PHENIX1.11refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→19.77 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2429 2682 5.22 %
Rwork0.2106 48722 -
obs0.2123 51404 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.72 Å2 / Biso mean: 41.2707 Å2 / Biso min: 16.65 Å2
Refinement stepCycle: final / Resolution: 2.1→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5778 0 56 418 6252
Biso mean--68.32 40.64 -
Num. residues----742
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.140.35841530.30922513266698
2.14-2.180.3861320.29092520265298
2.18-2.220.29441260.27822590271698
2.22-2.270.33751360.27532534267098
2.27-2.320.29241240.25392595271999
2.32-2.380.26831280.23772535266398
2.38-2.450.28731420.24092548269099
2.45-2.520.29271550.24892588274399
2.52-2.60.2871260.23762524265099
2.6-2.690.26431510.23432581273299
2.69-2.80.28031530.23052518267197
2.8-2.930.26941510.22532563271499
2.93-3.080.23161310.21212597272899
3.08-3.270.2471460.2032588273499
3.27-3.520.19031430.19362579272299
3.52-3.880.23831460.18252582272899
3.88-4.430.2131510.17862557270898
4.43-5.560.19651430.17862607275099
5.56-19.770.21771450.19542603274898
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)
11.53020.37340.31491.9431-0.69411.7953-0.13521.2446-0.156-1.00780.1249-0.15550.136-0.1748-0.02310.5269-0.05440.01720.7405-0.01780.245916.042537.82292.3875
22.44470.284-0.19411.9074-0.18680.8561-0.020.17680.4082-0.07760.0599-0.1089-0.04770.0112-0.04780.1911-0.02590.01460.24710.02140.208215.446848.885721.8408
32.0387-0.4259-0.12561.1127-0.30870.5764-0.04210.0038-0.09010.00960.0293-0.17630.07020.04080.01460.2662-0.0159-0.00350.2898-0.04360.198915.460736.112126.4292
43.0078-0.6782-0.03982.45250.43343.2324-0.08040.82810.1151-0.87080.0626-0.01710.00710.20410.03580.4302-0.0739-0.02050.43740.01470.215657.733455.89932.2135
52.48730.55190.19541.94570.14790.88820.01860.0368-0.4619-0.05830.10690.06910.0857-0.029-0.09710.1711-0.0216-0.04230.20650.01080.335858.473744.877321.8054
61.6943-0.26780.16821.3360.3381.09890.0127-0.1103-0.08620.03560.05840.0698-0.0803-0.1148-0.06010.2057-0.00530.00580.22960.07150.280358.322457.624426.3614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 97 )A4 - 97
2X-RAY DIFFRACTION2chain 'A' and (resid 98 through 273 )A98 - 273
3X-RAY DIFFRACTION3chain 'A' and (resid 274 through 374 )A274 - 374
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 97 )B4 - 97
5X-RAY DIFFRACTION5chain 'B' and (resid 98 through 273 )B98 - 273
6X-RAY DIFFRACTION6chain 'B' and (resid 274 through 374 )B274 - 374

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