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- PDB-7xpt: Crystal structrue of MtdL:GDP:Mn soaked with GDP-Glc -

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Basic information

Entry
Database: PDB / ID: 7xpt
TitleCrystal structrue of MtdL:GDP:Mn soaked with GDP-Glc
ComponentsTransglycosylse
KeywordsTRANSFERASE
Function / homologySTELLO-like / Reversibly glycosylated polypeptide family / Reversibly glycosylated polypeptide / metal ion binding / GDP-ALPHA-D-GLUCOSE / : / Transglycosylse
Function and homology information
Biological speciesMarinactinospora thermotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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

Downloads & links

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Assembly

Deposited unit
A: Transglycosylse
B: Transglycosylse
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9046
Polymers83,5842
Non-polymers1,3214
Water9,206511
1
A: Transglycosylse
hetero molecules

A: Transglycosylse
hetero molecules

B: Transglycosylse
hetero molecules

B: Transglycosylse
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,80912
Polymers167,1684
Non-polymers2,6418
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 area11890 Å2
ΔGint-67 kcal/mol
Surface area51650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.275, 98.825, 58.102
Angle α, β, γ (deg.)90.000, 96.770, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transglycosylse


Mass: 41791.895 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-GDG / GDP-ALPHA-D-GLUCOSE / GDP-ALPHA-D-GLUCOSE


Mass: 605.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N5O16P2 / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.1 M tri-sodium citrate pH 5.6, 10% (w/v) PEG 4000, 10% (w/v) isopropanol

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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: Jun 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→80.57 Å / Num. obs: 55455 / % possible obs: 90.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 32.73 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.041 / Rrim(I) all: 0.106 / Net I/σ(I): 11.1 / Num. measured all: 352445 / Scaling rejects: 20
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
2-2.056.30.9192641342010.8790.38811.793.7
8.94-80.575.70.03940397080.9980.0170.04330.697.9

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XPR

7xpr


Resolution: 2→57.7 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.259 2756 5.01 %
Rwork0.2152 52212 -
obs0.2174 54968 89.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.98 Å2 / Biso mean: 41.0174 Å2 / Biso min: 21.81 Å2
Refinement stepCycle: final / Resolution: 2→57.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5849 0 80 511 6440
Biso mean--40.57 44.07 -
Num. residues----750
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.030.36351500.28762860301099
2.03-2.050.354530.32641117117089
2.08-2.110.3797930.28221944203797
2.11-2.150.3181370.262924306199
2.15-2.20.32241320.26722874300699
2.2-2.240.35281030.27532100220394
2.26-2.310.34331160.28022291240796
2.31-2.370.33581650.24122847301298
2.37-2.440.29741520.23392878303099
2.44-2.520.32121510.25512865301698
2.52-2.610.2721400.24922887302799
2.61-2.710.2669800.25521531161152
2.71-2.840.33291290.23772885301498
2.84-2.990.28361750.24032860303599
2.99-3.170.27761830.2212857304099
3.17-3.420.24071800.21982845302598
3.42-3.760.24781390.19372873301298
3.76-4.310.20781770.17622880305799
4.31-5.430.21161580.17882904306299
5.43-57.70.22421430.19372990313399
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)
11.72530.173-0.08093.049-0.91342.7140.03170.42870.03-0.43840.0579-0.04340.0138-0.0093-0.1080.23030.00080.02550.4618-0.00660.209517.174938.74472.9934
21.4288-0.0304-0.08671.3314-0.24690.6778-0.00720.10630.2339-0.00530.0318-0.0292-0.1253-0.0113-0.02740.1991-0.03490.00960.3520.00370.236414.082348.270522.5791
33.56461.4417-1.54911.9109-0.59543.84920.0415-0.1462-0.1836-0.00440.0035-0.17140.13550.2993-0.04120.23650.0333-0.05560.39230.0020.320320.972230.297328.4689
40.5452-0.87130.72722.95810.46632.7399-0.56370.4504-0.2704-0.46620.36650.45550.3239-0.5480.24130.2976-0.03260.00850.5804-0.05270.25850.575846.54694.4255
54.58781.0075-0.96666.80840.23362.98550.00230.5901-0.4061-0.51750.069-0.36510.43610.1011-0.06130.37470.0225-0.01220.4844-0.08850.231160.388650.60530.7145
61.7882-0.3798-0.65416.43542.21063.3474-0.0840.67180.0726-1.0536-0.22340.1974-0.4067-0.20860.34760.4634-0.1174-0.0670.6550.00870.267557.727558.9209-2.7273
71.4076-0.97790.93377.18271.97344.53730.04590.22950.5135-0.4884-0.156-0.1373-0.3678-0.17020.14340.2911-0.01920.01030.38280.04430.326356.152663.551310.5253
82.51770.620.25431.5175-0.66973.11510.01130.1671-0.45-0.16290.06630.02230.3218-0.0336-0.07260.2618-0.0329-0.01160.3576-0.05130.467555.098141.049817.0426
92.0899-0.12390.24842.06620.54340.7409-0.00150.0112-0.2955-0.00720.0708-0.07520.09350.013-0.07430.2182-0.0324-0.0350.36180.02920.345360.866847.027823.2484
105.7987-1.4792-1.15153.38532.18924.85020.3133-0.30390.28560.17110.1266-0.18340.1260.0422-0.42330.1938-0.0206-0.06060.22590.01690.218367.478556.445830.1129
118.40455.19893.47524.83213.1012.65170.1973-0.70440.17760.127-0.2780.4734-0.0619-0.98140.09350.26970.0290.01510.60930.03110.396848.764661.962730.6015
122.13740.61191.75283.76260.08837.2341-0.017-0.22930.0799-0.03790.0625-0.0176-0.241-0.0927-0.08170.14560.00030.04990.2830.01520.200956.968966.613726.6228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 99 )A0 - 99
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 317 )A100 - 317
3X-RAY DIFFRACTION3chain 'A' and (resid 318 through 374 )A318 - 374
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 18 )B0 - 18
5X-RAY DIFFRACTION5chain 'B' and (resid 19 through 44 )B19 - 44
6X-RAY DIFFRACTION6chain 'B' and (resid 45 through 75 )B45 - 75
7X-RAY DIFFRACTION7chain 'B' and (resid 76 through 99 )B76 - 99
8X-RAY DIFFRACTION8chain 'B' and (resid 100 through 152 )B100 - 152
9X-RAY DIFFRACTION9chain 'B' and (resid 153 through 293 )B153 - 293
10X-RAY DIFFRACTION10chain 'B' and (resid 294 through 317 )B294 - 317
11X-RAY DIFFRACTION11chain 'B' and (resid 318 through 342 )B318 - 342
12X-RAY DIFFRACTION12chain 'B' and (resid 343 through 374 )B343 - 374

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