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- PDB-7xps: Crystal structrue of MtdL:GDP:Mn -

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Basic information

Entry
Database: PDB / ID: 7xps
TitleCrystal structrue of MtdL:GDP:Mn
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 / MOLECULAR REPLACEMENT / 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 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)84,5806
Polymers83,5842
Non-polymers9964
Water11,692649
1
A: Transglycosylse
B: Transglycosylse
hetero molecules

A: Transglycosylse
B: Transglycosylse
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,16012
Polymers167,1684
Non-polymers1,9938
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area10690 Å2
ΔGint-110 kcal/mol
Surface area50750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.694, 162.243, 116.496
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-713-

HOH

21B-723-

HOH

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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-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: 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.: 649 / 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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M tri-sodium citrate, pH 5.6, 15% (w/v) PEG 4000

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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: Oct 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→19.85 Å / Num. obs: 54465 / % possible obs: 99.5 % / Redundancy: 13.3 % / Biso Wilson estimate: 26.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.038 / Rrim(I) all: 0.14 / Net I/σ(I): 15.2 / Num. measured all: 723926 / 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
2.1-2.1613.70.9366084244570.9390.2610.9722.899.9
8.91-19.85120.025847870710.0070.02655.889.4

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Processing

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

7xpr


Resolution: 2.1→19.85 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2674 2734 5.05 %
Rwork0.2235 51454 -
obs0.2257 54188 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.69 Å2 / Biso mean: 33.051 Å2 / Biso min: 15.32 Å2
Refinement stepCycle: final / Resolution: 2.1→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5785 0 58 649 6492
Biso mean--57.45 39.31 -
Num. residues----741
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 (%)
2.1-2.140.43241470.308925232670100
2.14-2.170.30971600.27482539269999
2.17-2.220.32121380.282725462684100
2.22-2.260.47561290.3322557268699
2.26-2.310.30061360.26542550268699
2.31-2.360.27251480.24242550269899
2.36-2.420.29261380.24122573271199
2.42-2.490.29221340.23872484261898
2.49-2.560.29051260.23442579270599
2.56-2.640.311370.224225652702100
2.64-2.740.29231270.22552574270199
2.74-2.850.30211320.21632570270299
2.85-2.980.26991360.22182581271799
2.98-3.130.26491470.21372570271799
3.13-3.330.26791150.21482566268198
3.33-3.590.26431140.206126252739100
3.59-3.940.2251650.19972579274499
3.94-4.510.19161330.19432613274699
4.51-5.660.2451440.20342611275599
5.66-19.850.24191280.21512699282798
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)
11.29210.1995-0.32111.8995-0.10760.53370.0168-0.008-0.0319-0.01220.0353-0.21730.05170.0251-0.05250.21870.014-0.00880.1989-0.00660.181720.5409-13.7061-32.7739
24.01060.26780.5062.76240.34514.15120.1704-0.719-0.240.6389-0.1666-0.04660.22340.02420.00620.4415-0.0374-0.01260.3507-0.00850.210517.627323.0440.043
31.81830.0201-0.71241.4490.17271.90530.0116-0.2376-0.01030.29260.0189-0.1109-0.01980.1-0.03490.2851-0.0204-0.04770.2185-0.01380.267223.80626.0147-15.0917
41.29910.17170.04931.59710.05820.59120.02080.01020.0409-0.00090.0225-0.0527-0.03260.0214-0.04480.2642-0.01690.01050.2192-0.00750.235519.712521.3651-25.3042
51.8243-0.22340.48371.7105-0.13751.32420.05610.38890.0135-0.4518-0.0335-0.16890.10440.0715-0.01950.30470.010.0520.2292-0.00490.203519.4594-17.7492-52.3372
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 139 through 374 )B139 - 374
2X-RAY DIFFRACTION2chain 'A' and (resid 4 through 75 )A4 - 75
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 152 )A76 - 152
4X-RAY DIFFRACTION4chain 'A' and (resid 153 through 374 )A153 - 374
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 138 )B5 - 138

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