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- PDB-8hl8: Crystal structrue of MtdL R257K mutant -

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Basic information

Entry
Database: PDB / ID: 8hl8
TitleCrystal structrue of MtdL R257K mutant
ComponentsTransglycosylse
KeywordsTRANSFERASE
Function / homologySTELLO-like / Reversibly glycosylated polypeptide family / Reversibly glycosylated polypeptide / metal ion binding / : / Transglycosylse
Function and homology information
Biological speciesMarinactinospora thermotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionNov 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transglycosylse
C: Transglycosylse
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6384
Polymers83,5282
Non-polymers1102
Water2,360131
1
A: Transglycosylse
hetero molecules

A: Transglycosylse
hetero molecules

C: Transglycosylse
hetero molecules

C: Transglycosylse
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,2758
Polymers167,0564
Non-polymers2204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
crystal symmetry operation5_545x+1/2,y-1/2,z1
crystal symmetry operation7_545-x+1/2,y-1/2,-z+1/21
Buried area7650 Å2
ΔGint-47 kcal/mol
Surface area52190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.605, 162.405, 116.206
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Transglycosylse


Mass: 41763.879 Da / Num. of mol.: 2 / Mutation: R257K
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.83 %
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: Oct 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→19.84 Å / Num. obs: 32478 / % possible obs: 99.6 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.074 / Rrim(I) all: 0.2 / Χ2: 1 / Net I/σ(I): 7.8 / Num. measured all: 230290
Reflection shellResolution: 2.5→2.6 Å / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 1.303 / Num. measured all: 26291 / Num. unique obs: 3592 / CC1/2: 0.866 / Rpim(I) all: 0.515 / Rrim(I) all: 1.403 / Χ2: 0.97 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XPT

7xpt


Resolution: 2.5→19.84 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2956 1567 4.86 %
Rwork0.2565 --
obs0.2583 32243 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5777 0 2 131 5910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025925
X-RAY DIFFRACTIONf_angle_d0.4378093
X-RAY DIFFRACTIONf_dihedral_angle_d12.4452141
X-RAY DIFFRACTIONf_chiral_restr0.04892
X-RAY DIFFRACTIONf_plane_restr0.0041088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.580.32561160.33732744X-RAY DIFFRACTION99
2.58-2.670.34261390.32312759X-RAY DIFFRACTION99
2.67-2.780.35771440.30122755X-RAY DIFFRACTION99
2.78-2.910.33571500.29732756X-RAY DIFFRACTION100
2.91-3.060.31071190.2862804X-RAY DIFFRACTION99
3.06-3.250.33661360.29132756X-RAY DIFFRACTION99
3.25-3.50.35031580.26362768X-RAY DIFFRACTION99
3.5-3.850.30461720.24592766X-RAY DIFFRACTION99
3.85-4.40.26071150.22232842X-RAY DIFFRACTION100
4.4-5.520.25911570.21982833X-RAY DIFFRACTION99
5.52-19.840.23761610.22652893X-RAY DIFFRACTION99
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)
12.7807-0.04660.3343.18290.36642.7305-0.04760.73840.0287-0.80060.01-0.10820.20750.0134-0.00250.4831-0.0213-0.12210.5205-0.05950.355128.762514.0699-0.3666
21.4135-0.37820.56151.3680.27340.7367-0.050.5828-0.1023-0.43070.00190.4158-0.12690.02-0.07960.3980.0542-0.11150.25760.03250.400530.392119.94139.7249
32.01950.5141-0.0073.32840.02550.9095-0.00290.0414-0.04490.12290.02120.48270.0097-0.03170.01810.36450.0089-0.10260.29950.01440.485222.576311.960724.9504
41.32380.13230.11590.7909-0.75440.97820.22730.28780.275-0.5539-0.08320.204-0.03290.045-0.08040.31330.0698-0.10560.2304-0.05920.667625.09215.083520.7659
51.3060.51650.92832.2601-0.14782.0101-0.0389-0.16090.03770.32540.0273-0.3285-0.2645-0.04210.0120.31540.02340.00190.3489-0.0470.515239.141916.246729.1759
61.5303-0.62410.57061.3752-0.07811.1920.01320.457-0.0329-0.3922-0.0129-0.0664-0.21160.0866-0.02390.48520.00350.00970.401-0.02830.484120.933156.31218.0199
71.6670.1583-0.43641.45460.12151.0786-0.02850.048-0.0723-0.1220.0542-0.31690.04280.1007-0.05620.28190.0317-0.11270.250.01180.367919.668959.216525.6267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 138 )
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 258 )
4X-RAY DIFFRACTION4chain 'A' and (resid 259 through 293 )
5X-RAY DIFFRACTION5chain 'A' and (resid 294 through 374 )
6X-RAY DIFFRACTION6chain 'C' and (resid 4 through 152 )
7X-RAY DIFFRACTION7chain 'C' and (resid 153 through 374 )

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