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- PDB-8xgq: The co-crystal structure of LtpM with UDP -

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Basic information

Entry
Database: PDB / ID: 8xgq
TitleThe co-crystal structure of LtpM with UDP
ComponentsLtpM1
KeywordsTRANSFERASE / glucosyltransferase
Function / homologyAnkyrin repeat profile. / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / URIDINE-5'-DIPHOSPHATE / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsWei, T. / Xiao, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: The co-crystal structure of LtpM with UDP
Authors: Wei, T. / Xiao, J.
History
DepositionDec 15, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: LtpM1
A: LtpM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,6854
Polymers96,8762
Non-polymers8082
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.593, 64.925, 84.423
Angle α, β, γ (deg.)109.920, 94.240, 109.060
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 7 through 88 or resid 95...
21(chain B and (resid 7 through 88 or resid 95...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLUGLU(chain A and (resid 7 through 88 or resid 95...AB7 - 881 - 82
12ASPASPSERSER(chain A and (resid 7 through 88 or resid 95...AB95 - 26889 - 262
13ALAALAILEILE(chain A and (resid 7 through 88 or resid 95...AB270 - 400264 - 394
14PROPROPROPRO(chain A and (resid 7 through 88 or resid 95...AB402396
15GLYGLYHISHIS(chain A and (resid 7 through 88 or resid 95...AB404 - 430398 - 424
21SERSERGLUGLU(chain B and (resid 7 through 88 or resid 95...BA7 - 881 - 82
22ASPASPSERSER(chain B and (resid 7 through 88 or resid 95...BA95 - 11089 - 104
23ASPASPSERSER(chain B and (resid 7 through 88 or resid 95...BA115 - 268109 - 262
24ALAALAPROPRO(chain B and (resid 7 through 88 or resid 95...BA270 - 271264 - 265
25METMETALAALA(chain B and (resid 7 through 88 or resid 95...BA288 - 295282 - 289
26ALAALAALAALA(chain B and (resid 7 through 88 or resid 95...BA301295
27VALVALVALVAL(chain B and (resid 7 through 88 or resid 95...BA307 - 315301 - 309
28LEULEUASNASN(chain B and (resid 7 through 88 or resid 95...BA348 - 354342 - 348
29SERSERILEILE(chain B and (resid 7 through 88 or resid 95...BA356 - 400350 - 394
210PROPROPROPRO(chain B and (resid 7 through 88 or resid 95...BA402396
211GLYGLYHISHIS(chain B and (resid 7 through 88 or resid 95...BA404 - 430398 - 424

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Components

#1: Protein LtpM1


Mass: 48438.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Gene: D1H98_02725 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A3A6VV34
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
Has ligand of interestY
Has protein modificationN

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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: 2.84 Å3/Da / Density % sol: 62.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.44 M ammonium sulfate, 0.1 M BIS-TRIS pH 6.4, 0.1 M NaCl

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.04→50 Å / Num. obs: 19903 / % possible obs: 96.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 73.36 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.087 / Net I/σ(I): 13
Reflection shellResolution: 3.04→3.15 Å / Rmerge(I) obs: 0.466 / Num. unique obs: 1830 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold

Resolution: 3.04→28.29 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Phase error: 34.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3014 1988 10 %
Rwork0.2573 17890 -
obs0.2618 19878 95.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.72 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.04→28.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6061 0 50 0 6111
Biso mean--62.17 --
Num. residues----757
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2060X-RAY DIFFRACTION12.34TORSIONAL
12B2060X-RAY DIFFRACTION12.34TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.04-3.120.28891250.26771125125084
3.12-3.20.37041440.29531299144399
3.2-3.30.35311490.31821330147999
3.3-3.40.36751500.28981351150199
3.4-3.520.33951410.28451275141697
3.52-3.660.34311440.2921294143897
3.66-3.830.35551470.27251320146798
3.83-4.030.32291420.26931281142397
4.03-4.280.31331410.23441275141696
4.28-4.610.29041440.2481284142896
4.61-5.070.29051360.2351230136693
5.07-5.80.27281440.25511291143596
5.8-7.290.28651460.26941311145798
7.29-28.290.23911350.2191224135992

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