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- PDB-8hhd: Crystal structure of PaMurU -

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Basic information

Entry
Database: PDB / ID: 8hhd
TitleCrystal structure of PaMurU
ComponentsNucleotidyl transferase
KeywordsTRANSFERASE / MurU / N-acetylmuramate alpha-1-phosphate uridylyltransferase
Function / homologyglucose-1-phosphate thymidylyltransferase activity / : / Nucleotidyl transferase domain / Nucleotidyl transferase / biosynthetic process / Nucleotide-diphospho-sugar transferases / Nucleotidyltransferase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.27 Å
AuthorsShin, D.H. / Jo, S.R. / Kim, M.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1D1A1B07050781 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of PAMurU
Authors: Shin, D.H. / Jo, S.R. / Kim, M.S.
History
DepositionNov 16, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleotidyl transferase
B: Nucleotidyl transferase
C: Nucleotidyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3247
Polymers78,7983
Non-polymers5264
Water4,846269
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.509, 76.509, 97.935
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Nucleotidyl transferase / Nucleotidyltransferase / Nucleotidyltransferase family protein


Mass: 26265.969 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: rmlA / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1Y3LFE7, glucose-1-phosphate thymidylyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.06M NaCl, 0.1M HEPES pH8.0, 1.6M Ammonium sulfate, 0.1M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 29509 / % possible obs: 100 % / Redundancy: 11.4 % / Rsym value: 0.129 / Net I/σ(I): 16.2
Reflection shellResolution: 2.27→2.31 Å / Num. unique obs: 1478 / Rsym value: 0.501

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.27→32.65 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 24.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 1961 6.77 %
Rwork0.1797 --
obs0.1835 28978 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→32.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5108 0 30 269 5407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095260
X-RAY DIFFRACTIONf_angle_d1.1557145
X-RAY DIFFRACTIONf_dihedral_angle_d15.9451906
X-RAY DIFFRACTIONf_chiral_restr0.064763
X-RAY DIFFRACTIONf_plane_restr0.007950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.330.31191360.20661844X-RAY DIFFRACTION94
2.33-2.390.25551460.20261912X-RAY DIFFRACTION96
2.39-2.460.26231320.18321851X-RAY DIFFRACTION96
2.46-2.540.2541460.19121925X-RAY DIFFRACTION97
2.54-2.630.27051330.20441910X-RAY DIFFRACTION97
2.63-2.740.27691460.19341933X-RAY DIFFRACTION98
2.74-2.860.25191390.19461896X-RAY DIFFRACTION99
2.86-3.020.26041380.20361950X-RAY DIFFRACTION99
3.02-3.20.2621410.20251973X-RAY DIFFRACTION99
3.2-3.450.25971460.18341961X-RAY DIFFRACTION100
3.45-3.80.21291360.16161974X-RAY DIFFRACTION100
3.8-4.340.20751440.15011942X-RAY DIFFRACTION100
4.35-5.470.19771380.16021981X-RAY DIFFRACTION100
5.48-6.160.22021400.17951965X-RAY DIFFRACTION100

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