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- PDB-6t38: Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor -

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Basic information

Entry
Database: PDB / ID: 6t38
TitlePseudomonas aeruginosa RmlA in complex with allosteric inhibitor
ComponentsGlucose-1-phosphate thymidylyltransferase
KeywordsTRANSFERASE / RmlA / allostery / thymidylyltransferase / inhibitor
Function / homology
Function and homology information


glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / dTDP-rhamnose biosynthetic process / lipopolysaccharide core region biosynthetic process / extracellular polysaccharide biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
Glucose-1-phosphate thymidylyltransferase, short form / Nucleotidyl transferase domain / Nucleotidyl transferase / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
BROMIDE ION / Chem-MBK / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsAlphey, M.S. / Xiao, G. / Westwood, J.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustWT100209MA United Kingdom
CitationJournal: Bioorg.Med.Chem. / Year: 2021
Title: Next generation Glucose-1-phosphate thymidylyltransferase (RmlA) inhibitors: An extended SAR study to direct future design.
Authors: Xiao, G. / Alphey, M.S. / Tran, F. / Pirrie, L. / Milbeo, P. / Zhou, Y. / Bickel, J.K. / Kempf, O. / Kempf, K. / Naismith, J.H. / Westwood, N.J.
History
DepositionOct 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose-1-phosphate thymidylyltransferase
B: Glucose-1-phosphate thymidylyltransferase
C: Glucose-1-phosphate thymidylyltransferase
D: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,76925
Polymers134,6564
Non-polymers3,11221
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14520 Å2
ΔGint-194 kcal/mol
Surface area41310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.450, 90.890, 97.421
Angle α, β, γ (deg.)90.000, 95.430, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSVALVALAA2 - 29212 - 302
21LYSLYSVALVALBB2 - 29212 - 302
12LYSLYSTYRTYRAA2 - 29312 - 303
22LYSLYSTYRTYRCC2 - 29312 - 303
13LYSLYSVALVALAA2 - 29212 - 302
23LYSLYSVALVALDD2 - 29212 - 302
14LYSLYSVALVALBB2 - 29212 - 302
24LYSLYSVALVALCC2 - 29212 - 302
15LYSLYSTYRTYRBB2 - 29312 - 303
25LYSLYSTYRTYRDD2 - 29312 - 303
16LYSLYSVALVALCC4 - 29214 - 302
26HISHISVALVALDD17 - 29227 - 302

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glucose-1-phosphate thymidylyltransferase /


Mass: 33664.121 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rmlA, PA5163 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HU22, glucose-1-phosphate thymidylyltransferase

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Non-polymers , 5 types, 267 molecules

#2: Chemical
ChemComp-MBK / ~{N}-[6-(4-azanylbutylamino)-1-[(4-bromophenyl)methyl]-2,4-bis(oxidanylidene)pyrimidin-5-yl]-~{N}-methyl-benzenesulfonamide


Mass: 536.442 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H26BrN5O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 12% PEG 6000, 0.1 M MES PH 6, 0.1 M MGCL2, 0.15 M NA BR, 1% BETA-MERCAPTOETHANOL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 23, 2019 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→28.92 Å / Num. obs: 66426 / % possible obs: 99.8 % / Redundancy: 4.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.059 / Rrim(I) all: 0.133 / Net I/σ(I): 8.7 / Num. measured all: 320687 / Scaling rejects: 447
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
2.15-2.24.20.4031814343700.8530.2210.4623.198.5
10.08-28.924.60.06229536370.9910.0320.0718.892.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.574
Highest resolutionLowest resolution
Rotation24.08 Å2.36 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0257refinement
MOSFLMdata reduction
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FTV

5ftv


Resolution: 2.15→24.09 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.2011 / FOM work R set: 0.8237 / SU B: 5.729 / SU ML: 0.148 / SU R Cruickshank DPI: 0.2718 / SU Rfree: 0.2024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 3257 4.9 %RANDOM
Rwork0.2119 ---
obs0.2135 63148 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.76 Å2 / Biso mean: 23.301 Å2 / Biso min: 6.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å2-0.98 Å2
2---0.44 Å20 Å2
3---0.77 Å2
Refinement stepCycle: final / Resolution: 2.15→24.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8719 0 171 246 9136
Biso mean--27.3 23.52 -
Num. residues----1132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0139071
X-RAY DIFFRACTIONr_bond_other_d0.0020.0178312
X-RAY DIFFRACTIONr_angle_refined_deg1.331.6612342
X-RAY DIFFRACTIONr_angle_other_deg1.1791.59219231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67751122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55122.95444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.137151412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7281546
X-RAY DIFFRACTIONr_chiral_restr0.060.21145
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210215
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021875
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A83040.07
12B83040.07
21A83880.08
22C83880.08
31A81970.06
32D81970.06
41B83050.08
42C83050.08
51B85570.06
52D85570.06
61C79310.08
62D79310.08
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 239 -
Rwork0.246 4577 -
all-4816 -
obs--98.43 %

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