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

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Basic information

Entry
Database: PDB / ID: 6tqg
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 / 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
Chem-NVQ / Glucose-1-phosphate thymidylyltransferase / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 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
DepositionDec 16, 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)137,86720
Polymers134,6564
Non-polymers3,21016
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13500 Å2
ΔGint-123 kcal/mol
Surface area39660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.011, 137.920, 73.930
Angle α, β, γ (deg.)90.000, 102.980, 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: _ / Refine code: _

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
13ARGARGVALVALAA3 - 29213 - 302
23ARGARGVALVALDD3 - 29213 - 302
14LYSLYSTYRTYRBB2 - 29312 - 303
24LYSLYSTYRTYRCC2 - 29312 - 303
15ARGARGTYRTYRBB3 - 29313 - 303
25ARGARGTYRTYRDD3 - 29313 - 303
16ARGARGTYRTYRCC3 - 29313 - 303
26ARGARGTYRTYRDD3 - 29313 - 303

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Glucose-1-phosphate thymidylyltransferase


Mass: 33664.121 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Residues missing from the model due to missing electron density resulting from loop/sidechain flexibility
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: rmlA, rfbA, CAZ10_00575, E4V10_15605, IPC1492_24235, IPC605_02475, PAMH19_2921
Production host: Escherichia coli (E. coli)
References: UniProt: G3XCK4, UniProt: Q9HU22*PLUS, glucose-1-phosphate thymidylyltransferase
#2: Chemical
ChemComp-NVQ / ~{N}-[1-[(4-bromophenyl)methyl]-6-[3-(methylamino)propylamino]-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


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


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 11% PEG 6000, 0.15M MES pH6, 0.15M sodium bromide, 0.15M magnesium chloride, 1% B-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: 1.5417 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 3, 2019 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.45→29.57 Å / Num. obs: 49961 / % possible obs: 95.6 % / Redundancy: 5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.071 / Rrim(I) all: 0.164 / Net I/σ(I): 7.9
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
2.45-2.534.51.0491981744220.5570.5261.1791.392.1
9.8-29.574.90.04639408060.9980.0230.05221.695.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.585
Highest resolutionLowest resolution
Rotation29.57 Å2.66 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.7.4data scaling
MOLREPphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FTV

5ftv


Resolution: 2.45→29.57 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.885 / SU B: 22.571 / SU ML: 0.265 / SU R Cruickshank DPI: 0.5301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.53 / ESU R Free: 0.306
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2836 2551 5.1 %RANDOM
Rwork0.2571 ---
obs0.2585 47378 95.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 98.02 Å2 / Biso mean: 46.12 Å2 / Biso min: 12.55 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å21.74 Å2
2---0.76 Å20 Å2
3----1.92 Å2
Refinement stepCycle: final / Resolution: 2.45→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8281 0 188 106 8575
Biso mean--45.69 37.32 -
Num. residues----1069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0138660
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177931
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.63611765
X-RAY DIFFRACTIONr_angle_other_deg1.1261.57218325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62351058
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88323.043437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.149151355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7511544
X-RAY DIFFRACTIONr_chiral_restr0.0480.21083
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029714
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021810
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A82690.06
12B82690.06
21A78840.06
22C78840.06
31A79770.06
32D79770.06
41B78140.06
42C78140.06
51B79110.06
52D79110.06
61C78750.04
62D78750.04
LS refinement shellResolution: 2.45→2.514 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 188 -
Rwork0.347 3333 -
all-3521 -
obs--91.34 %
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)
10.7097-0.45950.35940.7890.17391.5037-0.1131-0.04450.07620.17810.3153-0.15840.20670.0666-0.20210.23060.0736-0.14630.19-0.06080.31484.7780.03833.506
21.19990.2668-0.56810.78360.09481.0129-0.011-0.11850.0301-0.13310.2684-0.1551-0.0990.1132-0.25740.2078-0.0761-0.10740.1396-0.05340.324410.405-28.3368.146
30.7363-0.55280.35990.9786-0.55370.85360.1459-0.039-0.1174-0.10920.17680.2607-0.0037-0.2157-0.32270.1510.0019-0.12690.11360.18030.4216-24.3125.54917.092
40.96480.6334-0.26581.5076-0.90640.7179-0.03910.06810.28-0.17860.3840.39850.2072-0.2376-0.34490.2016-0.15-0.2750.19910.21470.4273-22.841-33.05610.167
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 293
2X-RAY DIFFRACTION2B2 - 293
3X-RAY DIFFRACTION3C2 - 293
4X-RAY DIFFRACTION4D2 - 293

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