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- PDB-6t37: Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor -

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Basic information

Entry
Database: PDB / ID: 6t37
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-M9Z / Glucose-1-phosphate thymidylyltransferase / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.079 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)137,42918
Polymers134,6564
Non-polymers2,77214
Water8,341463
1
A: Glucose-1-phosphate thymidylyltransferase
B: Glucose-1-phosphate thymidylyltransferase
hetero molecules

A: Glucose-1-phosphate thymidylyltransferase
B: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,35816
Polymers134,6564
Non-polymers2,70212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15220 Å2
ΔGint-106 kcal/mol
Surface area39380 Å2
MethodPISA
2
C: Glucose-1-phosphate thymidylyltransferase
D: Glucose-1-phosphate thymidylyltransferase
hetero molecules

C: Glucose-1-phosphate thymidylyltransferase
D: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,50020
Polymers134,6564
Non-polymers2,84316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area14640 Å2
ΔGint-142 kcal/mol
Surface area39450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.910, 152.570, 134.720
Angle α, β, γ (deg.)90.000, 93.390, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

21C-432-

HOH

31C-525-

HOH

41D-415-

HOH

51D-498-

HOH

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
11ARGARGTYRTYRAA3 - 29313 - 303
21ARGARGTYRTYRBB3 - 29313 - 303
12LYSLYSTYRTYRAA2 - 29312 - 303
22LYSLYSTYRTYRCC2 - 29312 - 303
13LYSLYSTYRTYRAA2 - 29312 - 303
23LYSLYSTYRTYRDD2 - 29312 - 303
14ARGARGVALVALBB3 - 29213 - 302
24ARGARGVALVALCC3 - 29213 - 302
15ARGARGTYRTYRBB3 - 29313 - 303
25ARGARGTYRTYRDD3 - 29313 - 303
16LYSLYSTYRTYRCC2 - 29312 - 303
26LYSLYSTYRTYRDD2 - 29312 - 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 are due to flexibility and weak electron density
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-M9Z / ~{N}-[6-[3-[4-(aminomethyl)-1,2,3-triazol-1-yl]propylamino]-2,4-bis(oxidanylidene)-1-(phenylmethyl)pyrimidin-5-yl]-~{N}-methyl-benzenesulfonamide


Mass: 524.595 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H28N8O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / 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.: 463 / 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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 6, 2018 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.079→25.71 Å / Num. obs: 76533 / % possible obs: 99.2 % / Redundancy: 3.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.075 / Rrim(I) all: 0.143 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.079-2.122.70.61342800.5340.4540.76893.2
10.4-25.713.60.0615920.9930.0370.07193.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.7.3data scaling
MOLREPphasing
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FTV

5ftv


Resolution: 2.079→25.71 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.283 / SU ML: 0.159 / SU R Cruickshank DPI: 0.2394 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / ESU R Free: 0.185
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2419 3850 5 %RANDOM
Rwork0.2175 ---
obs0.2188 72677 99.11 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 80.68 Å2 / Biso mean: 31.529 Å2 / Biso min: 9.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20.22 Å2
2--0.73 Å20 Å2
3----0.99 Å2
Refinement stepCycle: final / Resolution: 2.079→25.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8762 0 180 463 9405
Biso mean--35.67 35.48 -
Num. residues----1144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0139154
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178315
X-RAY DIFFRACTIONr_angle_refined_deg1.311.66212473
X-RAY DIFFRACTIONr_angle_other_deg1.1931.59219217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76551140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66823.036448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91151391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9891545
X-RAY DIFFRACTIONr_chiral_restr0.0540.21160
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210383
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021908
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A88750.05
12B88750.05
21A87420.07
22C87420.07
31A88660.07
32D88660.07
41B84560.05
42C84560.05
51B86670.06
52D86670.06
61C86290.06
62D86290.06
LS refinement shellResolution: 2.079→2.133 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.318 256 -
Rwork0.312 5067 -
obs--93.88 %

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