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- PDB-4b4b: Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor -

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Basic information

Entry
Database: PDB / ID: 4b4b
TitlePseudomonas aeruginosa RmlA in complex with allosteric inhibitor
ComponentsGLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
KeywordsTRANSFERASE
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 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-GJB / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAlphey, M.S. / Pirrie, L. / Torrie, L.S. / Gardiner, M. / Sarkar, A. / Brenk, R. / Westwood, N.J. / Gray, D. / Naismith, J.H.
CitationJournal: ACS Chem. Biol. / Year: 2013
Title: Allosteric competitive inhibitors of the glucose-1-phosphate thymidylyltransferase (RmlA) from Pseudomonas aeruginosa.
Authors: Alphey, M.S. / Pirrie, L. / Torrie, L.S. / Boulkeroua, W.A. / Gardiner, M. / Sarkar, A. / Maringer, M. / Oehlmann, W. / Brenk, R. / Scherman, M.S. / McNeil, M. / Rejzek, M. / Field, R.A. / ...Authors: Alphey, M.S. / Pirrie, L. / Torrie, L.S. / Boulkeroua, W.A. / Gardiner, M. / Sarkar, A. / Maringer, M. / Oehlmann, W. / Brenk, R. / Scherman, M.S. / McNeil, M. / Rejzek, M. / Field, R.A. / Singh, M. / Gray, D. / Westwood, N.J. / Naismith, J.H.
History
DepositionJul 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references / Structure summary
Revision 1.2Mar 6, 2013Group: Database references
Revision 1.3Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)136,31315
Polymers134,6564
Non-polymers1,65611
Water4,378243
1
B: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
C: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
hetero molecules

B: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
C: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,50816
Polymers134,6564
Non-polymers1,85212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area15230 Å2
ΔGint-92.8 kcal/mol
Surface area42210 Å2
MethodPISA
2
A: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
D: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
hetero molecules

A: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
D: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,11814
Polymers134,6564
Non-polymers1,46110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area14900 Å2
ΔGint-95.3 kcal/mol
Surface area43730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.060, 154.240, 134.850
Angle α, β, γ (deg.)90.00, 92.78, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9995, -0.007248, -0.02961), (-0.006877, -0.9999, 0.0126), (-0.0297, -0.01239, -0.9995)5.144, -17.48, 67.93
2given(-0.9636, -0.007149, -0.2674), (0.01481, -0.9995, -0.02666), (-0.2671, -0.02965, 0.9632)62.33, -36.67, 7.883
3given(-0.9312, 0.008543, -0.3645), (-0.004044, -0.9999, -0.0131), (-0.3646, -0.01073, 0.9311)62.09, -36.13, 11.32

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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
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q9HU22, 1L-myo-inositol 1-phosphate cytidylyltransferase
#2: Chemical
ChemComp-GJB / 1-(2-phenylethyl)pyrimidine-2,4,6(1H,3H,5H)-trione


Mass: 232.235 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H12N2O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.97 % / Description: NONE
Crystal growpH: 6
Details: 4% PEG 6000, 0.1 M MES PH 6, 0.05 M MGCL2, 0.1 M NA BR, 1% BETA-MERCAPTOETHANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→59.1 Å / Num. obs: 72939 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.7
Reflection shellResolution: 2→2.15 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ARW

4arw


Resolution: 2.1→59.101 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.575 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2655 3645 5.07 %RANDOM
Rwork0.2262 ---
obs0.228 72228 94.882 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 55.553 Å2
Baniso -1Baniso -2Baniso -3
1-2.254 Å20 Å2-0.065 Å2
2--0.556 Å20 Å2
3----2.817 Å2
Refinement stepCycle: LAST / Resolution: 2.1→59.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9205 0 108 243 9556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.029544
X-RAY DIFFRACTIONr_bond_other_d0.0060.026474
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9912954
X-RAY DIFFRACTIONr_angle_other_deg1.3253.00115738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99351177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22324.302437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79151579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2181556
X-RAY DIFFRACTIONr_chiral_restr0.0820.21408
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110648
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021896
X-RAY DIFFRACTIONr_nbd_refined0.2160.21919
X-RAY DIFFRACTIONr_nbd_other0.1630.280
X-RAY DIFFRACTIONr_nbtor_refined0.1780.24628
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2201
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.4466.4499544
X-RAY DIFFRACTIONr_mcbond_other1.3456.596474
X-RAY DIFFRACTIONr_mcangle_it6.2849.58812950
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it9.61719.6243249
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.33631.4627295
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 263 -
Rwork0.281 5265 -
obs--99.892 %

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