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- PDB-3zll: Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor -

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Basic information

Entry
Database: PDB / ID: 3zll
TitlePseudomonas aeruginosa RmlA in complex with allosteric inhibitor
ComponentsGLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
KeywordsTRANSFERASE / THYMIDYLYLTRANSFERASE / ALLOSTERIC 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 / 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-4WF / Glucose-1-phosphate thymidylyltransferase / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionFeb 1, 2013Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 20, 2013ID: 4AS6
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Feb 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 1.3Dec 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)136,59318
Polymers134,6564
Non-polymers1,93714
Water8,215456
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9010 Å2
ΔGint-66.7 kcal/mol
Surface area51160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.090, 154.110, 134.670
Angle α, β, γ (deg.)90.00, 92.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2066-

HOH

21B-2051-

HOH

31C-2035-

HOH

41C-2071-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9994, -0.009546, -0.03356), (-0.009044, -0.9998, 0.01505), (-0.0337, -0.01474, -0.9993)5.109, -17.07, 67.95
2given(-0.9521, 0.01484, 0.3055), (0.02019, 0.9997, 0.01435), (-0.3052, 0.01983, -0.9521)39.08, -20.92, 72.58
3given(-0.9318, 0.01261, -0.3627), (-0.007392, -0.9998, -0.01577), (-0.3628, -0.01201, 0.9318)62.28, -35.48, 11.2

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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) / Plasmid: PET23A MODIFIED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: G3XCK4, UniProt: Q9HU22*PLUS, 1L-myo-inositol 1-phosphate cytidylyltransferase

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Non-polymers , 5 types, 470 molecules

#2: Chemical
ChemComp-4WF / 5-azanyl-6-oxidanyl-1-(phenylmethyl)pyrimidine-2,4-dione


Mass: 233.223 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H11N3O3
#3: 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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 51.9 % / Description: NONE
Crystal growpH: 6
Details: 4% PEG6000, 0.1M MES PH6, 0.05M MGCL2, 0.1M NABR, 1% B-ME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.96→45.3 Å / Num. obs: 88442 / % possible obs: 94.4 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.5
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.7 / % possible all: 91.6

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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→45.32 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.509 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24514 4150 5 %RANDOM
Rwork0.1994 ---
obs0.2017 78879 94.47 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.468 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å2-0.26 Å2
2---0.22 Å20 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 2→45.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9264 0 126 456 9846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.029609
X-RAY DIFFRACTIONr_bond_other_d0.0010.026503
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.9913039
X-RAY DIFFRACTIONr_angle_other_deg0.8653.00115826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91551179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7924.227440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.343151583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9431556
X-RAY DIFFRACTIONr_chiral_restr0.070.21416
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110703
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021909
X-RAY DIFFRACTIONr_nbd_refined0.210.22235
X-RAY DIFFRACTIONr_nbd_other0.1820.285
X-RAY DIFFRACTIONr_nbtor_refined0.1760.24656
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2218
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_it2.6655.1489607
X-RAY DIFFRACTIONr_mcbond_other0.7255.2716502
X-RAY DIFFRACTIONr_mcangle_it3.9877.66113037
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.4215.6773258
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.07625.1977681
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 247 -
Rwork0.25 5121 -
obs--84.14 %

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