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

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Basic information

Entry
Database: PDB / ID: 3zlk
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 / 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-Y46 / Glucose-1-phosphate thymidylyltransferase / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.952 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: 4ASP
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
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)136,28812
Polymers134,6564
Non-polymers1,6318
Water13,079726
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)136,28812
Polymers134,6564
Non-polymers1,6318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area13810 Å2
ΔGint-99.8 kcal/mol
Surface area44730 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)136,28812
Polymers134,6564
Non-polymers1,6318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area13620 Å2
ΔGint-105.4 kcal/mol
Surface area42690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.300, 155.000, 134.450
Angle α, β, γ (deg.)90.00, 92.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2092-

HOH

21C-2076-

HOH

31C-2079-

HOH

41D-2055-

HOH

51D-2107-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9375, 0.01101, -0.3479), (-0.006215, -0.9999, -0.01491), (-0.348, -0.01182, 0.9374)62.63, -36.3, 10.75
2given(0.9989, -0.005255, -0.04735), (-0.004625, -0.9999, 0.01339), (-0.04742, -0.01316, -0.9988)5.535, -17.53, 68.24
3given(-0.9534, 0.008598, 0.3016), (0.01161, 0.9999, 0.008208), (-0.3015, 0.01133, -0.9534)40.13, -20.66, 72.68

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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) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: G3XCK4, UniProt: Q9HU22*PLUS, 1L-myo-inositol 1-phosphate cytidylyltransferase
#2: Chemical
ChemComp-Y46 / N-(6-AMINO-1-BENZYL-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL)BENZENESULFONAMIDE


Mass: 372.398 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H16N4O4S
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 726 / 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: 2.58 Å3/Da / Density % sol: 52.3 % / 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 28, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→37.23 Å / Num. obs: 81490 / % possible obs: 85.5 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 28.17 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.7
Reflection shellResolution: 1.95→2 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2 / % possible all: 69

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Processing

Software
NameVersionClassification
REFMAC5.6.0017refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ARW

4arw


Resolution: 1.952→37.233 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.863 / SU B: 5.056 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2774 4049 5.03 %RANDOM
Rwork0.2329 ---
obs0.235 80615 84.744 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 30.897 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å2-0.374 Å2
2---0.283 Å20 Å2
3----0.093 Å2
Refinement stepCycle: LAST / Resolution: 1.952→37.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9206 0 108 726 10040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.029543
X-RAY DIFFRACTIONr_bond_other_d0.0010.026440
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.99212965
X-RAY DIFFRACTIONr_angle_other_deg0.8743.00215696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10951176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32524.289436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.617151577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7441556
X-RAY DIFFRACTIONr_chiral_restr0.0670.21406
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110689
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021939
X-RAY DIFFRACTIONr_nbd_refined0.220.22589
X-RAY DIFFRACTIONr_nbd_other0.2460.2118
X-RAY DIFFRACTIONr_nbtor_refined0.1760.24658
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2246
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_it1.6533.5369542
X-RAY DIFFRACTIONr_mcbond_other0.3823.6356440
X-RAY DIFFRACTIONr_mcangle_it2.6225.26712962
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4610.863245
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.79517.5238069
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: 1.952→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 236 -
Rwork0.317 4421 -
obs--67.21 %

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