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- PDB-5fuh: Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor -

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Basic information

Entry
Database: PDB / ID: 5fuh
TitlePseudomonas aeruginosa RmlA in complex with allosteric inhibitor
ComponentsGLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
KeywordsTRANSFERASE / THYMIDYLYL / ALLOSTERIC / INHIBITOR / PSEUDOMONAS
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-HKX / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAlphey, M.S. / Tran, F. / Westwood, N.J. / Naismith, J.H.
CitationJournal: To be Published
Title: Allosteric Competitive Inhibitors of the Glucose-1-Phosphate Thymidylyltransferase (Rmla) from Pseudomonas Aeruginosa.
Authors: Tran, F. / Alphey, M.S. / Westwood, N.J. / Naismith, J.H.
History
DepositionJan 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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)137,80920
Polymers134,6564
Non-polymers3,15216
Water10,305572
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)137,62518
Polymers134,6564
Non-polymers2,96814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area19360 Å2
ΔGint-89.6 kcal/mol
Surface area43800 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)137,99322
Polymers134,6564
Non-polymers3,33718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area20270 Å2
ΔGint-108.3 kcal/mol
Surface area43620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.460, 155.260, 134.830
Angle α, β, γ (deg.)90.00, 92.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2082-

HOH

21B-2054-

HOH

31B-2113-

HOH

41C-2063-

HOH

51C-2121-

HOH

61D-2041-

HOH

71D-2077-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9359, 0.01102, -0.3522), (-0.004872, -0.9998, -0.01834), (-0.3524, -0.01545, 0.9357)62.74, -35.89, 10.84
2given(0.9995, -0.001456, -0.03248), (-0.000964, -0.9999, 0.01515), (-0.0325, -0.01511, -0.9994)5.141, -17.38, 68.02
3given(-0.9564, 0.01034, 0.2918), (0.01355, 0.9999, 0.008977), (-0.2917, 0.01254, -0.9564)40.39, -20.73, 72.6

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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 (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q9HU22, glucose-1-phosphate thymidylyltransferase

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Non-polymers , 5 types, 588 molecules

#2: Chemical
ChemComp-HKX / N-[6-amino-1-(3-bromobenzyl)-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl]-N-methylbenzenesulfonamide


Mass: 465.321 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H17BrN4O4S
#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.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN-TERMINAL HIS-TAG PRESENT

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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: 2.59 Å3/Da / Density % sol: 52.58 % / 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: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2014 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.59→67.35 Å / Num. obs: 175397 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.5
Reflection shellResolution: 1.59→1.63 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.1 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ASJ

4asj


Resolution: 1.6→67.349 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.997 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME RESIDUES AT THE N-TERMINUS ARE DISORDERED. SOME RESIDUES HAVE BEEN MODELLED IN MULTIPLE CONFORMATIONS. THE BOUND INHIBITOR HAS PARTIAL ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME RESIDUES AT THE N-TERMINUS ARE DISORDERED. SOME RESIDUES HAVE BEEN MODELLED IN MULTIPLE CONFORMATIONS. THE BOUND INHIBITOR HAS PARTIAL OCCUPANCY. SOME EXTRA ELECTRON DENSITY IS OBSERVED IN THE PARTIALLY OCCUPIED INHIBITOR BINDING SITE, MOST LIKELY DUE TO WATERS BOUND WHEN INHIBITOR IS ABSENT. SOME EXTRA ELECTRON DENSITY IS OBSERVED NEAR THE MULTIPLE CONFORMATIONS OF GLN237, MOST LIKELY DUE TO WATERS BOUND WHEN SIDE CHAIN IS IN ALTERNATIVE CONFORMATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 8570 5.03 %RANDOM
Rwork0.202 ---
obs0.203 172334 99.18 %-
Solvent computationIon probe radii: 0.4 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 29.619 Å2
Baniso -1Baniso -2Baniso -3
1-0.557 Å20 Å2-0.468 Å2
2--0.307 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.6→67.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9267 0 188 572 10027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199752
X-RAY DIFFRACTIONr_bond_other_d0.0020.029311
X-RAY DIFFRACTIONr_angle_refined_deg1.311.99813258
X-RAY DIFFRACTIONr_angle_other_deg0.9133.00221421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95151204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69524.289443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.463151609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9971556
X-RAY DIFFRACTIONr_chiral_restr0.0730.21444
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111056
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022234
X-RAY DIFFRACTIONr_nbd_refined0.1910.24432
X-RAY DIFFRACTIONr_nbd_other0.1810.2152
X-RAY DIFFRACTIONr_nbtor_refined0.1680.29206
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.2454
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_it1.4132.784750
X-RAY DIFFRACTIONr_mcbond_other1.4122.784749
X-RAY DIFFRACTIONr_mcangle_it2.2834.1645934
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8163.055001
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9414.4727310
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: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 597 -
Rwork0.279 11749 -
obs--96.22 %

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