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- PDB-5fu8: Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor -

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Basic information

Entry
Database: PDB / ID: 5fu8
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-DH5 / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.2Jan 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)137,49716
Polymers134,6564
Non-polymers2,84012
Water11,584643
1
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)137,49716
Polymers134,6564
Non-polymers2,84012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area18630 Å2
ΔGint-88.6 kcal/mol
Surface area42610 Å2
MethodPISA
2
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)137,49716
Polymers134,6564
Non-polymers2,84012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area18870 Å2
ΔGint-90.4 kcal/mol
Surface area43030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.180, 154.480, 134.750
Angle α, β, γ (deg.)90.00, 92.34, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9368, 0.01033, -0.3497), (-0.006098, -0.9999, -0.01321), (-0.3498, -0.01024, 0.9368)62.49, -35.66, 10.87
2given(0.9991, -0.004631, -0.04188), (-0.003974, -0.9999, 0.01574), (-0.04195, -0.01556, -0.999)5.528, -17.15, 68.18
3given(-0.956, 0.00578, 0.2932), (0.009558, 0.9999, 0.01145), (-0.2931, 0.01375, -0.956)40.29, -20.69, 72.59

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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 (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q9HU22, glucose-1-phosphate thymidylyltransferase
#2: Chemical
ChemComp-DH5 / N-(6-amino-1-(4-bromo-3-methylbenzyl)-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-N-methylbenzenesulfonamide


Mass: 479.348 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H19BrN4O4S
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H2O
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: 2.57 Å3/Da / Density % sol: 52.12 % / 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 28, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→25.88 Å / Num. obs: 68251 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 7.486 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.4 / % possible all: 95.2

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Processing

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

4asj


Resolution: 2.2→134.637 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.891 / SU B: 7.496 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 3158 5.01 %RANDOM
Rwork0.2004 ---
obs0.203 63783 96.133 %-
Solvent computationIon probe radii: 0.4 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 26.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.748 Å20 Å2-0.463 Å2
2---0.056 Å20 Å2
3----0.652 Å2
Refinement stepCycle: LAST / Resolution: 2.2→134.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9226 0 168 643 10037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199631
X-RAY DIFFRACTIONr_bond_other_d0.0020.029162
X-RAY DIFFRACTIONr_angle_refined_deg1.511.99613087
X-RAY DIFFRACTIONr_angle_other_deg0.983.00221066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74551179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11124.282439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.389151581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9851556
X-RAY DIFFRACTIONr_chiral_restr0.0830.21417
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110931
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022203
X-RAY DIFFRACTIONr_nbd_refined0.2110.24688
X-RAY DIFFRACTIONr_nbd_other0.2090.2153
X-RAY DIFFRACTIONr_nbtor_refined0.1720.29248
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2522
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_it1.6032.5154710
X-RAY DIFFRACTIONr_mcbond_other1.6042.5154709
X-RAY DIFFRACTIONr_mcangle_it2.6773.7655879
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9422.7544919
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2254.0277204
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→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 216 -
Rwork0.345 4418 -
obs--94.94 %

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