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

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Basic information

Entry
Database: PDB / ID: 5fye
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 / 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-LD6 / Glucose-1-phosphate thymidylyltransferase / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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
DepositionMar 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Data collection
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Jan 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 / pdbx_struct_special_symmetry / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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)137,19716
Polymers134,6564
Non-polymers2,54012
Water4,972276
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)137,19716
Polymers134,6564
Non-polymers2,54012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area18200 Å2
ΔGint-97.2 kcal/mol
Surface area43000 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)137,19716
Polymers134,6564
Non-polymers2,54012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area18650 Å2
ΔGint-91.6 kcal/mol
Surface area43250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.290, 154.420, 134.620
Angle α, β, γ (deg.)90.00, 92.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2033-

HOH

21C-2024-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSVALVALAA2 - 29212 - 302
21LYSLYSVALVALBB2 - 29212 - 302
12HISHISTYRTYRAA-9 - 2933 - 303
22HISHISTYRTYRCC-8 - 2934 - 303
13LYSLYSTYRTYRAA2 - 29312 - 303
23LYSLYSTYRTYRDD2 - 29312 - 303
14LYSLYSVALVALBB2 - 29212 - 302
24LYSLYSVALVALCC2 - 29212 - 302
15LYSLYSTYRTYRBB2 - 29312 - 303
25LYSLYSTYRTYRDD2 - 29312 - 303
16LYSLYSTYRTYRCC2 - 29312 - 303
26LYSLYSTYRTYRDD2 - 29312 - 303

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(-0.9356, 0.007378, -0.353), (-0.003027, -0.9999, -0.01288), (-0.353, -0.01098, 0.9355)62.44, -35.83, 10.95
2given(0.9991, -0.005756, -0.04281), (-0.005064, -0.9999, 0.01624), (-0.0429, -0.016, -0.999)5.511, -17.2, 68.14
3given(-0.9553, 0.0105, 0.2955), (0.01382, 0.9999, 0.009149), (-0.2953, 0.01282, -0.9553)40.19, -20.65, 72.6

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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: G3XCK4, UniProt: Q9HU22*PLUS, glucose-1-phosphate thymidylyltransferase
#2: Chemical
ChemComp-LD6 / N-(6-Amino-1-(3-fluorobenzyl)-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-N-methylbenzenesulfonamide


Mass: 404.415 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H17FN4O4S
#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.: 276 / 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: 52.13 % / Description: NONE
Crystal growpH: 6
Details: 4% PEG 6000, 0.1 M MES PH6, 0.05 M MGCL2, 0.1 M 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: Mar 23, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→27.8 Å / Num. obs: 48194 / % possible obs: 94.3 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 15.13 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.5 / % possible all: 94.4

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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: 2.4→134.512 Å / Cor.coef. Fo:Fc: 0.841 / Cor.coef. Fo:Fc free: 0.81 / SU B: 10.109 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.704 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME RESIDUES AT THE N-TERMINI ARE DISORDERED AND HAVE BEEN OMITTED FROM THE MODEL. RESIDUES D192-D197 WERE NOT CLEARLY DEFINED AND HAVE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME RESIDUES AT THE N-TERMINI ARE DISORDERED AND HAVE BEEN OMITTED FROM THE MODEL. RESIDUES D192-D197 WERE NOT CLEARLY DEFINED AND HAVE BEEN OMITTED FROM THE MODEL. THE BOUND COMPOUND HAS BEEN MODELLED IN THE PREDOMINANT CONFORMATION. SEVERAL RESIDUES HAVE BEEN MODELLED IN WITH ALTERNATE CONFORMATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2831 2407 5.09 %RANDOM
Rwork0.2434 ---
obs0.245 48146 94.068 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 32.002 Å2
Baniso -1Baniso -2Baniso -3
1-0.607 Å20 Å2-0.585 Å2
2---0.554 Å20 Å2
3----0.007 Å2
Refinement stepCycle: LAST / Resolution: 2.4→134.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9183 0 164 276 9623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0199583
X-RAY DIFFRACTIONr_bond_other_d0.0090.029111
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.99413020
X-RAY DIFFRACTIONr_angle_other_deg1.5783.00220947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42551172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40924.292438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92151570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0081555
X-RAY DIFFRACTIONr_chiral_restr0.0930.21412
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02110874
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022201
X-RAY DIFFRACTIONr_nbd_refined0.2090.23988
X-RAY DIFFRACTIONr_nbd_other0.2290.2153
X-RAY DIFFRACTIONr_nbtor_refined0.1760.29102
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2382
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1250.21
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_it2.9083.0254685
X-RAY DIFFRACTIONr_mcbond_other2.9083.0254684
X-RAY DIFFRACTIONr_mcangle_it4.4854.5285846
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0523.2984898
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8444.8157170
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A350980.08
12B350980.08
21A353900.09
22C353900.09
31A339200.11
32D339200.11
41B349100.09
42C349100.09
51B340700.1
52D340700.1
61C343360.1
62D343360.1
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 170 -
Rwork0.264 3407 -
obs--94.082 %

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