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- PDB-9szl: PaMurU in complex with Ca2+ and UDPNAM (uridine diphosphate N-ace... -

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Basic information

Entry
Database: PDB / ID: 9szl
TitlePaMurU in complex with Ca2+ and UDPNAM (uridine diphosphate N-acetyl muramic acid)
ComponentsN-acetylmuramate alpha-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / Pseudonomas aeruginosa Peptidoglycan recycling pathway Bacteria cell wall
Function / homology
Function and homology information


N-acetyl-alpha-D-muramate 1-phosphate uridylyltransferase / peptidoglycan turnover / peptidoglycan biosynthetic process / nucleotidyltransferase activity / cell wall organization / regulation of cell shape / response to antibiotic / metal ion binding
Similarity search - Function
: / : / Nucleotidyl transferase domain / Nucleotidyl transferase / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
DIPHOSPHATE / Chem-EPZ / TRIETHYLENE GLYCOL / N-acetylmuramate alpha-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsJimenez-Faraco, E. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2023-153118OB-I00 Spain
CitationJournal: Acs Catalysis / Year: 2026
Title: Catalytic Cycle of N-Acetylmuramic Acid-alpha-1-Phosphate Uridylyltransferase MurU of Pseudomonas aeruginosa
Authors: Jimenez-Faraco, E. / El-Araby, A.M. / Feltzer, R. / Nguyen, V.T. / Mobashery, S. / Hermoso, J.A.
History
DepositionOct 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: N-acetylmuramate alpha-1-phosphate uridylyltransferase
A: N-acetylmuramate alpha-1-phosphate uridylyltransferase
B: N-acetylmuramate alpha-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,48618
Polymers78,2353
Non-polymers3,25115
Water3,333185
1
C: N-acetylmuramate alpha-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1626
Polymers26,0781
Non-polymers1,0845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: N-acetylmuramate alpha-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1626
Polymers26,0781
Non-polymers1,0845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: N-acetylmuramate alpha-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1626
Polymers26,0781
Non-polymers1,0845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.352, 51.407, 72.652
Angle α, β, γ (deg.)90.689, 90.707, 102.554
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 3 molecules CAB

#1: Protein N-acetylmuramate alpha-1-phosphate uridylyltransferase / MurNAc-1P uridylyltransferase / MurNAc-alpha-1P uridylyltransferase


Mass: 26078.389 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: murU, PA0597 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9I5U0, N-acetyl-alpha-D-muramate 1-phosphate uridylyltransferase

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Non-polymers , 5 types, 200 molecules

#2: Chemical ChemComp-EPZ / (2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid


Mass: 679.416 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H31N3O19P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: HEPES 0.1M pH=7.5, 0.2M NaCl 25% PEG3350 / PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 17, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.09→50.17 Å / Num. obs: 39760 / % possible obs: 92.5 % / Redundancy: 3.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.112 / Net I/σ(I): 7.7
Reflection shellResolution: 2.09→2.15 Å / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3083 / CC1/2: 0.706 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
Aimless0.7.15data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→50.169 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 12.187 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / ESU R: 0.255 / ESU R Free: 0.207
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2492 1945 4.892 %
Rwork0.1993 37813 -
all0.202 --
obs-39758 92.544 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.762 Å2
Baniso -1Baniso -2Baniso -3
1-0.081 Å20.09 Å22.159 Å2
2---0.05 Å21.184 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.09→50.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5101 0 195 185 5481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0125414
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165041
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.8667363
X-RAY DIFFRACTIONr_angle_other_deg0.5841.7711590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.845663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.967548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99210807
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.19710244
X-RAY DIFFRACTIONr_chiral_restr0.0860.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026415
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021215
X-RAY DIFFRACTIONr_nbd_refined0.2250.21190
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.24848
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22567
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22789
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0090.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1630.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1810.224
X-RAY DIFFRACTIONr_nbd_other0.2380.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2010.218
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0920.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0740.21
X-RAY DIFFRACTIONr_mcbond_it2.3792.6562667
X-RAY DIFFRACTIONr_mcbond_other2.3782.6562667
X-RAY DIFFRACTIONr_mcangle_it3.3964.7543325
X-RAY DIFFRACTIONr_mcangle_other3.3964.7553326
X-RAY DIFFRACTIONr_scbond_it3.3173.032747
X-RAY DIFFRACTIONr_scbond_other3.2853.0262740
X-RAY DIFFRACTIONr_scangle_it4.985.4014038
X-RAY DIFFRACTIONr_scangle_other4.925.394026
X-RAY DIFFRACTIONr_lrange_it6.20128.8845956
X-RAY DIFFRACTIONr_lrange_other6.18728.4285935
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.09-2.1440.3081430.25727890.2632390.9360.95390.52180.239
2.144-2.2030.3131390.23527380.23930380.9430.96394.70050.215
2.203-2.2670.2911680.24426960.24730100.9460.95995.14950.222
2.267-2.3360.2521500.2327050.23129830.9570.96695.7090.208
2.336-2.4130.2821230.20524970.20927680.9550.97494.65320.189
2.413-2.4970.3111370.21924470.22427390.940.9794.3410.204
2.497-2.5910.2861260.21623770.21926570.9470.97294.2040.2
2.591-2.6970.2551080.20323050.20625700.9630.97693.89110.191
2.697-2.8160.2741170.19421320.19824120.9560.97793.24210.185
2.816-2.9530.2451150.19920210.20223110.960.97692.42750.193
2.953-3.1120.223570.18519450.18622020.9670.97990.91740.181
3.112-3.30.293790.20618110.2121100.9390.97489.57350.203
3.3-3.5270.252640.20216740.20419810.9610.97987.73350.205
3.527-3.8080.241770.213700.20218370.9650.97778.76970.199
3.808-4.1690.166680.15713300.15716850.9850.98682.96740.165
4.169-4.6570.17610.14914270.1515560.9850.98795.62980.159
4.657-5.370.231760.17711980.1813160.9710.98496.80850.192
5.37-6.5580.317630.22610650.23111550.9460.97697.66230.242
6.558-9.1960.191490.1828150.1838810.9740.9898.07040.199
9.196-50.1690.241250.2354710.2365090.9760.97297.4460.239
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4379-0.06590.02020.3478-0.06810.2056-0.06960.0007-0.0258-0.01640.04740.0254-0.0130.03110.02220.0401-0.02260.01640.0245-0.00130.016815.261318.22973.6372
20.2284-0.0127-0.18780.4173-0.18350.67360.050.02420.04390.0389-0.0241-0.00750.02680.0021-0.02590.04280.00370.01690.00440.00410.01254.8992-3.973626.1738
30.46010.1144-0.05160.3446-0.17290.48610.02060.00470.0193-0.00860.0201-0.00790.0006-0.0241-0.04070.0493-0.0270.01080.0164-0.0040.008-5.4337-15.955-17.9334
Refinement TLS groupSelection: ALL

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