PDB-9sqf: PaMurU in complex with Mn2+ and UTP substrate

ID or keywords:

Entry

Database: PDB / ID: 9sqf

Title

PaMurU in complex with Mn2+ and UTP substrate

Components

N-acetylmuramate alpha-1-phosphate uridylyltransferase

Keywords

TRANSFERASE / 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

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Jimenez-Faraco, E. / Hermoso, J.A.

Funding support

Spain, 1items

Citation

Journal: 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

Deposition	Sep 22, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 29, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9sqf.cif.gz	350.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9sqf.ent.gz	216.3 KB	Display	PDB format
PDBx/mmJSON format	9sqf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sq/9sqf ftp://data.pdbj.org/pub/pdb/validation_reports/sq/9sqf	HTTPS FTP

-
Related structure data

Related structure data	9smvC 9sqdC 9sqeC 9sqgC 9szkC 9szlC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1)

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

80 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: N-acetylmuramate alpha-1-phosphate uridylyltransferase

hetero molecules

defined by author
Evidence: equilibrium centrifugation, ultracentrifugation (SV-AUC)
26.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: N-acetylmuramate alpha-1-phosphate uridylyltransferase

hetero molecules

defined by author
26.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

B: N-acetylmuramate alpha-1-phosphate uridylyltransferase

hetero molecules

defined by author
26.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	51.943, 51.957, 73.117
Angle α, β, γ (deg.)	89.885, 89.557, 77.559
Int Tables number	1
Space group name H-M	P1

#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
#2: Chemical	ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE Mass: 484.141 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₉H₁₅N₂O₁₅P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: UTP*YM
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.46 Å³/Da / Density % sol: 50.06 %
Crystal grow	Temperature: 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

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.7712 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.7712 Å / Relative weight: 1
Reflection	Resolution: 2.1→50.74 Å / Num. obs: 40882 / % possible obs: 93.8 % / Redundancy: 3.5 % / CC_1/2: 0.978 / R_merge(I) obs: 0.121 / Net I/σ(I): 8.3
Reflection shell	Resolution: 2.1→2.16 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.423 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3225 / CC_1/2: 0.708 / % possible all: 89.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
autoPROC		data reduction
Aimless	0.7.15	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→50.74 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.909 / SU B: 13.706 / SU ML: 0.175 / Cross valid method: FREE R-VALUE / ESU R: 0.246 / ESU R Free: 0.205
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2515	1921	4.7 %
R_work	0.2012	38954	-
all	0.204	-	-
obs	-	40875	93.827 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 28.569 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.399 Å²	0.503 Å²	-1.098 Å²
2-	-	-0.169 Å²	0.945 Å²
3-	-	-	-0.011 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→50.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5122	0	93	221	5436

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	5337
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4974
X-RAY DIFFRACTION	r_angle_refined_deg	1.732	1.856	7265
X-RAY DIFFRACTION	r_angle_other_deg	0.562	1.759	11426
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.997	5	667
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.098	5	48
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.941	10	810
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.341	10	246
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	776
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	6433
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1219
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	1118
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.204	0.2	4630
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	2547
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	2696
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.171	0.2	238
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.092	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.196	0.2	65
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.168	0.2	34
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.007	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.224	2.472	2680
X-RAY DIFFRACTION	r_mcbond_other	2.221	2.472	2680
X-RAY DIFFRACTION	r_mcangle_it	3.441	4.435	3343
X-RAY DIFFRACTION	r_mcangle_other	3.441	4.435	3344
X-RAY DIFFRACTION	r_scbond_it	2.631	2.76	2657
X-RAY DIFFRACTION	r_scbond_other	2.631	2.76	2658
X-RAY DIFFRACTION	r_scangle_it	4.104	4.948	3922
X-RAY DIFFRACTION	r_scangle_other	4.104	4.948	3923
X-RAY DIFFRACTION	r_lrange_it	6.035	27.393	5861
X-RAY DIFFRACTION	r_lrange_other	6.037	26.723	5833

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.1-2.154	0.314	132	0.283	2750	X-RAY DIFFRACTION	89.726
2.154-2.213	0.26	128	0.255	2668	X-RAY DIFFRACTION	90.2226
2.213-2.277	0.32	122	0.237	2684	X-RAY DIFFRACTION	91.0743
2.277-2.347	0.271	164	0.24	2556	X-RAY DIFFRACTION	91.4593
2.347-2.424	0.249	83	0.225	2565	X-RAY DIFFRACTION	92.2006
2.424-2.509	0.31	110	0.228	2484	X-RAY DIFFRACTION	93.0082
2.509-2.604	0.338	99	0.222	2407	X-RAY DIFFRACTION	93.3333
2.604-2.71	0.299	134	0.211	2298	X-RAY DIFFRACTION	93.9359
2.71-2.83	0.264	121	0.187	2171	X-RAY DIFFRACTION	94.2434
2.83-2.967	0.262	99	0.197	2163	X-RAY DIFFRACTION	94.8825
2.967-3.127	0.251	105	0.201	2021	X-RAY DIFFRACTION	95.2082
3.127-3.316	0.249	92	0.199	1966	X-RAY DIFFRACTION	95.4988
3.316-3.544	0.275	98	0.218	1805	X-RAY DIFFRACTION	96.1597
3.544-3.826	0.226	74	0.195	1723	X-RAY DIFFRACTION	96.4056
3.826-4.189	0.199	75	0.154	1581	X-RAY DIFFRACTION	96.8421
4.189-4.68	0.201	97	0.153	1438	X-RAY DIFFRACTION	97.0904
4.68-5.396	0.257	53	0.168	1263	X-RAY DIFFRACTION	97.2653
5.396-6.59	0.251	65	0.221	1083	X-RAY DIFFRACTION	98.4563
6.59-9.243	0.193	51	0.163	835	X-RAY DIFFRACTION	99.3274
9.243-50.74	0.15	19	0.225	494	X-RAY DIFFRACTION	99.8055

Refinement TLS params.

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

ID	L11 (°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)
1	0.3748	0.0063	-0.0028	0.3442	-0.0197	0.3757	0.0488	-0.0273	-0.0147	-0.0316	-0.055	-0.0015	-0.0361	0.0321	0.0062	0.0515	0.0096	-0.0044	0.0166	0.0042	0.0145	-15.0007	18.508	3.5119
2	0.2777	-0.0176	0.1571	0.6986	-0.0271	0.8918	0.0155	0.0394	0.0185	0.0206	-0.0189	0.0241	0.0254	-0.0356	0.0033	0.0291	0.0249	-0.0011	0.0321	-0	0.0025	-26.5135	41.1074	-18.1295
3	0.508	-0.1111	0.0165	0.3651	-0.1231	0.5609	-0.0419	-0.0532	0.031	-0.0212	0.0799	0.0099	0.0063	-0.0006	-0.038	0.0201	-0.0042	-0.0108	0.0404	0.0102	0.014	-36.2601	54.6508	26.1761

Refinement TLS group

Selection: ALL

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi