PDB-8rhi: Lytic Transglycosylase MltD of Pseudomonas aeruginosa in a ternar...

ID or keywords:

Entry

Database: PDB / ID: 8rhi

Title

Lytic Transglycosylase MltD of Pseudomonas aeruginosa in a ternary complex bound to Bulgecin A and chito-tetraose

Components

LysM peptidoglycan-binding domain-containing protein

Keywords

LYASE / Lytic transglycosylase / Bacterial cell-wall / bulgecin A

Function / homology

Function and homology information

Lyases; Carbon-oxygen lyases; Acting on polysaccharides / lytic transglycosylase activity / peptidoglycan metabolic process /

membrane
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.98 Å

Authors

Miguel-Ruano, V. / Hermoso, J.A.

Funding support

Spain, 1items

Citation

Journal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural characterization of lytic transglycosylase MltD of Pseudomonas aeruginosa, a target for the natural product bulgecin A.
Authors: Miguel-Ruano, V. / Feltzer, R. / Batuecas, M.T. / Ramachandran, B. / El-Araby, A.M. / Avila-Cobian, L.F. / De Benedetti, S. / Mobashery, S. / Hermoso, J.A.

History

Deposition	Dec 15, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 17, 2024	Provider: repository / Type: Initial release
Revision 1.1	Apr 24, 2024	Group: Database references / Category: citation / Item: _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8rhi.cif.gz	317.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8rhi.ent.gz	196.2 KB	Display	PDB format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rh/8rhi ftp://data.pdbj.org/pub/pdb/validation_reports/rh/8rhi	HTTPS FTP

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Related structure data

Related structure data	8rheC 8rhfC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#211 - Jul 2017 Pilus Machine similarity (4) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: LysM peptidoglycan-binding domain-containing protein

B: LysM peptidoglycan-binding domain-containing protein

hetero molecules

80.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: equilibrium centrifugation, Velocity sedimentation analytical ultracentrifugation

Unit cell

Length a, b, c (Å)	45.248, 117.036, 120.146
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LEU / End label comp-ID: LEU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 63 - 337 / Label seq-ID: 8 - 282

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Protein , 1 types, 2 molecules AB

#1: Protein	LysM peptidoglycan-binding domain-containing protein / Membrane-bound lytic murein transglycosylase D / Murein transglycosylase Mass: 38579.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Histidine tag and TEV cleavage site in the N-t region. MltD construction form residues 76 to 393. Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: mltD, CAZ10_25765, CGU42_31890, GNQ48_00460, GUL26_19730, IPC1295_05870, PAERUG_P19_London_7_VIM_2_05_10_06006 Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 References: UniProt: A0A0C7CWY9, Lyases; Carbon-oxygen lyases; Acting on polysaccharides

#1: Protein

LysM peptidoglycan-binding domain-containing protein / Membrane-bound lytic murein transglycosylase D / Murein transglycosylase

Mass: 38579.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Histidine tag and TEV cleavage site in the N-t region. MltD construction form residues 76 to 393.
Source: (gene. exp.)

Pseudomonas aeruginosa (bacteria)
Gene: mltD, CAZ10_25765, CGU42_31890, GNQ48_00460, GUL26_19730, IPC1295_05870, PAERUG_P19_London_7_VIM_2_05_10_06006
Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3
References: UniProt: A0A0C7CWY9,

Lyases; Carbon-oxygen lyases; Acting on polysaccharides

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Sugars , 2 types, 2 molecules

#2: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide

/ Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

#3: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...

Type: oligosaccharide

/ Mass: 830.786 Da / Num. of mol.: 1 / Source method: obtained synthetically

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1/a4-b1_b4-c1_c4-d1	WURCS	PDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}	LINUCS	PDB-CARE

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Non-polymers , 3 types, 197 molecules

#4: Chemical	ChemComp-BLG / 4-O-(4-O-SULFONYL-N-ACETYLGLUCOSAMININYL)-5-METHYLHYDROXY-L-PROLINE-TAURINE / BULGECIN A Mass: 552.551 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₆H₃₀N₃O₁₄S₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.06 Å³/Da / Density % sol: 40.19 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES pH 6.5, 25% w/v PEG 550 MME, and 10 mM zinc sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.98→83.84 Å / Num. obs: 47136 / % possible obs: 87.8 % / Redundancy: 13.13 % / CC_1/2: 0.9992 / Net I/σ(I): 16.72
Reflection shell	Resolution: 1.98→2.03 Å / Mean I/σ(I) obs: 1.696 / Num. unique obs: 2355 / CC_1/2: 0.6743 / % possible all: 96.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0411	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.98→83.835 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.955 / SU B: 7.824 / SU ML: 0.111 / Cross valid method: FREE R-VALUE / ESU R: 0.172 / ESU R Free: 0.145
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2155	2232	4.937 %
R_work	0.1902	42976	-
all	0.191	-	-
obs	-	45208	99.634 %

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: 49.644 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.081 Å²	-0 Å²	0 Å²
2-	-	-0.478 Å²	0 Å²
3-	-	-	-0.603 Å²

Refinement step

Cycle: LAST / Resolution: 1.98→83.835 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4423	0	165	186	4774

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	4710
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4336
X-RAY DIFFRACTION	r_angle_refined_deg	1.026	1.682	6425
X-RAY DIFFRACTION	r_angle_other_deg	0.364	1.593	9953
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.778	5	548
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.231	5	46
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	2.188	5	8
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.229	10	740
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.908	10	240
X-RAY DIFFRACTION	r_chiral_restr	0.053	0.2	711
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	5541
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1165
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	1020
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	3977
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	2324
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.071	0.2	2498
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.159	0.2	227
X-RAY DIFFRACTION	r_metal_ion_refined	0.108	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.132	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.159	0.2	74
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.141	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	2.248	3.942	2200
X-RAY DIFFRACTION	r_mcbond_other	2.248	3.942	2201
X-RAY DIFFRACTION	r_mcangle_it	3.717	7.075	2744
X-RAY DIFFRACTION	r_mcangle_other	3.716	7.075	2745
X-RAY DIFFRACTION	r_scbond_it	2.788	4.317	2510
X-RAY DIFFRACTION	r_scbond_other	2.785	4.316	2508
X-RAY DIFFRACTION	r_scangle_it	4.604	7.775	3681
X-RAY DIFFRACTION	r_scangle_other	4.603	7.775	3682
X-RAY DIFFRACTION	r_lrange_it	6.986	39.442	5424
X-RAY DIFFRACTION	r_lrange_other	6.975	39.258	5385
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.119	0.05	8733

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.11888	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.11888	0.05009

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.98-2.031	0.302	136	0.266	2984	0.267	3282	0.932	0.95	95.064	0.252
2.031-2.087	0.274	137	0.245	3096	0.247	3233	0.952	0.961	100	0.224
2.087-2.147	0.279	164	0.232	2984	0.235	3148	0.95	0.965	100	0.209
2.147-2.214	0.229	146	0.226	2874	0.226	3020	0.968	0.968	100	0.199
2.214-2.286	0.23	153	0.21	2824	0.211	2977	0.97	0.972	100	0.18
2.286-2.366	0.222	142	0.197	2720	0.198	2862	0.972	0.977	100	0.162
2.366-2.456	0.222	137	0.181	2604	0.183	2741	0.968	0.98	100	0.15
2.456-2.556	0.241	132	0.191	2552	0.193	2684	0.966	0.978	100	0.159
2.556-2.669	0.213	154	0.185	2430	0.187	2584	0.975	0.981	100	0.156
2.669-2.799	0.241	122	0.177	2327	0.18	2449	0.97	0.982	100	0.155
2.799-2.951	0.183	117	0.189	2188	0.189	2305	0.979	0.979	100	0.165
2.951-3.129	0.252	98	0.202	2137	0.204	2235	0.964	0.975	100	0.184
3.129-3.345	0.222	109	0.204	1988	0.205	2097	0.963	0.973	100	0.192
3.345-3.613	0.206	107	0.184	1842	0.185	1950	0.98	0.98	99.9487	0.179
3.613-3.957	0.231	107	0.18	1687	0.183	1794	0.969	0.981	100	0.183
3.957-4.422	0.182	75	0.162	1596	0.163	1671	0.982	0.984	100	0.174
4.422-5.104	0.185	72	0.169	1396	0.17	1468	0.983	0.984	100	0.189
5.104-6.246	0.195	37	0.19	1218	0.19	1255	0.978	0.98	100	0.21
6.246-8.808	0.208	50	0.172	951	0.173	1003	0.98	0.983	99.8006	0.199
8.808-83.835	0.198	36	0.216	567	0.215	604	0.979	0.963	99.8344	0.277

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	0.4406	0.113	-0.1252	0.1861	0.1953	0.5043	-0.0093	0.0205	-0.0275	0.0076	0.0158	-0.0203	0.0184	0.0009	-0.0065	0.0042	0.0176	0.0118	0.1025	0.03	0.1209	15.3046	-19.4359	-11.1922
2	0.2238	-0.2816	0.5463	1.0513	-0.2147	1.6579	-0.124	-0.0328	0.0384	-0.0035	0.0434	-0.0803	-0.3898	-0.0593	0.0806	0.1098	0.0066	-0.0273	0.0737	0.0657	0.0845	9.8783	4.4411	-26.9914

Refinement TLS group

Selection: ALL

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