PDB-5a5x: Crystal Structure of Se-Met MltF from Pseudomonas aeruginosa

ID or keywords:

Entry

Database: PDB / ID: 5a5x

Title

Crystal Structure of Se-Met MltF from Pseudomonas aeruginosa

Components

(MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F) x 2

Keywords

HYDROLASE / LYTIC TRANSGLYCOSILOSE / CELL WALL RECYCLING

Function / homology

Function and homology information

: / lytic transglycosylase activity / peptidoglycan catabolic process / cell wall organization / cell outer membrane / cell wall macromolecule catabolic process
Similarity search - Function

Biological species

PSEUDOMONAS AERUGINOSA PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.801 Å

Authors

Dominguez-Gil, T. / Acebron, I. / Hermoso, J.A.

Citation

Journal: Structure / Year: 2016
Title: Activation by Allostery in Cell-Wall Remodeling by a Modular Membrane-Bound Lytic Transglycosylase from Pseudomonas aeruginosa.
Authors: Dominguez-Gil, T. / Lee, M. / Acebron-Avalos, I. / Mahasenan, K.V. / Hesek, D. / Dik, D.A. / Byun, B. / Lastochkin, E. / Fisher, J.F. / Mobashery, S. / Hermoso, J.A.

History

Deposition	Jun 23, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 12, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 22, 2017	Group: Atomic model / Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5a5x.cif.gz	359.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5a5x.ent.gz	304.3 KB	Display	PDB format
PDBx/mmJSON format	5a5x.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a5/5a5x ftp://data.pdbj.org/pub/pdb/validation_reports/a5/5a5x	HTTPS FTP

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Related structure data

Related structure data	5aa1C 5aa2C 5aa3C 5aa4C C: citing same article (ref.)
Similar structure data	5aa2-1 5aa3-1 5aa3-8 5aa3-6 5aa1-3 5aa2-4 5aa3-4 5aa3-12 5aa2-2 6jj4-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F

B: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F

hetero molecules

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

1

A: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F

hetero molecules

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

2

B: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F

hetero molecules

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

Unit cell

Length a, b, c (Å)	166.993, 134.977, 48.749
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F / MUREIN LYASE F Mass: 51868.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) References: UniProt: Q9HXN1, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Protein	MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F / MUREIN LYASE F Mass: 51760.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) References: UniProt: Q9HXN1, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 675 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.87 Å³/Da / Density % sol: 57.11 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97778
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97778 Å / Relative weight: 1
Reflection	Resolution: 1.8→54.17 Å / Num. obs: 102963 / % possible obs: 99.7 % / Observed criterion σ(I): 1.5 / Redundancy: 5.5 % / B_iso Wilson estimate: 29.21 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 15.5
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 5.3 % / R_merge(I) obs: 0.787 / Mean I/σ(I) obs: 1.9 / % possible all: 98

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Processing

Software

Name: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 1.801→43.443 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 21.54 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2175	5053	4.9 %
R_work	0.1795	-	-
obs	0.1813	102550	99.55 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.801→43.443 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6709	0	28	675	7412

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6914
X-RAY DIFFRACTION	f_angle_d	1.008	9339
X-RAY DIFFRACTION	f_dihedral_angle_d	13.794	2620
X-RAY DIFFRACTION	f_chiral_restr	0.041	984
X-RAY DIFFRACTION	f_plane_restr	0.004	1230

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 (%)
1.8006-1.821	0.3014	155	0.2707	3129	X-RAY DIFFRACTION	97
1.821-1.8424	0.3186	154	0.2622	3222	X-RAY DIFFRACTION	100
1.8424-1.8649	0.2895	139	0.262	3252	X-RAY DIFFRACTION	100
1.8649-1.8885	0.3014	183	0.2469	3201	X-RAY DIFFRACTION	100
1.8885-1.9134	0.2455	173	0.2307	3217	X-RAY DIFFRACTION	100
1.9134-1.9396	0.2518	163	0.2271	3219	X-RAY DIFFRACTION	100
1.9396-1.9673	0.2568	164	0.222	3207	X-RAY DIFFRACTION	100
1.9673-1.9967	0.2562	144	0.2151	3231	X-RAY DIFFRACTION	100
1.9967-2.0279	0.2522	157	0.216	3262	X-RAY DIFFRACTION	100
2.0279-2.0611	0.2598	177	0.2045	3176	X-RAY DIFFRACTION	100
2.0611-2.0966	0.2359	138	0.1967	3242	X-RAY DIFFRACTION	99
2.0966-2.1348	0.2124	177	0.192	3228	X-RAY DIFFRACTION	99
2.1348-2.1758	0.2064	166	0.1838	3198	X-RAY DIFFRACTION	99
2.1758-2.2202	0.2135	184	0.1834	3252	X-RAY DIFFRACTION	99
2.2202-2.2685	0.2326	174	0.1776	3155	X-RAY DIFFRACTION	100
2.2685-2.3213	0.2264	210	0.1816	3252	X-RAY DIFFRACTION	100
2.3213-2.3793	0.2021	163	0.183	3194	X-RAY DIFFRACTION	100
2.3793-2.4436	0.2399	171	0.1818	3302	X-RAY DIFFRACTION	100
2.4436-2.5155	0.2374	168	0.1806	3207	X-RAY DIFFRACTION	100
2.5155-2.5967	0.1902	164	0.1787	3257	X-RAY DIFFRACTION	100
2.5967-2.6895	0.2128	176	0.1815	3242	X-RAY DIFFRACTION	100
2.6895-2.7972	0.2352	177	0.1875	3225	X-RAY DIFFRACTION	100
2.7972-2.9245	0.2314	185	0.1922	3271	X-RAY DIFFRACTION	100
2.9245-3.0786	0.2575	166	0.1873	3276	X-RAY DIFFRACTION	100
3.0786-3.2714	0.212	170	0.1819	3298	X-RAY DIFFRACTION	100
3.2714-3.5239	0.2245	169	0.1766	3283	X-RAY DIFFRACTION	100
3.5239-3.8784	0.2177	176	0.1668	3301	X-RAY DIFFRACTION	100
3.8784-4.4391	0.1769	171	0.1493	3333	X-RAY DIFFRACTION	99
4.4391-5.5909	0.1947	174	0.1539	3340	X-RAY DIFFRACTION	99
5.5909-43.4558	0.1867	165	0.1688	3525	X-RAY DIFFRACTION	99

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	2.2305	-0.1598	-0.0898	1.2556	-0.5431	0.7015	0.0019	0.6778	-0.5254	-0.2145	-0.0481	0.0264	0.211	-0.1041	0.0388	0.3021	0.001	-0.0145	0.3723	-0.1724	0.3825	-17.6807	23.8267	10.8752
2	1.099	0.0172	-0.269	1.6777	0.8716	2.5842	-0.0165	0.1451	-0.415	0.1575	0.003	0.1905	0.1721	-0.3132	0.1203	0.3157	-0.0259	-0.0001	0.2404	-0.0488	0.3772	-26.2838	21.7679	26.8121
3	1.2657	-0.1377	-0.2162	2.1208	0.8528	2.3426	-0.0588	0.0927	-0.3149	0.2534	0.0258	0.1736	0.2052	-0.0126	0.0487	0.2366	-0.0283	0.0116	0.1421	-0.0504	0.288	-26.2396	26.1277	29.0623
4	1.0483	0.9949	0.6507	0.7783	0.6892	0.407	-0.1576	0.3308	-0.0966	-0.1598	0.295	-0.0724	-0.0696	0.6702	-0.0995	0.3319	-0.0495	-0.0322	0.5362	0.0087	0.556	-4.8405	27.4457	26.0774
5	2.9007	-0.2133	0.4903	0.9569	-0.0948	1.1614	0.0892	0.0747	0.0899	-0.0458	-0.0919	-0.1997	0.0064	0.0916	-0.0095	0.2067	0.0028	-0.0151	0.2244	-0.0058	0.2236	1.0317	45.1466	18.3114
6	1.5544	-0.0594	0.8749	1.4718	0.3463	0.9054	-0.0216	-0.2628	0.0942	0.3471	-0.0348	0.2347	0.0835	-0.0862	0.0319	0.2766	-0.0428	0.0665	0.2584	-0.0169	0.2138	-52.8373	54.3314	41.5267
7	1.9561	0.0727	-1.5453	1.2957	0.6927	1.918	-0.1215	0.2752	-0.2364	-0.1019	-0.0329	0.1608	0.0551	-0.1524	0.1462	0.2251	-0.04	-0.0156	0.3064	0.0252	0.1858	-51.5065	49.708	24.8054
8	2.3045	0.7344	-0.9062	1.3529	-0.1095	1.2591	-0.1266	0.4703	-0.057	-0.1166	0.1285	0.0542	0.0592	-0.0254	0.0222	0.2203	-0.0529	-0.0207	0.3072	-0.022	0.1264	-46.7033	49.7823	23.9035
9	6.8314	2.8125	1.1324	1.0618	0.4127	0.1655	0.6869	0.3002	0.251	0.0913	-0.1953	0.153	-0.0234	0.0785	-0.452	0.4285	-0.0067	0.0288	0.2573	0.0683	0.526	-45.865	69.343	32.1962
10	1.4986	-0.079	0.4048	2.6614	0.2709	1.3938	-0.0412	-0.0083	0.4231	0.0985	0.0722	-0.3173	-0.0379	0.0298	-0.0447	0.1865	-0.0091	0.003	0.1902	-0.0183	0.2534	-30.1822	71.2648	46.0047

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 25 THROUGH 85 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 86 THROUGH 131 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 132 THROUGH 241 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 242 THROUGH 263 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 264 THROUGH 444 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 29 THROUGH 85 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 86 THROUGH 131 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 132 THROUGH 241 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 242 THROUGH 262 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 263 THROUGH 445 )

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