PDB-4uz2: Crystal structure of the N-terminal LysM domains from the putativ...

ID or keywords:

Entry

Database: PDB / ID: 4uz2

Title

Crystal structure of the N-terminal LysM domains from the putative NlpC/P60 D,L endopeptidase from T. thermophilus

Components

CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN

Keywords

HYDROLASE

Function / homology

Function and homology information

NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology

Biological species

THERMUS THERMOPHILUS HB8 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Wong, J.E.M.M. / Blaise, M.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2015
Title: An Intermolecular Binding Mechanism Involving Multiple Lysm Domains Mediates Carbohydrate Recognition by an Endopeptidase.
Authors: Wong, J.E.M.M. / Midtgaard, S.R. / Gysel, K. / Thygesen, M.B. / Sorensen, K.K. / Jensen, K.J. / Stougaard, J. / Thirup, S. / Blaise, M.

History

Deposition	Sep 4, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 11, 2015	Group: Database references
Revision 1.2	Mar 25, 2015	Group: Database references
Revision 1.3	Jan 17, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4	May 8, 2024	Group: Data collection / Database references / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4uz2.cif.gz	167.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4uz2.ent.gz	137.2 KB	Display	PDB format
PDBx/mmJSON format	4uz2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4uz2_validation.pdf.gz	448.5 KB	Display	wwPDB validaton report
Full document	4uz2_full_validation.pdf.gz	450.8 KB	Display
Data in XML	4uz2_validation.xml.gz	15.4 KB	Display
Data in CIF	4uz2_validation.cif.gz	21.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uz/4uz2 ftp://data.pdbj.org/pub/pdb/validation_reports/uz/4uz2	HTTPS FTP

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Related structure data

Related structure data	4uz3C 4xcmC C: citing same article (ref.)
Similar structure data	2bv2-d 5ujl-d 3v3x-2 5ujn-d 5ltl-d 5o6s-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 - HomologyF&H Search

Related structure data

4uz3C

4xcmC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#211 - Jul 2017 Pilus Machine similarity (4)

Deposited unit

A: CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN

B: CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN

C: CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN

D: CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN

43.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN

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

2

B: CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN

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

3

C: CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN

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

4

D: CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN

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

Unit cell

Length a, b, c (Å)	122.930, 122.930, 76.810
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	94
Space group name H-M	P4₂2₁2

#1: Protein	CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN / P60_TTH Mass: 10971.500 Da / Num. of mol.: 4 / Fragment: LYSM DOMAIN, RESIDUES 15-114 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS HB8 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA 2 / References: UniProt: Q5SLM7
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN / P60_TTH

Mass: 10971.500 Da / Num. of mol.: 4 / Fragment: LYSM DOMAIN, RESIDUES 15-114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

THERMUS THERMOPHILUS HB8 (bacteria) / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA 2 / References: UniProt: Q5SLM7

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.31 Å³/Da / Density % sol: 62.8 % / Description: NONE
Crystal grow	Details: 28& PEG MME 2000, 0.1M POTASSIUM THIOCYANATE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.976
Detector	Date: Nov 27, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 2.5→20 Å / Num. obs: 20666 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 11.7 % / B_iso Wilson estimate: 46.94 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 24.14
Reflection shell	Resolution: 2.5→2.6 Å / Redundancy: 11.9 % / R_merge(I) obs: 0.81 / Mean I/σ(I) obs: 3.2 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.5→19.796 Å / SU ML: 0.35 / σ(F): 1.36 / Phase error: 28.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2552	1999	9.7 %
R_work	0.212	-	-
obs	0.2163	20657	99.03 %

Solvent computation

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

Displacement parameters

B_iso mean: 71 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→19.796 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3047	0	0	82	3129

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3095
X-RAY DIFFRACTION	f_angle_d	0.549	4198
X-RAY DIFFRACTION	f_dihedral_angle_d	11.153	1184
X-RAY DIFFRACTION	f_chiral_restr	0.021	493
X-RAY DIFFRACTION	f_plane_restr	0.003	546

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 (%)
2.5001-2.5625	0.3337	139	0.3033	1313	X-RAY DIFFRACTION	100
2.5625-2.6316	0.3253	141	0.2688	1300	X-RAY DIFFRACTION	100
2.6316-2.7089	0.3266	140	0.2802	1308	X-RAY DIFFRACTION	100
2.7089-2.7961	0.3516	143	0.2689	1335	X-RAY DIFFRACTION	100
2.7961-2.8957	0.2868	141	0.2544	1318	X-RAY DIFFRACTION	100
2.8957-3.0113	0.3308	141	0.2567	1315	X-RAY DIFFRACTION	100
3.0113-3.1478	0.3239	143	0.2621	1327	X-RAY DIFFRACTION	99
3.1478-3.313	0.2945	141	0.2379	1328	X-RAY DIFFRACTION	99
3.313-3.5195	0.2678	143	0.2231	1331	X-RAY DIFFRACTION	99
3.5195-3.7895	0.2299	142	0.2077	1324	X-RAY DIFFRACTION	99
3.7895-4.1677	0.2287	142	0.1845	1330	X-RAY DIFFRACTION	99
4.1677-4.7634	0.2038	145	0.1705	1347	X-RAY DIFFRACTION	98
4.7634-5.9739	0.2199	145	0.197	1361	X-RAY DIFFRACTION	98
5.9739-19.7968	0.2267	153	0.1742	1421	X-RAY DIFFRACTION	97

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	4.0443	-5.1562	0.5358	8.6327	1.8524	3.1278	-0.3613	-0.0372	1.8334	-0.898	-0.6573	1.8649	-0.901	-1.4469	0.8449	0.6924	0.1786	-0.2309	0.7331	-0.1779	0.883	-30.9331	11.5184	-20.0158
2	5.6143	-2.5046	0.4842	4.0061	0.7429	1.5928	-0.7325	0.1983	0.9961	-0.9265	-0.348	1.892	-0.411	-0.6166	1.0075	0.9305	0.2208	-0.3548	0.7567	-0.1756	1.3125	-29.9427	18.9976	-17.6589
3	5.3735	0.9298	2.1263	5.5433	-1.8547	6.2063	-0.3382	0.4241	-0.1352	-0.8872	0.2638	-0.1083	-0.0468	0.3803	0.0529	0.5329	0.141	0.1058	0.4724	0.0314	0.3271	-2.3815	16.0308	-11.4676
4	5.8911	1.3314	-0.4379	8.1404	-2.2724	6.8019	0.1932	0.2968	0.2305	-0.2629	-0.1019	-0.391	-0.104	0.2866	-0.0947	0.4425	0.243	0.1493	0.4941	0.0414	0.372	-2.8148	18.1932	-7.8598
5	5.5157	0.0912	-2.2749	2.2172	-1.6643	5.6475	0.0851	-1.2948	0.205	-0.0575	-0.2389	-0.7055	-0.3002	0.7824	0.1564	0.8937	-0.2079	-0.1009	0.9191	0.0492	0.8043	33.0778	21.6219	-19.0916
6	4.6146	-4.0291	5.3141	4.0462	-4.4092	6.2597	-1.4755	0.4409	2.183	0.3877	-0.8666	-0.8903	-0.5282	0.7366	2.2175	0.5604	-0.0011	-0.1317	0.6214	0.0357	0.8332	23.6056	21.3151	-21.0992
7	4.3401	0.9908	0.2423	4.7868	1.8433	5.2152	-0.2459	-0.5369	0.0883	0.4153	0.5364	0.2186	0.1331	-0.5346	-0.2905	0.441	0.0289	0.0077	0.5901	0.0741	0.3237	4.0998	20.1139	-28.4238
8	8.2383	-1.6701	-4.1187	6.7676	2.2024	2.3804	0.3839	-0.0962	0.4476	-0.2179	0.1611	0.0308	-0.3429	-0.437	-0.3558	0.5104	-0.0589	0.0096	0.5403	0.077	0.287	4.4648	21.7185	-33.9026
9	5.6991	-2.7471	2.8413	6.0543	-3.3228	4.1858	-0.0488	0.474	0.7181	-0.2016	0.1823	0.2958	-0.878	-0.2865	-0.1218	0.9969	0.188	0.0447	0.7359	0.0692	0.7031	-12.1143	35.0988	-10.1934
10	2.9249	1.2943	-0.9553	6.0724	2.2786	4.4625	0.1349	-0.5884	0.1304	-0.0913	-0.4944	-0.0137	-0.1222	0.3362	0.328	0.3604	0.1946	0.0139	0.6408	0.1138	0.3088	-3.1863	17.2505	10.4666
11	3.9757	2.7449	4.3637	2.439	3.1741	4.7913	0.4591	-0.2373	-0.5904	-0.6244	0.6538	1.0399	-0.1904	-1.4712	-1.0092	1.0498	-0.1789	-0.0814	0.8602	0.2359	0.7427	-35.7245	-10.9472	-50.6104
12	8.0716	0.8848	4.3885	3.8711	4.4814	6.611	0.2821	-0.5858	-1.8843	-1.0257	1.3205	0.1329	0.416	0.6003	-1.2294	0.7857	-0.5432	-0.1228	0.9866	0.3306	0.94	-34.5826	-19.9369	-47.1622
13	7.2178	5.5162	-0.7624	5.1444	-0.2646	0.1875	-0.2992	-1.4334	0.0521	-0.9758	0.8061	1.5779	0.9427	-2.5278	-0.3752	0.7433	-0.3189	-0.2368	1.6175	0.3928	1.4519	-44.2516	-14.5604	-46.4379
14	3.6513	-5.0729	3.0479	7.5013	-4.1357	2.5052	1.4329	0.0194	0.3363	0.1072	-0.0123	1.2526	0.1464	-0.7126	-1.4023	0.488	-0.0487	0.0395	0.9824	0.2095	0.6762	-33.5388	-11.5703	-40.5921
15	3.8673	2.3906	3.9414	8.536	2.4626	6.9132	-0.5379	-0.0558	0.6206	0.1535	0.549	0.3359	-1.1749	0.51	-0.1186	0.5067	-0.0883	0.0631	0.3223	-0.0478	0.2995	-14.4589	-5.4053	-31.8129
16	6.6393	0.6347	0.2097	5.0444	3.1573	2.0546	0.3573	0.3257	0.9968	0.0588	-0.308	0.232	-1.1287	-0.7638	-0.074	0.6231	0.0954	0.0305	0.5541	-0.0908	0.3583	-20.6756	-0.8634	-27.2246
17	6.5695	-0.4589	1.8962	2.7477	1.9555	2.1435	-0.3234	-1.6708	-0.6181	1.4413	0.0714	0.562	0.9039	-1.5914	0.222	0.5214	-0.0652	0.0946	0.8696	0.0361	0.3789	-21.7026	-9.9119	-21.5391
18	6.5542	1.1436	-5.2389	5.58	-0.0533	4.2923	-0.3444	-0.92	-0.8048	0.691	-0.0134	-0.0848	0.7474	1.224	0.2626	0.5523	-0.0081	0.0456	0.7322	-0.0011	0.3545	-11.1355	-10.0653	-23.1632
19	6.8439	-3.9192	1.5133	3.6942	0.5474	5.6849	-0.5949	-0.2645	-1.139	1.1054	0.0179	1.7312	0.1178	-0.7202	0.5313	0.5161	-0.0394	0.2067	0.4742	-0.1004	0.5538	-24.7685	-9.0257	-28.8779

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'C' AND (RESID 16 THROUGH 26 )
2	X-RAY DIFFRACTION	2	CHAIN 'C' AND (RESID 27 THROUGH 64 )
3	X-RAY DIFFRACTION	3	CHAIN 'C' AND (RESID 65 THROUGH 93 )
4	X-RAY DIFFRACTION	4	CHAIN 'C' AND (RESID 94 THROUGH 113 )
5	X-RAY DIFFRACTION	5	CHAIN 'D' AND (RESID 16 THROUGH 56 )
6	X-RAY DIFFRACTION	6	CHAIN 'D' AND (RESID 57 THROUGH 64 )
7	X-RAY DIFFRACTION	7	CHAIN 'D' AND (RESID 65 THROUGH 93 )
8	X-RAY DIFFRACTION	8	CHAIN 'D' AND (RESID 94 THROUGH 111 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 15 THROUGH 64 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 65 THROUGH 114 )
11	X-RAY DIFFRACTION	11	CHAIN 'A' AND (RESID 16 THROUGH 26 )
12	X-RAY DIFFRACTION	12	CHAIN 'A' AND (RESID 27 THROUGH 37 )
13	X-RAY DIFFRACTION	13	CHAIN 'A' AND (RESID 38 THROUGH 56 )
14	X-RAY DIFFRACTION	14	CHAIN 'A' AND (RESID 57 THROUGH 64 )
15	X-RAY DIFFRACTION	15	CHAIN 'A' AND (RESID 65 THROUGH 74 )
16	X-RAY DIFFRACTION	16	CHAIN 'A' AND (RESID 75 THROUGH 85 )
17	X-RAY DIFFRACTION	17	CHAIN 'A' AND (RESID 86 THROUGH 93 )
18	X-RAY DIFFRACTION	18	CHAIN 'A' AND (RESID 94 THROUGH 104 )
19	X-RAY DIFFRACTION	19	CHAIN 'A' AND (RESID 105 THROUGH 114 )

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