PDB-5zqc: Crystal Structure of Penicillin-Binding Protein D2 from Listeria ...

ID or keywords:

Entry

Database: PDB / ID: 5zqc

Title

Crystal Structure of Penicillin-Binding Protein D2 from Listeria monocytogenes in the Ampicillin bound form

Components

Lmo2812 protein

Keywords

ANTIBIOTIC /

Listeria monocytogenes /

hypothetical /

penicillin-binding protein / LmPBPD2 / lmo2812

Function / homology

Function and homology information

serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape /

Biological species

Listeria monocytogenes EGD-e (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.702 Å

Authors

Jeong, J.H. / Kim, Y.G.

Funding support

Korea, Republic Of, 1items

Citation

Journal: Antimicrob. Agents Chemother. / Year: 2018
Title: Crystal Structures of Penicillin-Binding Protein D2 from Listeria monocytogenes and Structural Basis for Antibiotic Specificity
Authors: Jeong, J.H. / Cha, H.J. / Kim, Y.G.

History

Deposition	Apr 18, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 1, 2018	Provider: repository / Type: Initial release
Revision 1.1	Aug 22, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Sep 12, 2018	Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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

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Related structure data

Related structure data	5zqaSC 5zqbC 5zqdC 5zqeC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5zqd-2 5zqb-4 5zqe-2 5zqe-8 5zqe-6 1xk2-1 5zqb-2 5zqd-5 5zqe-1 1xk1-1 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

5zqaSC

5zqbC

5zqdC

5zqeC

S: Starting model for refinement

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	#29 - May 2002 Penicillin-binding Proteins similarity (2) #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) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Lmo2812 protein

B: Lmo2812 protein

C: Lmo2812 protein

D: Lmo2812 protein

hetero molecules

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

1

A: Lmo2812 protein

hetero molecules

defined by author
Evidence: gel filtration
30.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Lmo2812 protein

hetero molecules

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

3

C: Lmo2812 protein

hetero molecules

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

4

D: Lmo2812 protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	74.884, 98.850, 77.441
Angle α, β, γ (deg.)	90.00, 104.21, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Lmo2812 protein Mass: 30091.605 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: It contains covalently bound Ampicillin molecules Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria) Strain: EGD-e / Gene: lmo2812 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y3M3
#2: Chemical	ChemComp-AIX / (2R,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form) Mass: 351.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₆H₂₁N₃O₄S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.31 Å³/Da / Density % sol: 46.72 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2M sodium formate, 20%(wt/vol) PEG 3350

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Data collection

Diffraction	Mean temperature: 200 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2016
Radiation	Monochromator: Double crystal SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.702→30.004 Å / Num. obs: 110772 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / B_iso Wilson estimate: 18.42 Å² / CC_1/2: 0.994 / R_merge(I) obs: 0.1085 / R_pim(I) all: 0.053 / R_rim(I) all: 0.1214 / Net I/σ(I): 12.72
Reflection shell	Resolution: 1.702→1.763 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.2697 / Mean I/σ(I) obs: 2.58 / Num. unique obs: 10025 / CC_1/2: 0.766 / R_pim(I) all: 0.1802 / R_rim(I) all: 0.327 / % possible all: 84

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5ZQA

5zqa

Resolution: 1.702→30.004 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.53 / Phase error: 27.59

	R_factor	Num. reflection	% reflection
R_free	0.2597	1991	1.8 %
R_work	0.2227	-	-
obs	0.2233	110757	92.64 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.702→30.004 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7415	0	120	292	7827

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7629
X-RAY DIFFRACTION	f_angle_d	0.838	10298
X-RAY DIFFRACTION	f_dihedral_angle_d	5.108	4599
X-RAY DIFFRACTION	f_chiral_restr	0.048	1223
X-RAY DIFFRACTION	f_plane_restr	0.005	1304

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 (%)
1.7018-1.7443	0.3435	119	0.2855	6922	X-RAY DIFFRACTION	83
1.7443-1.7915	0.3082	138	0.2705	7252	X-RAY DIFFRACTION	87
1.7915-1.8442	0.2948	140	0.2575	7213	X-RAY DIFFRACTION	87
1.8442-1.9037	0.2871	133	0.241	7390	X-RAY DIFFRACTION	88
1.9037-1.9717	0.2832	135	0.2319	7704	X-RAY DIFFRACTION	92
1.9717-2.0506	0.2566	143	0.22	7826	X-RAY DIFFRACTION	94
2.0506-2.1439	0.2901	143	0.2243	7998	X-RAY DIFFRACTION	95
2.1439-2.2569	0.2283	152	0.205	8046	X-RAY DIFFRACTION	96
2.2569-2.3983	0.2868	145	0.2181	8047	X-RAY DIFFRACTION	96
2.3983-2.5834	0.2733	153	0.2257	8263	X-RAY DIFFRACTION	98
2.5834-2.8432	0.2774	153	0.2314	8239	X-RAY DIFFRACTION	99
2.8432-3.2541	0.2495	158	0.2269	8268	X-RAY DIFFRACTION	98
3.2541-4.0982	0.2408	138	0.2086	7829	X-RAY DIFFRACTION	93
4.0982-30.0085	0.228	141	0.2097	7769	X-RAY DIFFRACTION	91

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	4.8646	-0.3746	1.0179	0.878	-1.2192	1.7878	-0.3569	0.081	1.1053	0.2624	0.04	-0.4429	-0.5872	-0.1123	0.1718	0.1644	0.0046	-0.0132	0.2004	-0.0091	0.4164	378.871	21.1829	121.5329
2	2.036	1.0401	-0.014	1.7848	0.1624	0.7153	-0.044	0.0437	0.1421	-0.0615	0.0072	0.1125	-0.0171	-0.0503	0.036	0.1276	0.0317	-0.0073	0.1778	0.0197	0.1742	363.8302	5.8508	116.3175
3	5.5617	0.7079	0.658	4.5083	1.198	3.2415	0.2435	-0.0041	-0.3207	0.152	-0.0612	-0.9759	0.2996	0.8171	-0.076	0.1525	0.0451	0.0008	0.3059	0.0154	0.4403	372.7042	-15.0028	116.4555
4	0.4433	1	-0.4949	2.1423	-0.9219	1.2037	-0.0303	0.0783	-0.0413	-0.0488	0.0331	0.0372	0.0167	-0.0415	-0.0025	0.1211	-0.0034	-0.004	0.2293	0.0203	0.1952	365.8065	-0.4515	110.9707
5	2.0189	0.6732	-0.1699	1.6657	-0.2941	0.4348	0.0352	-0.096	0.188	0.098	-0.0358	-0.0213	-0.0325	-0.0109	0.007	0.1294	0.0139	-0.0051	0.1945	-0.0345	0.1748	370.9172	8.2268	125.3871
6	1.7337	-0.7393	-0.2789	1.5211	-0.1002	0.8849	-0.0239	-0.0702	-0.1939	0.0084	-0.0063	0.0117	0.0439	-0.0225	0.0282	0.1112	-0.0244	-0.007	0.1681	0.0285	0.2175	329.7339	6.681	129.7557
7	1.7403	1.9665	-1.8312	5.0273	-0.7378	2.8075	-0.2322	0.0198	0.3807	0.1045	0.1806	-0.8538	-0.3327	0.683	0.0321	0.1847	-0.0965	0.003	0.2733	-0.0186	0.6341	335.1514	30.8227	128.8299
8	0.6558	-0.9146	0.1594	3.0436	-1.2513	1.3381	-0.0666	-0.1046	0.0644	0.1911	0.1139	0.0792	-0.0656	-0.0641	-0.0398	0.1221	-0.0089	-0.0077	0.1871	-0.0107	0.1762	328.5358	16.3835	135.9723
9	1.4246	-0.3807	-0.2758	1.5338	0.0059	0.9488	-0.0009	0.027	-0.1297	-0.0617	-0.0286	-0.0478	0.0059	0.0559	0.0341	0.1063	-0	-0.0064	0.1458	0.0004	0.1445	333.4597	7.3655	121.7818
10	1.6245	-1.1146	-0.3434	1.1961	-0.1695	0.6669	-0.0944	0.0437	-0.2719	0.0813	-0.0219	0.0991	0.0731	0.0028	0.1142	0.1255	-0.0177	-0.012	0.1246	-0.0002	0.1891	338.4428	3.2576	91.3288
11	2.1861	0.5614	-0.8312	4.4817	1.1426	3.2656	0.1131	0.0431	0.4126	0.2598	0.0771	-0.6869	-0.1054	0.5515	-0.1075	0.1425	-0.0244	-0.022	0.1499	-0.0013	0.2605	340.212	23.8683	91.0115
12	1.1281	-0.3223	-0.3065	1.5197	0.1831	1.2115	-0.0114	-0.0026	0.0137	0.1071	-0.0201	-0.006	0.0387	0.0717	0.0301	0.1124	0.0013	-0.0048	0.1552	0.0123	0.1655	337.2006	9.5751	92.8963
13	3.7751	0.9024	1.0756	2.6701	1.3335	2.2362	-0.0129	-0.0178	-0.103	-0.0084	0.0344	-0.1007	0.0209	0.015	-0.0111	0.127	0.0112	-0.002	0.1385	0.0282	0.1432	346.3364	1.2026	83.8157
14	4.5274	0.1879	-0.1483	1.2051	-0.6957	2.043	-0.0659	-0.1564	0.4223	0.1256	0.0967	0.1375	-0.3881	-0.0387	-0.0478	0.1838	0.0109	-0.0107	0.1208	0.0046	0.2442	383.7387	18.4045	81.5598
15	2.2383	0.2712	-0.1659	1.2264	0.397	0.8518	0.0584	0.0941	0.0917	0.0025	-0.1179	0.1842	0.0327	-0.1045	0.066	0.1722	0.0053	-0.0046	0.1668	0.0107	0.1143	367.1669	-5.1783	77.309
16	1.9976	-0.341	0.1797	5.2602	1.9455	4.2993	0.091	-0.021	0.005	0.0312	0.0237	-0.2884	0.0303	0.3471	-0.1168	0.1415	0.0158	0.0014	0.1876	0.0115	0.1793	378.4766	-14	79.5782
17	0.911	0.3849	0.2287	0.8944	0.3465	0.9253	0.0024	-0.013	0.0671	-0.0499	0.0031	-0.0393	0.0026	-0.0155	-0.0085	0.1247	0.0031	0.002	0.1391	0.0109	0.1639	378.1255	3.5521	81.2544

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 24 through 38 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 39 through 84 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 85 through 103 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 104 through 170 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 171 through 270 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 25 through 84 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 85 through 103 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 104 through 170 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 171 through 270 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 24 through 84 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 85 through 119 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 120 through 217 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 218 through 270 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 23 through 56 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 57 through 84 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 85 through 116 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 117 through 270 )

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