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

ID or keywords:

Entry

Database: PDB / ID: 5zqb

Title

Crystal Structure of Penicillin-Binding Protein D2 from Listeria monocytogenes in the Penicillin G 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 / proteolysis / metal ion binding
Similarity search - Function

Biological species

Listeria monocytogenes EGD-e (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.896 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	Jul 25, 2018	Provider: repository / Type: Initial release
Revision 1.1	Aug 22, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _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
Revision 1.4	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5zqb.cif.gz	385.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5zqb_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	5zqb_full_validation.pdf.gz	1.6 MB	Display
Data in XML	5zqb_validation.xml.gz	40.2 KB	Display
Data in CIF	5zqb_validation.cif.gz	56.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zq/5zqb ftp://data.pdbj.org/pub/pdb/validation_reports/zq/5zqb	HTTPS FTP

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Related structure data

Related structure data	5zqaSC 5zqcC 5zqdC 5zqeC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5zqe-4 5zqe-8 5zqe-1 5zqe-7 5zqe-3 5zqd-7 5zqd-4 5zqe-2 5zqd-6 5zqd-8 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

5zqcC

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

3

C: Lmo2812 protein

hetero molecules

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

4

D: Lmo2812 protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	74.716, 98.900, 77.453
Angle α, β, γ (deg.)	90.00, 104.30, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Lmo2812 protein Mass: 30091.605 Da / Num. of mol.: 4 / Fragment: UNP residues 21-272 Source method: isolated from a genetically manipulated source 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-PNM / OPEN FORM - PENICILLIN G Mass: 336.406 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₆H₂₀N₂O₄S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.3 Å³/Da / Density % sol: 46.61 %
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 315 / Detector: CCD / Date: Jul 7, 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: 1.896→29.9 Å / Num. obs: 84701 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / B_iso Wilson estimate: 21.17 Å² / CC_1/2: 0.992 / R_merge(I) obs: 0.1492 / R_pim(I) all: 0.06362 / R_rim(I) all: 0.1625 / Net I/σ(I): 13.88
Reflection shell	Resolution: 1.897→1.965 Å / Redundancy: 6.5 % / R_merge(I) obs: 0.4808 / Mean I/σ(I) obs: 4.46 / Num. unique obs: 8075 / CC_1/2: 0.838 / R_pim(I) all: 0.202 / R_rim(I) all: 0.5223 / % possible all: 94

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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: 1.896→29.894 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 23.99

	R_factor	Num. reflection	% reflection
R_free	0.2489	1984	2.34 %
R_work	0.2004	-	-
obs	0.2015	84701	98.06 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.896→29.894 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7479	0	140	401	8020

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7715
X-RAY DIFFRACTION	f_angle_d	0.84	10414
X-RAY DIFFRACTION	f_dihedral_angle_d	3.1	4659
X-RAY DIFFRACTION	f_chiral_restr	0.047	1228
X-RAY DIFFRACTION	f_plane_restr	0.004	1323

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 (%)
1.8963-1.9437	0.2855	134	0.2291	5590	X-RAY DIFFRACTION	93
1.9437-1.9962	0.263	141	0.2104	5857	X-RAY DIFFRACTION	98
1.9962-2.055	0.2586	137	0.1973	5837	X-RAY DIFFRACTION	97
2.055-2.1213	0.2556	144	0.197	5859	X-RAY DIFFRACTION	97
2.1213-2.1971	0.2467	146	0.1907	5895	X-RAY DIFFRACTION	98
2.1971-2.285	0.2461	139	0.1922	5904	X-RAY DIFFRACTION	98
2.285-2.389	0.2589	145	0.1948	5921	X-RAY DIFFRACTION	99
2.389-2.5149	0.2559	143	0.2018	5931	X-RAY DIFFRACTION	99
2.5149-2.6723	0.2443	139	0.2082	5957	X-RAY DIFFRACTION	99
2.6723-2.8785	0.2452	145	0.21	5918	X-RAY DIFFRACTION	99
2.8785-3.1679	0.2529	140	0.2078	5962	X-RAY DIFFRACTION	99
3.1679-3.6256	0.2128	144	0.2023	5956	X-RAY DIFFRACTION	99
3.6256-4.5653	0.2575	145	0.1784	6043	X-RAY DIFFRACTION	99
4.5653-29.8972	0.2531	142	0.2112	6087	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	3.0764	0.714	-0.6732	1.7954	0.1416	2.2871	-0.1585	0.0778	-0.4484	-0.068	-0.0099	-0.1126	0.2622	-0.0476	0.1178	0.1328	0.0009	0.0084	0.122	-0.0358	0.1602	-0.0814	4.9646	23.3355
2	1.9415	0.6897	-0.4434	3.0595	0.463	1.6146	-0.0229	0.0379	0.1606	-0.1015	0.0351	0.2058	-0.094	-0.0782	-0.0147	0.1183	0.0078	-0.0141	0.1032	0.0206	0.0952	9.9871	32.6653	20.1575
3	0.7944	0.3996	-0.466	1.2286	-0.4798	0.9664	0.0011	0.0147	-0.0349	-0.0838	-0.0284	0.0066	0.0173	0.0269	0.0229	0.0936	0.0068	-0.0028	0.1183	-0.0183	0.1185	8.8543	22.1134	19.7605
4	3.0613	-0.2709	0.7273	2.2642	-0.5574	2.0362	-0.0131	0.0804	-0.0314	0.0094	0.044	0.1095	0.0598	-0.045	-0.0303	0.085	-0.0008	0.0081	0.0802	-0.0118	0.0708	-0.3095	13.7608	28.7856
5	1.2369	-0.7218	0.1225	1.0616	-0.0596	0.6367	-0.0718	0.0074	0.2064	-0.0183	0.0412	-0.0927	-0.1078	0.0624	0.0428	0.1343	-0.0328	0.0101	0.1267	-0.013	0.1355	44.8671	19.777	33.102
6	2.3445	-0.3048	0.9722	3.3416	-0.0082	2.9301	-0.0385	-0.201	-0.0617	0.1516	0.0474	0.2234	0.0788	-0.2412	0.0187	0.1121	-0.0078	0.0323	0.1051	0.0052	0.1092	43.2181	-0.0318	34.4421
7	2.4549	-0.2821	-0.2916	3.115	0.254	1.7493	-0.0458	-0.1919	0.2026	0.334	0.0026	-0.0701	-0.1406	0.0669	0.0408	0.1746	0.0164	-0.0119	0.1272	-0.0368	0.0953	45.1889	15.6302	44.9931
8	1.8132	-0.238	0.1881	1.2022	0.1214	0.7696	0.0493	0.1241	0.0477	-0.0517	-0.0375	0.0327	0.0061	0.0039	0.0012	0.1021	-0.003	0.0097	0.1268	0.0112	0.1044	41.3283	18.0557	25.2644
9	1.4942	0.875	-0.0426	1.8052	0.0758	0.701	-0.0058	0.0151	-0.1407	0.0681	-0.0045	0.0061	0.0484	-0.0073	0.0133	0.1142	0.0178	0.0062	0.1111	-0.0125	0.1095	-2.9265	18.8688	58.0205
10	2.7961	0.0067	-0.3108	3.7434	-0.2301	2.6612	-0.0359	0.0754	0.1995	-0.0449	0.1332	0.4499	-0.0622	-0.313	-0.0552	0.1164	0.0151	-0.0184	0.1306	0.0214	0.1907	-5.5551	39.2672	59.5905
11	1.2344	0.6754	-0.2745	3.3439	0.8295	0.8816	0.0102	0.1847	0.0081	-0.3348	-0.0467	-0.0647	-0.0269	-0.0439	0.0337	0.13	-0.0049	-0.0112	0.1416	-0.0069	0.067	-1.9138	26.524	47.9442
12	0.8643	0.047	-0.3037	1.2842	0.0844	0.3028	0.0372	-0.0178	-0.0783	0.1079	-0.0667	0.0414	-0.0213	-0.0791	0.0353	0.1053	-0.0091	-0.0052	0.1271	-0.0008	0.0865	-6.4579	19.9289	65.876
13	1.1798	-0.7567	0.0915	1.4277	-0.1684	0.7221	-0.0403	-0.0175	0.1369	0.0217	0.0144	-0.0865	-0.0434	0.0329	0.0278	0.1006	-0.0266	0.0018	0.1397	-0.0115	0.1294	34.4918	21.9892	70.1223
14	4.3842	-0.0252	1.0525	4.386	-2.0789	4.3113	-0.154	-0.5219	0.0699	0.1409	0.0879	0.7488	-0.0279	-0.9759	0.1817	0.1387	-0.0197	0.0364	0.2942	-0.0016	0.319	27.8467	-1.4243	72.3022
15	1.137	-0.502	-0.3958	2.4183	0.7875	1.488	-0.043	-0.1101	-0.0087	0.129	0.0181	-0.0016	0.0268	0.0397	0.0227	0.107	-0.0035	-0.0017	0.1217	0.0061	0.1017	35.8574	12.1605	76.7053
16	1.6089	-0.4385	0.1366	1.1623	-0.1246	0.5833	0.0035	0.0891	0.0495	-0.0819	-0.0078	0.0523	-0.0103	-0.0047	0.0146	0.1229	-0.0135	-0.005	0.1353	0.0099	0.0979	30.8514	20.7609	62.2527

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 24 through 56 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 57 through 119 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 120 through 217 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 218 through 270 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 24 through 84 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 85 through 130 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 131 through 170 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 171 through 270 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 24 through 84 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 85 through 119 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 120 through 170 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 171 through 270 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 24 through 84 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 85 through 103 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 104 through 170 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 171 through 270 )

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