PDB-5e2h: Crystal Structure of D-alanine Carboxypeptidase AmpC from Mycobac...

ID or keywords:

Entry

Database: PDB / ID: 5e2h

Title

Crystal Structure of D-alanine Carboxypeptidase AmpC from Mycobacterium smegmatis

Components

Beta-lactamase

Keywords

HYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function

Biological species

Mycobacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Kim, Y. / Hatzos-Skintges, C. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of D-alanine Carboxypeptidase AmpC from Mycobacterium smegmatis
Authors: Kim, Y. / Hatzos-Skintges, C. / Endres, M. / Babnigg, G. / Joachimiak, A.

History

Deposition	Oct 1, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5e2h.cif.gz	445.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5e2h.ent.gz	370.1 KB	Display	PDB format
PDBx/mmJSON format	5e2h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5e2h_validation.pdf.gz	454.5 KB	Display	wwPDB validaton report
Full document	5e2h_full_validation.pdf.gz	458.9 KB	Display
Data in XML	5e2h_validation.xml.gz	46 KB	Display
Data in CIF	5e2h_validation.cif.gz	68.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e2/5e2h ftp://data.pdbj.org/pub/pdb/validation_reports/e2/5e2h	HTTPS FTP

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Related structure data

Related structure data	5e2g
Similar structure data	4u0t-6 3wrz-2 3o86-1 3ws5-2 6tzf-2 3wrt-2 6tzh-3 4u0t-5 5gsc-2 3ws1-3 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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: MCSG-APC115002

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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)

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

C: Beta-lactamase

hetero molecules

117 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-lactamase

hetero molecules

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

2

B: Beta-lactamase

hetero molecules

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

3

C: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	127.779, 73.682, 113.413
Angle α, β, γ (deg.)	90.00, 90.19, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Beta-lactamase Mass: 38797.172 Da / Num. of mol.: 3 / Fragment: residues 27-380 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_3978 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QZC8, beta-lactamase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 803 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.32 Å³/Da / Density % sol: 46.95 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Calcium Chloride, 0.1 M Tris:HCl pH 8.5, 25% (w/v) PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97926 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 95577 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / R_sym value: 0.092 / Net I/σ(I): 14.34
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 3 % / R_merge(I) obs: 0.68 / Mean I/σ(I) obs: 1.66 / % possible all: 96

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Processing

Software

Name	Version	Classification
PHENIX	(1.10pre_2104: ???)	refinement
HKL-3000		data scaling
HKL-3000		phasing
SBC-Collect		data collection

Refinement

Method to determine structure:

SAD / Resolution: 1.8→32.551 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.65 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1972	4547	4.76 %	random
R_work	0.1635	-	-	-
obs	0.1651	95551	96.72 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→32.551 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8058	0	12	803	8873

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	8735
X-RAY DIFFRACTION	f_angle_d	0.924	11951
X-RAY DIFFRACTION	f_dihedral_angle_d	14.799	5231
X-RAY DIFFRACTION	f_chiral_restr	0.056	1311
X-RAY DIFFRACTION	f_plane_restr	0.007	1614

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 (%)
1.7927-1.8131	0.3405	116	0.296	2324	X-RAY DIFFRACTION	76
1.8131-1.8344	0.3089	166	0.2807	3071	X-RAY DIFFRACTION	96
1.8344-1.8568	0.3117	143	0.2491	3018	X-RAY DIFFRACTION	97
1.8568-1.8803	0.2584	160	0.2294	3026	X-RAY DIFFRACTION	97
1.8803-1.905	0.2409	147	0.2152	2969	X-RAY DIFFRACTION	97
1.905-1.9311	0.2489	150	0.2094	3052	X-RAY DIFFRACTION	97
1.9311-1.9587	0.2322	124	0.2042	3052	X-RAY DIFFRACTION	97
1.9587-1.9879	0.2574	155	0.1971	3037	X-RAY DIFFRACTION	97
1.9879-2.019	0.2291	161	0.1837	3002	X-RAY DIFFRACTION	97
2.019-2.0521	0.2032	160	0.1922	3079	X-RAY DIFFRACTION	97
2.0521-2.0874	0.2342	148	0.1921	2984	X-RAY DIFFRACTION	97
2.0874-2.1254	0.251	220	0.1858	2965	X-RAY DIFFRACTION	97
2.1254-2.1663	0.2243	117	0.1792	3153	X-RAY DIFFRACTION	98
2.1663-2.2105	0.2585	117	0.1698	3020	X-RAY DIFFRACTION	97
2.2105-2.2585	0.2106	174	0.1664	3032	X-RAY DIFFRACTION	98
2.2585-2.3111	0.2131	164	0.168	3053	X-RAY DIFFRACTION	98
2.3111-2.3688	0.2186	148	0.1752	3099	X-RAY DIFFRACTION	98
2.3688-2.4329	0.2169	155	0.1672	3029	X-RAY DIFFRACTION	98
2.4329-2.5044	0.2485	149	0.1793	3096	X-RAY DIFFRACTION	98
2.5044-2.5852	0.2056	171	0.1629	3008	X-RAY DIFFRACTION	98
2.5852-2.6776	0.2355	156	0.1659	3076	X-RAY DIFFRACTION	98
2.6776-2.7847	0.1946	136	0.1706	3105	X-RAY DIFFRACTION	98
2.7847-2.9114	0.2102	137	0.1661	3111	X-RAY DIFFRACTION	98
2.9114-3.0648	0.1902	136	0.1727	3137	X-RAY DIFFRACTION	98
3.0648-3.2566	0.1965	146	0.1664	3057	X-RAY DIFFRACTION	98
3.2566-3.5078	0.191	132	0.1531	3158	X-RAY DIFFRACTION	98
3.5078-3.8603	0.18	153	0.1461	3108	X-RAY DIFFRACTION	98
3.8603-4.4177	0.1209	168	0.1226	3101	X-RAY DIFFRACTION	98
4.4177-5.5614	0.1647	172	0.1275	3106	X-RAY DIFFRACTION	98
5.5614-32.5565	0.1724	166	0.1556	2976	X-RAY DIFFRACTION	92

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	1.2684	0.0158	0.8102	1.1221	0.4023	2.9221	-0.0349	0.0009	0.0269	0.0642	0.1133	-0.0179	0.2564	0.3625	-0.046	0.1312	0.0453	0.0106	0.2278	0.0043	0.2068	84.2812	13.1137	-2.1612
2	3.6357	1.0007	1.5764	3.347	0.4081	3.8519	-0.175	-0.5415	0.2443	0.5479	0.1223	-0.1803	0.0433	0.1861	0.0512	0.3745	0.2112	-0.06	0.5085	-0.063	0.2687	91.3764	15.5022	22.5277
3	1.6529	-0.5652	0.319	2.0646	0.1878	1.7242	-0.1056	-0.0762	0.1164	0.0335	0.1605	-0.2628	0.043	0.5312	-0.0331	0.1542	0.0351	-0.0075	0.3499	-0.0077	0.2362	92.9599	14.0458	0.1254
4	1.4213	-0.5702	0.2643	1.6458	-0.022	2.5733	-0.1183	-0.2591	-0.1661	0.2639	0.1263	0.1483	0.3727	0.0893	-0.0236	0.1913	0.0583	0.0298	0.2119	0.0377	0.2268	76.6503	6.5951	6.4317
5	1.3161	-0.0325	-0.0901	1.1121	0.5194	2.3718	0.0632	0.1959	-0.0437	0.0278	-0.031	-0.0436	0.1623	0.3147	-0.0277	0.1522	0.0502	-0.0039	0.1899	0.0234	0.197	85.0523	12.3802	-36.0634
6	2.2378	0.0797	-0.2283	4.8489	1.7795	2.8085	0.0947	0.7355	-0.2057	-0.3897	-0.1508	0.0656	0.0887	0.151	0.0554	0.3099	0.1567	-0.0244	0.6222	-0.0676	0.2419	85.9187	5.5984	-60.3626
7	1.8371	-1.0463	-0.0468	0.8462	0.2012	3.0615	0.0641	0.385	-0.406	0.2109	-0.0362	0.0912	0.5516	0.6494	-0.0626	0.4001	0.1841	-0.0192	0.4558	-0.0921	0.3585	92.2714	-0.42	-46.2876
8	8.8734	4.5901	-4.5508	5.4968	-1.282	4.9223	0.1429	-0.389	-0.7155	0.2275	-0.2197	-0.0926	0.5179	0.3238	0.0709	0.3672	0.0621	-0.0556	0.2002	0.0429	0.2769	86.0989	0.7719	-30.5403
9	4.4925	0.9035	-1.5333	3.027	1.6843	5.0203	0.1006	0.3784	-0.0462	-0.0629	-0.1155	0.295	0.3199	-0.1593	-0.0097	0.2144	0.0078	-0.0153	0.1779	-0.0078	0.25	72.9994	3.9052	-40.6311
10	0.9554	-0.2837	0.1467	1.1772	0.2573	1.2341	0.0433	0.2719	0.0728	-0.0995	-0.0328	-0.1857	0.1216	0.3179	0.0177	0.1745	0.0584	0.0207	0.3131	0.0264	0.2262	94.5066	15.406	-40.4476
11	1.2865	-0.647	-1.1646	3.1048	2.1587	3.6756	0.0009	0.5249	0.2419	-0.1951	-0.0259	-0.015	-0.2177	0.5665	0.0308	0.2262	0.0375	0.013	0.47	0.1528	0.2715	88.1452	25.4805	-49.7644
12	2.0683	0.1448	-0.0956	2.7477	-0.3278	2.1462	0.0596	0.042	0.1804	0.0432	-0.1119	-0.0352	-0.0737	0.1794	0.0416	0.1199	0.0255	0.011	0.1639	0.025	0.1919	82.8397	21.4737	-37.0687
13	1.0917	-0.0898	-0.7334	1.5796	0.2339	2.4909	0.1201	-0.0574	0.0777	0.3084	-0.084	0.0455	-0.4376	0.0994	0.019	0.2968	-0.0156	-0.0161	0.1287	-0.0002	0.2037	64.1916	50.1378	-35.8652
14	2.503	-0.6252	-1.0068	2.618	0.7634	3.0562	0.1401	-0.4479	-0.1626	0.7246	-0.1529	0.6046	-0.3042	-0.2326	0.051	0.7028	-0.0821	0.1094	0.2693	-0.0215	0.3348	55.4241	51.3544	-15.6554
15	1.695	0.7087	-0.1872	2.1364	0.0526	1.8139	0.152	-0.0163	0.145	0.2687	-0.0871	0.2004	-0.4097	-0.207	-0.0558	0.3062	0.0517	0.013	0.1717	-0.007	0.2218	58.6084	55.1339	-37.5301
16	1.1606	0.3655	-0.2527	2.0622	-0.0581	2.8667	0.0537	-0.1528	-0.0507	0.4156	-0.09	-0.1967	-0.2475	0.334	-0.0036	0.2525	-0.0365	-0.0679	0.1691	0.0193	0.2332	73.8204	45.2324	-31.7576

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 90 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 91 through 145 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 146 through 250 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 251 through 353 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 0 through 90 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 91 through 145 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 146 through 171 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 172 through 192 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 193 through 216 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 217 through 269 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 270 through 302 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 303 through 353 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 0 through 109 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 110 through 145 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 146 through 250 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 251 through 353 )

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