PDB-5hnm: Crystal structure of vancomycin resistance D,D-pentapeptidase Van...

ID or keywords:

Entry

Database: PDB / ID: 5hnm

Title

Crystal structure of vancomycin resistance D,D-pentapeptidase VanY E175A mutant from VanB-type resistance cassette in complex with Zn(II)

Components

D-alanyl-D-alanine carboxypeptidase

Keywords

HYDROLASE / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / NIAID / ALPHA+BETA PROTEIN / METALLOPEPTIDASE / HEDGEHOG/DD-PEPTIDASE FOLD / MEROPS M15B SUBFAMILY / ZN2+-DEPENDENT / VANCOMYCIN RESISTANCE / ANTIBIOTIC RESISTANCE

Function / homology

Function and homology information

Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Enterococcus faecalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Stogios, P.J. / Chun, J. / Wawrzak, Z. / Evdokimova, E. / Di Leo, R. / Yim, V. / Courvalin, P. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: To be published
Authors: Stogios, P.J.

History

Deposition	Jan 18, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 10, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 23, 2016	Group: Structure summary
Revision 1.2	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5hnm.cif.gz	459.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5hnm.ent.gz	380.6 KB	Display	PDB format
PDBx/mmJSON format	5hnm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5hnm_validation.pdf.gz	491.8 KB	Display	wwPDB validaton report
Full document	5hnm_full_validation.pdf.gz	498.8 KB	Display
Data in XML	5hnm_validation.xml.gz	44.3 KB	Display
Data in CIF	5hnm_validation.cif.gz	61.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hn/5hnm ftp://data.pdbj.org/pub/pdb/validation_reports/hn/5hnm	HTTPS FTP

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Related structure data

Related structure data	4murS S: Starting model for refinement
Similar structure data	5zhw-2 6ms8-7 5wl4-4 4jzr-d 5wl8-1 5jyj-d 5n04-d 4psq-2 5zhf-1 2gf9-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) 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: CSGID-IDP91871

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#192 - Dec 2015 Vancomycin similarity (1)

Deposited unit

A: D-alanyl-D-alanine carboxypeptidase

B: D-alanyl-D-alanine carboxypeptidase

C: D-alanyl-D-alanine carboxypeptidase

D: D-alanyl-D-alanine carboxypeptidase

E: D-alanyl-D-alanine carboxypeptidase

F: D-alanyl-D-alanine carboxypeptidase

hetero molecules

135 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: D-alanyl-D-alanine carboxypeptidase

hetero molecules

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

2

B: D-alanyl-D-alanine carboxypeptidase

hetero molecules

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

3

C: D-alanyl-D-alanine carboxypeptidase

hetero molecules

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

4

D: D-alanyl-D-alanine carboxypeptidase

hetero molecules

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

5

E: D-alanyl-D-alanine carboxypeptidase

hetero molecules

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

6

F: D-alanyl-D-alanine carboxypeptidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	55.709, 77.319, 85.865
Angle α, β, γ (deg.)	101.34, 108.13, 90.06
Int Tables number	1
Space group name H-M	P1

#1: Protein	D-alanyl-D-alanine carboxypeptidase / DD-peptidase Mass: 22385.615 Da / Num. of mol.: 6 / Fragment: UNP residues 72-268 / Mutation: E175A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (strain ATCC 700802 / V583) (bacteria) Strain: ATCC 700802 / V583 / Gene: vanYB, EF_2297 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q47746, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 531 / 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: 2.56 Å³/Da / Density % sol: 51.96 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.5 M ammonium sulfate, 4% sucrose, 0.01 M magnesium chloride

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.3→18.878 Å / Num. obs: 58200 / % possible obs: 98.3 % / Redundancy: 3 % / R_merge(I) obs: 0.084 / Net I/σ(I): 8.3
Reflection shell	Resolution: 2.3→2.42 Å / Redundancy: 3 % / R_merge(I) obs: 0.412 / Mean I/σ(I) obs: 2.7 / % possible all: 97.7

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
SCALA		data scaling
PHENIX		phasing
PHENIX		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4MUR

4mur

Resolution: 2.3→18.878 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2753	2941	5.04 %	Random selection
R_work	0.2191	-	-	-
obs	0.2219	58200	95.81 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→18.878 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8669	0	26	531	9226

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	8961
X-RAY DIFFRACTION	f_angle_d	0.652	12164
X-RAY DIFFRACTION	f_dihedral_angle_d	11.883	3272
X-RAY DIFFRACTION	f_chiral_restr	0.033	1288
X-RAY DIFFRACTION	f_plane_restr	0.003	1598

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 (%)
2.3-2.3261	0.3446	185	0.3121	3631	X-RAY DIFFRACTION	95
2.3261-2.3534	0.3328	168	0.2946	3499	X-RAY DIFFRACTION	95
2.3534-2.3821	0.3307	169	0.2851	3604	X-RAY DIFFRACTION	95
2.3821-2.4122	0.3567	192	0.2806	3561	X-RAY DIFFRACTION	95
2.4122-2.4439	0.3498	169	0.2899	3525	X-RAY DIFFRACTION	95
2.4439-2.4773	0.3317	184	0.2867	3590	X-RAY DIFFRACTION	95
2.4773-2.5126	0.3087	179	0.2886	3599	X-RAY DIFFRACTION	95
2.5126-2.55	0.3703	202	0.2694	3507	X-RAY DIFFRACTION	95
2.55-2.5897	0.3284	209	0.2731	3528	X-RAY DIFFRACTION	95
2.5897-2.6321	0.3212	199	0.2732	3553	X-RAY DIFFRACTION	95
2.6321-2.6774	0.3246	191	0.2562	3596	X-RAY DIFFRACTION	95
2.6774-2.7259	0.3048	207	0.2508	3514	X-RAY DIFFRACTION	96
2.7259-2.7782	0.3294	194	0.2565	3604	X-RAY DIFFRACTION	95
2.7782-2.8347	0.3571	172	0.2617	3554	X-RAY DIFFRACTION	96
2.8347-2.8961	0.3022	211	0.2504	3589	X-RAY DIFFRACTION	95
2.8961-2.9632	0.3048	170	0.2342	3626	X-RAY DIFFRACTION	96
2.9632-3.0371	0.3093	198	0.2444	3522	X-RAY DIFFRACTION	96
3.0371-3.1188	0.2919	173	0.2434	3626	X-RAY DIFFRACTION	96
3.1188-3.2102	0.2763	175	0.2341	3609	X-RAY DIFFRACTION	96
3.2102-3.3132	0.3005	247	0.2323	3566	X-RAY DIFFRACTION	96
3.3132-3.431	0.2854	195	0.2163	3595	X-RAY DIFFRACTION	96
3.431-3.5675	0.3008	193	0.1951	3585	X-RAY DIFFRACTION	96
3.5675-3.7287	0.2674	193	0.201	3659	X-RAY DIFFRACTION	97
3.7287-3.9236	0.2681	169	0.1941	3605	X-RAY DIFFRACTION	97
3.9236-4.1669	0.2216	191	0.1799	3598	X-RAY DIFFRACTION	97
4.1669-4.4847	0.2196	206	0.1683	3611	X-RAY DIFFRACTION	97
4.4847-4.9287	0.2016	213	0.1633	3580	X-RAY DIFFRACTION	97
4.9287-5.6253	0.2467	195	0.1859	3664	X-RAY DIFFRACTION	97
5.6253-7.026	0.219	183	0.212	3648	X-RAY DIFFRACTION	97
7.026-18.8791	0.2549	178	0.195	3600	X-RAY DIFFRACTION	96

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	4.1919	5.7933	-5.0812	8.1472	-6.8	8.6931	-0.4161	0.4475	-0.3786	-0.1058	0.054	-0.2369	-0.1418	-0.0075	0.1456	0.3127	0.0218	0.0394	0.2673	-0.071	0.6582	-19.9533	48.9176	-77.4819
2	2.8624	-0.3125	0.5603	3.9719	-1.9538	3.6927	-0.213	-0.3408	-0.1341	0.2276	0.1537	0.0226	-0.1088	-0.0742	0.0652	0.251	0.0618	0.0308	0.224	-0.0084	0.2626	-35.9094	51.5293	-71.477
3	6.1056	-2.9237	1.6556	4.5249	-5.7055	8.3758	0.0358	-0.2996	0.3613	-0.2907	-0.0752	-0.3158	0.4245	-0.0724	0.0057	0.3614	-0.0771	-0.0079	0.2302	-0.0332	0.4193	-30.1224	70.7419	-90.0121
4	4.735	-0.8718	-0.4525	1.4613	-0.4791	3.2158	-0.094	-0.4178	0.7577	0.2014	0.0659	-0.2146	-0.7519	0.0301	-0.0042	0.4619	-0.0086	0.0121	0.2552	-0.0682	0.3383	-26.2029	59.7992	-67.8076
5	8.4291	1.3383	-1.552	3.1354	-2.9473	3.776	0.2906	0.643	0.1005	-0.4008	0.0805	0.0759	0.2438	0.7555	-0.3091	0.2675	0.0563	0.0044	0.3525	-0.0175	0.5462	-48.077	86.1844	-78.7207
6	6.4793	-5.8131	-2.0338	8.4993	-1.0791	3.2901	-0.0137	0.7564	-0.707	-0.1724	0.2277	-0.3874	1.0077	0.0184	0.0143	0.4769	0.0701	-0.0543	0.3097	-0.2415	0.5207	-64.5275	82.0484	-74.6934
7	0.3285	-0.0529	0.1694	1.6821	-0.9474	3.335	-0.0544	0.0283	0.0425	-0.0542	0.0116	-0.0292	-0.0767	-0.0772	0.0264	0.2101	0.0103	-0.0067	0.2737	-0.0075	0.2807	-61.257	96.1895	-76.6678
8	7.5724	0.154	-1.6973	1.2332	-0.1393	5.8611	-0.066	-0.2103	0.1834	0.058	-0.003	-0.278	-0.4182	0.3872	0.03	0.2541	-0.0494	-0.0338	0.2221	-0.0128	0.3399	-50.3979	96.9148	-66.5958
9	6.0068	4.8889	-3.6495	9.6252	-1.9296	2.5593	0.526	0.1768	0.1235	0.6063	-0.0272	1.0551	-0.5483	-1.1467	-0.5494	0.3832	0.0596	0.0598	0.5053	-0.0176	0.5294	-69.169	76.7021	-42.4803
10	0.4466	0.0519	-0.7788	2.9314	-3.6458	6.7098	0.2091	0.0607	-0.043	-0.3541	-0.0763	0.0947	0.4464	-0.0185	-0.1318	0.5048	0.0466	-0.0484	0.3685	-0.0302	0.3247	-56.2632	68.071	-43.6996
11	2.667	0.7427	0.4698	3.746	-1.3642	5.3961	0.0665	-0.1573	-0.1817	0.4725	-0.1119	-0.4221	-0.0736	0.2665	0.0356	0.4798	0.1183	-0.1101	0.4515	-0.0126	0.3399	-52.345	79.7575	-44.1227
12	9.6889	4.5694	-3.6936	4.6024	-3.847	3.6698	0.0438	-1.7766	0.3704	2.0671	-0.6434	0.113	-1.5454	0.4624	0.6099	0.8553	0.0998	-0.1089	0.5931	-0.0503	0.4802	-63.0577	88.0397	-39.2749
13	8.3344	4.7986	-7.925	6.7369	-3.5646	8.3821	-0.1975	-0.1849	-0.1116	-0.3842	0.5604	0.3321	0.6151	-1.1706	-0.3927	0.6058	0.1704	-0.074	1.0455	0.1005	0.5941	-41.0812	112.1819	-45.2513
14	0.0496	0.333	0.2571	1.4777	-3.6254	8.6979	0.2352	0.1267	-0.043	-0.2738	-0.043	0.0635	0.9414	-0.2264	-0.1476	0.7229	0.1188	0.0388	0.5337	-0.0462	0.4396	-25.6406	107.5652	-43.4411
15	9.167	7.7023	0.7407	8.0721	-2.2691	5.3312	0.1042	-0.2799	-1.7768	-0.2654	-1.0067	-1.929	-0.1601	1.2517	0.7197	0.6293	0.3083	0.0875	1.0472	0.0056	0.7636	-13.4288	118.7855	-43.7712
16	3.0289	0.7027	0.2899	5.3718	-2.6681	2.8319	0.3172	-0.3028	0.2799	0.4795	-0.0621	0.2957	-0.7782	-0.5427	-0.2519	0.6758	0.2202	0.0573	0.7233	-0.0371	0.3168	-29.3627	122.5302	-41.4393
17	7.1376	-6.486	-3.9439	6.2265	3.3849	2.3821	-1.0109	-0.6568	-0.7183	0.7344	0.5273	0.7023	0.8757	-0.2927	0.3606	0.5098	0.07	0.1865	0.4823	0.1834	0.7598	-62.2787	45.9372	-81.3686
18	5.3443	1.3307	0.4505	5.1902	-1.4371	4.6277	-0.036	0.3871	-0.1469	-0.0294	0.2907	0.1553	0.3164	0.0486	-0.1777	0.223	0.0007	0.0402	0.2115	0.0088	0.2471	-45.8954	49.6705	-92.1575
19	7.1473	-6.0807	-3.8435	8.7195	6.0371	6.8828	-0.3647	0.1478	0.6037	0.341	0.265	-0.5559	0.0178	0.2791	0.0686	0.2809	0.029	0.0224	0.2976	0.0595	0.3197	-52.7124	64.5496	-70.5722
20	4.0019	0.8926	-1.2148	3.3762	-0.0959	4.3448	-0.0594	0.4132	0.3653	-0.0914	0.0804	0.3106	-0.3798	-0.3671	-0.026	0.2713	0.0235	0.0085	0.2379	0.0756	0.348	-57.4052	58.0458	-90.9308
21	7.2467	-6.3743	-5.0624	8.5906	5.2817	7.7851	0.0431	-0.0837	0.0769	-0.0252	-0.0785	-0.9837	0.4625	-0.5116	-0.0068	0.3451	-0.0944	0.0132	0.2355	0.0793	0.3974	-35.3418	87.2285	-82.6364
22	4.5889	1.0289	-1.056	3.9528	-2.6407	3.1478	-0.1908	0.8893	-0.1952	-0.4606	0.2757	0.0607	-0.1126	0.3225	-0.084	0.257	-0.0957	-0.0036	0.4258	-0.0205	0.2376	-18.6422	88.7658	-92.6579
23	2.3894	0.823	0.9723	4.1333	6.0426	9.0036	-0.0547	0.206	0.4088	-0.1921	-0.199	0.4883	-0.3796	-0.3772	0.2617	0.2201	-0.0011	0.0141	0.2792	0.0497	0.3233	-25.6241	103.4221	-72.2068
24	4.2244	0.8502	-0.5654	2.4625	-0.2673	3.7054	-0.0567	0.9907	0.699	-0.165	0.2999	0.1446	-0.7138	-0.5421	-0.2055	0.4122	0.0231	0.0602	0.4451	0.195	0.3977	-29.1972	97.9579	-93.8115

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 88:106)
2	X-RAY DIFFRACTION	2	(chain A and resid 107:156)
3	X-RAY DIFFRACTION	3	(chain A and resid 157:176)
4	X-RAY DIFFRACTION	4	(chain A and resid 177:266)
5	X-RAY DIFFRACTION	5	(chain B and resid 88:103)
6	X-RAY DIFFRACTION	6	(chain B and resid 104:114)
7	X-RAY DIFFRACTION	7	(chain B and resid 115:204)
8	X-RAY DIFFRACTION	8	(chain B and resid 205:268)
9	X-RAY DIFFRACTION	9	(chain C and resid 88:102)
10	X-RAY DIFFRACTION	10	(chain C and resid 103:186)
11	X-RAY DIFFRACTION	11	(chain C and resid 187:255)
12	X-RAY DIFFRACTION	12	(chain C and resid 256:265)
13	X-RAY DIFFRACTION	13	(chain D and resid 88:107)
14	X-RAY DIFFRACTION	14	(chain D and resid 108:203)
15	X-RAY DIFFRACTION	15	(chain D and resid 204:211)
16	X-RAY DIFFRACTION	16	(chain D and resid 212:266)
17	X-RAY DIFFRACTION	17	(chain E and resid 87:106)
18	X-RAY DIFFRACTION	18	(chain E and resid 107:146)
19	X-RAY DIFFRACTION	19	(chain E and resid 147:176)
20	X-RAY DIFFRACTION	20	(chain E and resid 177:266)
21	X-RAY DIFFRACTION	21	(chain F and resid 87:107)
22	X-RAY DIFFRACTION	22	(chain F and resid 108:146)
23	X-RAY DIFFRACTION	23	(chain F and resid 147:186)
24	X-RAY DIFFRACTION	24	(chain F and resid 187:266)

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