PDB-5tr7: Crystal structure of a putative D-alanyl-D-alanine carboxypeptida...

ID or keywords:

Entry

Database: PDB / ID: 5tr7

Title

Crystal structure of a putative D-alanyl-D-alanine carboxypeptidase from Vibrio cholerae O1 biovar eltor str. N16961

Components

D-alanyl-D-alanine carboxypeptidase

Muramoylpentapeptide carboxypeptidase

Keywords

PENICILLIN-BINDING PROTEIN /

PBP5 / penicil-binding protein /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID /

TRANSFERASE

Function / homology

Function and homology information

serine-type D-Ala-D-Ala carboxypeptidase /

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

Biological species

Vibrio cholerae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Shatsman, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: Crystal structure of a putative D-alanyl-D-alanine carboxypeptidase from Vibrio cholerae O1 biovar eltor str. N16961
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Shatsman, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Oct 25, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 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_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5tr7.cif.gz	309.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5tr7.ent.gz	251.1 KB	Display	PDB format
PDBx/mmJSON format	5tr7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tr/5tr7 ftp://data.pdbj.org/pub/pdb/validation_reports/tr/5tr7	HTTPS FTP

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Related structure data

Related structure data	1nzoS S: Starting model for refinement
Similar structure data	2fdr-d 2ydd-d 4wc9-d 6azi-d 2a8n-d 3g8a-4 5owf-d 1xk5-d 1es2-d 1z4o-2 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-idp01407

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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: D-alanyl-D-alanine carboxypeptidase

B: D-alanyl-D-alanine carboxypeptidase

C: D-alanyl-D-alanine carboxypeptidase

hetero molecules

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

1

A: D-alanyl-D-alanine carboxypeptidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	88.749, 88.749, 85.425
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	B
2	3	C

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ALA	ALA	PHE	PHE	A	A	34 - 281	3 - 250
2	1	ALA	ALA	PHE	PHE	B	B	34 - 281	3 - 250
1	2	ASP	ASP	GLU	GLU	A	A	33 - 283	2 - 252
2	2	ASP	ASP	GLU	GLU	C	C	33 - 283	2 - 252
1	3	ALA	ALA	PHE	PHE	B	B	34 - 281	3 - 250
2	3	ALA	ALA	PHE	PHE	C	C	34 - 281	3 - 250

NCS ensembles :

ID
3
1
2

#1: Protein	D-alanyl-D-alanine carboxypeptidase / Muramoylpentapeptide carboxypeptidase Mass: 37390.117 Da / Num. of mol.: 3 / Fragment: UNP residues 32-372 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O1 biovar eltor str. N16961 / Gene: VC0947 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic References: UniProt: A0A0H7A7Y4, UniProt: Q9KTF5*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-NO2 / NITRITE ION / Nitrite Mass: 46.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 81 / 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 grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Sodium Nitrate, 0.1 M Bis-Tris propane, 20% PEG3350

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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: Oct 5, 2016 / Details: 3.0 Undulator
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.05→30 Å / Num. obs: 47191 / % possible obs: 100 % / Redundancy: 5.8 % / CC_1/2: 0.97 / R_merge(I) obs: 0.066 / Net I/σ(I): 36.6
Reflection shell	Resolution: 2.05→2.09 Å / Redundancy: 5.7 % / R_merge(I) obs: 0.75 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0155	refinement
HKL-2000		data reduction
HKL-2000		data scaling
BALBES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1NZO

1nzo

Resolution: 2.05→30 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.951 / SU B: 17.21 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.18 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23774	2246	4.8 %	RANDOM
R_work	0.19086	-	-	-
obs	0.19321	44920	99.94 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 65.043 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.77 Å²	1.38 Å²	0 Å²
2-	-	2.77 Å²	0 Å²
3-	-	-	-8.98 Å²

Refinement step

Cycle: 1 / Resolution: 2.05→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5772	0	43	81	5896

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.019	5919
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	5568
X-RAY DIFFRACTION	r_angle_refined_deg	2.028	1.952	7982
X-RAY DIFFRACTION	r_angle_other_deg	0.993	3	12827
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.324	5	750
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.259	25.305	262
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.942	15	1017
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.573	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.132	0.2	884
X-RAY DIFFRACTION	r_gen_planes_refined	0.027	0.02	6769
X-RAY DIFFRACTION	r_gen_planes_other	0.021	0.02	1326
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	3.844	3.692	3006
X-RAY DIFFRACTION	r_mcbond_other	3.841	3.69	3005
X-RAY DIFFRACTION	r_mcangle_it	4.927	5.521	3754
X-RAY DIFFRACTION	r_mcangle_other	4.927	5.522	3755
X-RAY DIFFRACTION	r_scbond_it	4.789	4.156	2913
X-RAY DIFFRACTION	r_scbond_other	4.784	4.156	2913
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	6.44	6.061	4229
X-RAY DIFFRACTION	r_long_range_B_refined	8.086	44.163	6629
X-RAY DIFFRACTION	r_long_range_B_other	8.086	44.16	6629
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number
1	1	A	16068
1	2	B	16068
2	1	A	16224
2	2	C	16224
3	1	B	16066
3	2	C	16066

LS refinement shell

Resolution: 2.05→2.104 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.346	180	-
R_work	0.366	3271	-
obs	-	-	100 %

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	2.2201	-2.105	0.9188	10.516	1.6973	2.4226	0.0437	-0.2856	-0.094	0.6065	0.1675	-0.2101	0.1637	0.1429	-0.2112	0.1271	-0.1051	-0.0327	0.1928	0.0107	0.0232	-37.6964	60.4256	16.215
2	0.3621	-0.2161	0.6111	1.9092	-0.2754	1.9121	0.0634	0.0387	0.0544	-0.0584	0.0039	-0.2124	-0.2031	0.5247	-0.0673	0.1295	-0.1451	0.0512	0.2819	-0.0321	0.159	-33.0069	69.4326	-3.599
3	2.2538	0.6742	-2.6471	1.7143	-0.7729	3.2093	0.0371	0.1624	-0.1857	-0.4728	-0.1327	-0.0293	-0.086	-0.0736	0.0956	0.409	-0.032	-0.0151	0.2604	-0.0775	0.2405	-37.11	65.8926	-17.7199
4	0.7558	-0.3955	0.0209	1.7884	0.2385	3.1629	0.111	-0.0102	-0.0203	-0.2633	0.0043	-0.0846	-0.0632	0.5632	-0.1153	0.0834	-0.0539	0.0195	0.1562	-0.0217	0.0631	-35.6945	67.3829	-2.6703
5	2.8368	-0.9584	0.2627	3.4023	0.731	3.8599	0.0282	0.1047	-0.2669	0.3904	-0.0583	-0.0944	0.1573	0.1886	0.0301	0.0894	-0.0514	-0.018	0.0952	0.0022	0.0698	-41.8519	59.2681	6.5494
6	3.163	0.5245	-1.7962	7.7005	5.702	7.7383	-0.0064	-0.2432	-0.3546	0.3551	-0.1836	0.5643	0.2118	0.2021	0.1899	0.2229	-0.0957	0.0278	0.2008	0.0059	0.2507	-46.0718	57.9359	15.7676
7	2.7246	5.2611	0.6275	11.3019	-2.0969	10.2702	-0.2792	-0.0588	-0.1692	-0.5636	0.3185	-0.3504	-0.3435	-1.0252	-0.0393	0.4755	-0.0318	0.0725	0.3338	-0.0225	0.1075	-43.151	52.6383	-38.814
8	0.3586	0.38	-0.8571	2.1131	0.6264	4.7114	-0.0722	-0.0759	-0.0044	-0.1301	0.5101	-0.2711	-0.3805	0.6524	-0.4379	0.1919	0.007	0.0335	0.4306	-0.1011	0.3525	-34.6092	36.6905	-19.6736
9	1.2533	0.1084	-2.5649	2.3409	1.3486	6.4332	-0.0438	0.3437	0.0699	0.0413	0.1374	0.1827	0.0269	-0.6626	-0.0936	0.064	0.0537	0.0062	0.3798	0.0342	0.2261	-47.1212	33.6176	-17.9311
10	2.7003	-1.5323	1.404	2.5325	-0.0183	6.2	-0.3179	-0.0464	-0.1725	-0.2894	0.6504	0.2798	-0.9328	-1.0117	-0.3325	0.2822	0.0456	0.0011	0.6852	0.1098	0.1786	-50.0973	41.6824	-25.897
11	1.9474	3.1044	1.6179	6.4288	3.7229	6.4712	-0.3872	-0.1965	-0.122	-1.1436	0.2877	-0.1552	-1.2758	-0.6749	0.0995	0.3336	-0.0453	-0.0053	0.4905	0.0178	0.1848	-45.0267	41.0255	-32.6488
12	3.0031	-0.8571	0.4456	8.6917	4.9107	5.4142	-0.1471	-0.2359	0.1728	-0.2816	0.1885	0.3112	-0.7884	-0.9909	-0.0415	0.471	0.1761	-0.0241	0.5194	0.1261	0.0775	-48.5637	46.7222	-35.3734
13	9.6772	-2.0054	-20.458	3.7137	4.8009	43.3549	-0.0988	-0.7103	0.2341	0.6124	0.5888	0.1355	0.3601	1.5896	-0.49	0.3134	0.0989	-0.0275	0.1549	-0.0265	0.3477	-10.7487	27.6012	-0.2541
14	0.7057	-0.1784	0.1526	1.4752	-1.1597	3.7185	-0.0776	-0.0086	0.0509	0.0219	-0.2006	-0.3817	0.3251	0.416	0.2782	0.058	0.0499	0.0282	0.1042	0.0652	0.6995	3.6044	37.3649	-20.2604
15	0.8619	-0.6133	0.2538	1.3223	-0.331	3.2538	-0.1053	0.0311	0.2754	-0.06	-0.1056	-0.3297	0.4127	0.3431	0.2109	0.0959	0.0383	0.0429	0.0907	0.0625	0.7079	2.3175	39.1195	-24.5132
16	8.8396	-4.3947	-1.0528	4.359	2.8697	3.0309	-0.2843	0.0401	0.5041	-0.2613	-0.3131	0.1086	-0.2113	-0.6377	0.5973	0.2433	-0.0475	0.0378	0.4288	-0.1343	0.5093	-10.2712	39.512	-15.4431
17	0.2354	0.5675	0.4035	2.1004	-0.0085	5.3408	-0.0238	-0.149	-0.0618	-0.0145	-0.3195	0.0353	0.221	-0.4371	0.3433	0.0502	0.0296	-0.0128	0.1354	-0.0915	0.6031	-8.9152	33.712	-11.2867
18	3.8002	1.3257	-1.1539	8.2606	4.2389	3.1709	0.1574	-0.3186	-0.0367	0.2222	-0.3205	0.2903	0.0099	-0.108	0.1631	0.0753	-0.02	0.0234	0.2593	-0.0247	0.3357	-10.484	39.5184	1.1193

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	34 - 52
2	X-RAY DIFFRACTION	2	A	53 - 99
3	X-RAY DIFFRACTION	3	A	100 - 122
4	X-RAY DIFFRACTION	4	A	123 - 225
5	X-RAY DIFFRACTION	5	A	226 - 267
6	X-RAY DIFFRACTION	6	A	268 - 282
7	X-RAY DIFFRACTION	7	B	34 - 40
8	X-RAY DIFFRACTION	8	B	41 - 191
9	X-RAY DIFFRACTION	9	B	192 - 216
10	X-RAY DIFFRACTION	10	B	217 - 236
11	X-RAY DIFFRACTION	11	B	237 - 258
12	X-RAY DIFFRACTION	12	B	259 - 282
13	X-RAY DIFFRACTION	13	C	33 - 38
14	X-RAY DIFFRACTION	14	C	39 - 105
15	X-RAY DIFFRACTION	15	C	106 - 223
16	X-RAY DIFFRACTION	16	C	224 - 235
17	X-RAY DIFFRACTION	17	C	236 - 274
18	X-RAY DIFFRACTION	18	C	275 - 283

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