PDB-6q71: Crystal structure of the alanine racemase Bsu17640 from Bacillus ...

ID or keywords:

Entry

Database: PDB / ID: 6q71

Title

Crystal structure of the alanine racemase Bsu17640 from Bacillus subtilis in the presence of Bis-Tris propane

Components

Alanine racemase 2

Keywords

ISOMERASE /

racemase /

alanine racemase

Function / homology

Function and homology information

alanine racemase / D-alanine biosynthetic process /

alanine racemase activity / peptidoglycan biosynthetic process /

pyridoxal phosphate binding /

cytosol
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.92 Å

Authors

Bernardo-Garcia, N. / Gago, F. / Hermoso, J.A.

Citation

Journal: Org.Biomol.Chem. / Year: 2019
Title: Cold-induced aldimine bond cleavage by Tris in Bacillus subtilis alanine racemase.
Authors: Bernardo-Garcia, N. / Sanchez-Murcia, P.A. / Espaillat, A. / Martinez-Caballero, S. / Cava, F. / Hermoso, J.A. / Gago, F.

History

Deposition	Dec 12, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 24, 2019	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2019	Group: Data collection / Database references Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Jan 24, 2024	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_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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_symmetry / _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 / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6q71.cif.gz	329 KB	Display	PDBx/mmCIF format
PDB format	pdb6q71.ent.gz	269.4 KB	Display	PDB format
PDBx/mmJSON format	6q71.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/q7/6q71 ftp://data.pdbj.org/pub/pdb/validation_reports/q7/6q71	HTTPS FTP

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Related structure data

Related structure data	5irpSC 6q70C 6q72C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1qrr-1 4wr3-2 2rjh-2 3e5p-1 1nsc-d 4qhr-d 1w3y-d 4xbj-1 4cpz-1 5fag-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Alanine racemase 2

B: Alanine racemase 2

hetero molecules

88.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	73.241, 73.241, 333.534
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	95
Space group name H-M	P4₃22

Components on special symmetry positions

ID	Model	Components
1	1	B-780- HOH

#1: Protein	Alanine racemase 2 / Mass: 43708.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: D3Z87_09640 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A386RMP5, UniProt: P94494*PLUS
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 577 / 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: 2.57 Å³/Da / Density % sol: 52.14 %
Crystal grow	Temperature: 290 K / Method: microbatch / pH: 8.5 / Details: PEG 4000, Bis-Tris propane, MgCl2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97934 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 1.92→49.6 Å / Num. obs: 70977 / % possible obs: 100 % / Redundancy: 12.9 % / R_merge(I) obs: 0.05 / Net I/σ(I): 16.6
Reflection shell	Resolution: 1.92→2 Å

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XDS		data reduction
Aimless		data scaling
Coot		model building
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5IRP

5irp

Resolution: 1.92→49.317 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.57

	R_factor	Num. reflection	% reflection
R_free	0.2315	3642	5.14 %
R_work	0.204	-	-
obs	0.2055	70845	99.99 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.92→49.317 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6050	0	11	571	6632

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.018	6169
X-RAY DIFFRACTION	f_angle_d	1.671	8342
X-RAY DIFFRACTION	f_dihedral_angle_d	16.896	3731
X-RAY DIFFRACTION	f_chiral_restr	0.24	956
X-RAY DIFFRACTION	f_plane_restr	0.008	1046

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 (%)
1.92-1.9453	0.3726	160	0.3581	2509	X-RAY DIFFRACTION	100
1.9453-1.972	0.3295	125	0.3306	2552	X-RAY DIFFRACTION	100
1.972-2.0001	0.3774	135	0.3137	2534	X-RAY DIFFRACTION	100
2.0001-2.03	0.317	132	0.2907	2567	X-RAY DIFFRACTION	100
2.03-2.0617	0.3227	114	0.2842	2510	X-RAY DIFFRACTION	100
2.0617-2.0955	0.299	138	0.2591	2591	X-RAY DIFFRACTION	100
2.0955-2.1316	0.2723	131	0.2469	2502	X-RAY DIFFRACTION	100
2.1316-2.1704	0.249	147	0.2448	2543	X-RAY DIFFRACTION	100
2.1704-2.2122	0.2817	144	0.2367	2544	X-RAY DIFFRACTION	100
2.2122-2.2573	0.3221	133	0.2432	2539	X-RAY DIFFRACTION	100
2.2573-2.3064	0.2933	130	0.25	2580	X-RAY DIFFRACTION	100
2.3064-2.36	0.263	150	0.2463	2550	X-RAY DIFFRACTION	100
2.36-2.4191	0.2614	139	0.2269	2524	X-RAY DIFFRACTION	100
2.4191-2.4845	0.2602	132	0.2282	2577	X-RAY DIFFRACTION	100
2.4845-2.5576	0.2503	155	0.2334	2541	X-RAY DIFFRACTION	100
2.5576-2.6401	0.2423	125	0.2269	2588	X-RAY DIFFRACTION	100
2.6401-2.7345	0.2633	145	0.2247	2581	X-RAY DIFFRACTION	100
2.7345-2.8439	0.2661	133	0.2204	2561	X-RAY DIFFRACTION	100
2.8439-2.9734	0.2448	132	0.2187	2603	X-RAY DIFFRACTION	100
2.9734-3.1301	0.2489	145	0.2105	2587	X-RAY DIFFRACTION	100
3.1301-3.3262	0.2517	149	0.2129	2631	X-RAY DIFFRACTION	100
3.3262-3.5829	0.208	135	0.188	2591	X-RAY DIFFRACTION	100
3.5829-3.9433	0.1998	142	0.1575	2645	X-RAY DIFFRACTION	100
3.9433-4.5136	0.155	143	0.1442	2664	X-RAY DIFFRACTION	100
4.5136-5.6853	0.1587	167	0.1474	2697	X-RAY DIFFRACTION	100
5.6853-49.3337	0.224	161	0.1913	2892	X-RAY DIFFRACTION	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	2.2046	-2.7423	0.1921	6.1544	-0.9002	0.7419	-0.0595	0.0568	0.4433	0.4149	-0.0566	-0.8303	-0.1352	0.1056	0.0884	0.3117	-0.0455	0.0268	0.2241	-0.0677	0.3383	45.8685	48.0644	358.9627
2	1.3732	-0.426	-0.41	0.8779	-0.2217	0.9272	0.067	-0.1969	0.0759	-0.0162	0.0295	-0.0246	-0.1609	-0.0424	-0.1002	0.2921	0.0002	0.0311	0.2303	-0.0151	0.2185	25.656	48.8222	362.2349
3	1.9822	0.0925	-0.7682	1.5792	-0.5719	2.7998	0.1366	-0.2481	-0.0631	-0.125	-0.0448	0.2811	-0.0768	-0.2034	-0.0811	0.2333	0.0602	-0.0091	0.2644	0.0176	0.2681	10.0418	49.5056	356.9913
4	5.7669	-1.53	-4.6541	1.2279	1.6872	5.3463	0.3743	0.3276	0.2651	-0.2516	-0.1318	0.1009	-0.2186	-0.3697	-0.2104	0.5329	0.1474	-0.027	0.3089	0.0377	0.3911	10.6903	59.9216	345.162
5	1.0167	-0.6227	-0.0401	1.4872	-0.2328	0.393	0.1786	0.0904	0.256	-0.3388	-0.0613	-0.1963	-0.1703	-0.0103	-0.0935	0.357	0.0315	0.0863	0.1817	-0.0092	0.263	34.1806	53.3256	349.4711
6	0.7076	-0.744	-0.1764	0.9533	0.7158	0.7715	0.2773	0.211	0.2978	-0.4971	-0.0991	-0.5581	-0.1109	0.1629	-0.1563	0.439	0.0533	0.1778	0.2553	0.0165	0.4151	54.1843	32.4895	343.9296
7	1.5095	-0.6555	0.0455	2.4865	0.2902	1.8955	0.1367	-0.1564	0.1678	-0.0788	-0.091	-0.2151	-0.0496	-0.0501	-0.0398	0.3148	-0.0136	0.0622	0.1786	-0.0145	0.2573	41.6594	42.624	356.2062
8	1.081	-0.8364	-0.31	2.0836	0.2596	0.6838	0.0366	-0.1024	-0.1863	-0.0022	0.054	0.2351	0.1522	0.0099	-0.0647	0.3004	-0.0394	-0.0562	0.1712	0.0211	0.2473	32.8626	14.3317	358.6313
9	1.4813	-0.2815	-0.2129	1.4672	0.1677	1.2301	0.0391	-0.2794	0.0748	0.1093	0.1347	-0.3665	0.0282	0.2595	-0.1278	0.269	0.0144	-0.0369	0.3114	-0.0629	0.2646	53.2964	20.9288	366.3873
10	2.2572	-0.7052	-0.0812	1.4337	0.0359	0.6986	0.0629	-0.1194	-0.0131	-0.1576	0.0213	-0.2764	0.1193	0.1905	-0.0644	0.3504	0.0638	-0.0137	0.2719	-0.0331	0.3035	55.9549	10.6901	353.4246
11	1.9139	-1.5681	-0.2773	2.5469	0.6405	0.6571	0.1183	0.1499	-0.2672	-0.2149	-0.1115	0.3786	0.1108	0.022	0.0138	0.3562	-0.0072	-0.112	0.2325	-0.0203	0.3064	25.0179	18.7257	346.7337
12	4.255	0.5898	1.3816	3.7654	0.9222	2.7401	0.2479	0.4631	0.0291	-0.6053	-0.2943	0.2713	-0.0039	-0.2411	0.1109	0.6035	0.1889	-0.1311	0.4046	-0.028	0.2891	12.5736	44.1804	337.1235
13	0.9882	-0.2647	0.3525	0.984	-0.1017	0.6664	0.2251	0.2415	-0.2884	-0.5681	-0.1351	0.4513	0.1415	-0.0929	-0.0757	0.4875	0.0432	-0.1481	0.2499	-0.0544	0.3689	19.2823	30.1466	344.0682
14	1.5494	-0.5134	-0.0338	2.4338	-0.0296	0.6998	0.1251	-0.0537	-0.1942	-0.0988	-0.1781	0.2163	-0.0384	0.0103	-0.002	0.3311	-0.0091	-0.0362	0.1908	-0.0093	0.2952	29.5247	23.0618	355.7443

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 25 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 107 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 108 through 178 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 179 through 198 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 199 through 262 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 263 through 358 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 359 through 386 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 56 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 57 through 120 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 121 through 236 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 237 through 262 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 263 through 281 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 282 through 358 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 359 through 386 )

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