PDB-5irp: Crystal structure of the alanine racemase Bsu17640 from Bacillus ...

ID or keywords:

Entry

Database: PDB / ID: 5irp

Title

Crystal structure of the alanine racemase Bsu17640 from Bacillus subtilis

Components

Alanine racemase 2

Keywords

ISOMERASE / racemase / PLP

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: 2.1 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	Mar 14, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Mar 29, 2017	Provider: repository / Type: Initial release
Revision 2.0	Apr 24, 2019	Group: Atomic model / Data collection / Database references Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_database_proc Item: _atom_site.occupancy / _citation.country ..._atom_site.occupancy / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.1	May 8, 2019	Group: Advisory / Data collection / Database references Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_validate_close_contact Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.2	Jan 10, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_label_seq_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_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 2.3	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5irp.cif.gz	333.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5irp_validation.pdf.gz	496.7 KB	Display	wwPDB validaton report
Full document	5irp_full_validation.pdf.gz	500.3 KB	Display
Data in XML	5irp_validation.xml.gz	36.4 KB	Display
Data in CIF	5irp_validation.cif.gz	55.1 KB	Display
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Related structure data

Related structure data	6q70C 6q71C 6q72C 3ha1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6q70-d 6q72-1 3uw6-2 1l6f-d 4ecl-1 3w7u-1 1sft-d 4ils-2 3gfr-d 1niu-d 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
Related items in Molecule of the Month	#263 - Nov 2021 Acetohydroxyacid Synthase similarity (1)

Deposited unit

A: Alanine racemase 2

B: Alanine racemase 2

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	72.888, 72.888, 332.833
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	A-413- MG
2	1	B-412- MG
3	1	A-501- HOH
4	1	B-501- HOH

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Protein , 1 types, 2 molecules AB

#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 (strain 168) (bacteria) Gene: alr2, yncD, BSU17640 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P94494, alanine racemase

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Non-polymers , 8 types, 707 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-UAH / (5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate / 4'-deformyl pyidoxal phosphote Mass: 219.132 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₁₀NO₅P
#4: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Mg
#8: Chemical	ChemComp-CO2 / CARBON DIOXIDE Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO₂
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 668 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.53 Å³/Da / Density % sol: 51.41 %
Crystal grow	Temperature: 290 K / Method: microbatch / pH: 8.5 Details: 15% PEG 4000 0.2M Magnesium Chloride 0.1M Tris pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 30, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.1→49.15 Å / Num. obs: 53961 / % possible obs: 100 % / Redundancy: 11.4 % / R_merge(I) obs: 0.096 / Net I/σ(I): 21.5
Reflection shell	Resolution: 2.1→2.21 Å / Redundancy: 10.2 % / R_merge(I) obs: 0.553 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
Aimless		data scaling
Coot		model building
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3HA1

3ha1

Resolution: 2.1→49.15 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.34

	R_factor	Num. reflection	% reflection
R_free	0.1986	2734	5.08 %
R_work	0.1544	-	-
obs	0.1567	53832	99.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→49.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6018	0	116	668	6802

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6247
X-RAY DIFFRACTION	f_angle_d	0.807	8433
X-RAY DIFFRACTION	f_dihedral_angle_d	15.815	3782
X-RAY DIFFRACTION	f_chiral_restr	0.052	962
X-RAY DIFFRACTION	f_plane_restr	0.005	1051

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 (%)
2.1-2.1362	0.2607	156	0.2013	2471	X-RAY DIFFRACTION	100
2.1362-2.1751	0.234	146	0.1773	2480	X-RAY DIFFRACTION	100
2.1751-2.2169	0.2291	106	0.1648	2523	X-RAY DIFFRACTION	100
2.2169-2.2622	0.2018	131	0.1667	2528	X-RAY DIFFRACTION	100
2.2622-2.3114	0.2199	138	0.1621	2466	X-RAY DIFFRACTION	100
2.3114-2.3651	0.2226	151	0.1618	2520	X-RAY DIFFRACTION	100
2.3651-2.4243	0.2477	115	0.1592	2534	X-RAY DIFFRACTION	100
2.4243-2.4898	0.2184	134	0.1541	2496	X-RAY DIFFRACTION	100
2.4898-2.5631	0.2235	150	0.16	2510	X-RAY DIFFRACTION	100
2.5631-2.6458	0.2177	156	0.1617	2504	X-RAY DIFFRACTION	100
2.6458-2.7404	0.236	119	0.163	2547	X-RAY DIFFRACTION	100
2.7404-2.8501	0.2352	135	0.1633	2535	X-RAY DIFFRACTION	100
2.8501-2.9798	0.2146	117	0.174	2551	X-RAY DIFFRACTION	100
2.9798-3.1368	0.2455	125	0.1636	2586	X-RAY DIFFRACTION	100
3.1368-3.3333	0.1985	125	0.1656	2581	X-RAY DIFFRACTION	100
3.3333-3.5906	0.1835	136	0.1442	2551	X-RAY DIFFRACTION	100
3.5906-3.9518	0.1901	150	0.134	2595	X-RAY DIFFRACTION	100
3.9518-4.5233	0.147	144	0.1234	2622	X-RAY DIFFRACTION	100
4.5233-5.6975	0.1571	153	0.1354	2649	X-RAY DIFFRACTION	100
5.6975-49.1663	0.174	147	0.1682	2849	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	0.4872	-0.6517	0.2248	2.7042	-0.5932	0.2957	0.1075	-0.1693	0.2526	-0.0062	0.0193	-0.1504	-0.1219	0.045	-0.0619	0.3283	-0.0427	0.0578	0.128	-0.049	0.1746	35.9673	50.5622	359.6233
2	3.1379	0.6633	0.0859	3.3179	-1.0946	2.448	0.1059	-0.3093	-0.0901	0.0303	0.0872	0.4606	0.0836	-0.4399	-0.1857	0.2259	-0.0282	0.0352	0.2269	0.0184	0.1917	12.9213	45.0933	364.9002
3	2.3933	0.4427	-1.408	1.8743	-1.43	3.3328	0.2286	0.0322	0.1355	-0.2386	-0.0157	0.2402	-0.1633	-0.3316	-0.1907	0.2826	0.0622	-0.0368	0.1474	-0.0121	0.209	11.1683	54.8067	348.9904
4	0.9599	-0.6072	0.3075	0.8926	-0.1805	0.2899	0.0996	-0.0018	0.1313	-0.2906	-0.05	-0.1484	-0.1081	-0.0236	-0.0109	0.3204	-0.0082	0.0924	0.0895	-0.0131	0.2222	34.1763	53.5344	348.7864
5	0.0549	-0.2638	0.0228	1.7642	0.1371	0.5608	0.167	0.0496	0.1728	-0.4794	-0.0511	-0.4115	-0.1179	0.1834	-0.0722	0.4191	0.0009	0.1684	0.1497	0.0085	0.3237	55.1886	30.9218	343.2563
6	2.0141	0.7402	-0.0376	2.6975	0.1419	0.771	0.1677	-0.14	0.1963	-0.1896	-0.1603	-0.2699	-0.1317	0.0991	-0.1166	0.4253	-0.0128	0.1098	0.0322	0.0065	0.2449	43.1496	43.5616	351.4652
7	0.9645	-1.5394	0.1802	4.9827	-0.0021	0.6971	0.0095	-0.0293	-0.2517	0.1387	-0.0102	0.3196	0.1708	-0.013	0.0306	0.3281	-0.0476	-0.019	0.0914	0.0115	0.1842	32.0297	14.5481	356.7712
8	1.9334	-0.2738	-0.1071	1.182	0.4253	1.4353	0.1549	-0.2202	-0.0362	-0.0222	0.0146	-0.2177	0.1323	0.3009	-0.1563	0.2644	-0.0024	-0.0094	0.1475	0.0079	0.1906	54.0516	14.529	357.3976
9	2.8695	-2.5876	-0.8826	2.9778	0.9414	0.2949	0.0613	0.1084	-0.2325	-0.2474	-0.1188	0.3478	0.0177	-0.0521	0.092	0.3243	-0.0116	-0.1038	0.1352	-0.0153	0.2299	25.0206	18.8297	346.2349
10	8.9686	0.1931	1.5639	2.8325	-0.4565	2.5118	0.3398	0.5229	-0.1421	-0.61	-0.1196	0.3878	-0.0893	-0.2823	-0.2126	0.4917	0.1088	-0.1376	0.2206	-0.0142	0.2359	12.2506	44.0541	336.5492
11	1.8179	0.5958	-0.2059	2.0601	0.2674	0.7551	0.0827	0.157	-0.0658	-0.5011	-0.0828	0.3485	0.0384	-0.1159	0.011	0.4121	0.0171	-0.113	0.1393	-0.0229	0.2565	18.2801	32.171	344.0613
12	2.7183	0.7056	-0.5502	4.5439	-0.3387	1.145	0.1043	-0.0792	-0.0405	-0.1774	-0.1307	0.2715	-0.022	0.026	0.0119	0.2776	0.017	-0.0436	0.0654	-0.0132	0.1936	28.3135	22.6135	351.0004

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 75 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 76 through 132 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 133 through 198 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 199 through 262 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 263 through 345 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 346 through 386 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 46 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 47 through 236 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 237 through 262 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 263 through 282 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 283 through 345 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 346 through 386 )

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