PDB-8brr: Crystal structure of a variant of penicillin G acylase from Bacil...

ID or keywords:

Entry

Database: PDB / ID: 8brr

Title

Crystal structure of a variant of penicillin G acylase from Bacillaceae i. s. sp. FJAT-27231 with reduced surface entropy and additionally engineered crystal contact

Components

(Penicillin G ...) x 2

Keywords

HYDROLASE / Penicillin / Acylase / Surface entropy reduction / Crystal contact engineering / Crystallizability

Function / homology

Function and homology information

hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / antibiotic biosynthetic process / metal ion binding
Similarity search - Function

Biological species

Bacillus sp. FJAT-27231 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Wichmann, J. / Mayer, J. / Mattes, H. / Lukat, P. / Blankenfeldt, W. / Biedendieck, R.

Funding support

Germany, 1items

Citation

Journal: Cryst.Growth Des. / Year: 2023
Title: Multistep Engineering of a Penicillin G Acylase for Systematic Improvement of Crystallization Efficiency
Authors: Wichmann, J. / Mayer, J. / Hintmann, M. / Lukat, P. / Blankenfeldt, W. / Biedendieck, R.

History

Deposition	Nov 23, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 3, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8brr.cif.gz	846 KB	Display	PDBx/mmCIF format
PDB format	pdb8brr.ent.gz	711.4 KB	Display	PDB format
PDBx/mmJSON format	8brr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8brr_validation.pdf.gz	464.1 KB	Display	wwPDB validaton report
Full document	8brr_full_validation.pdf.gz	468.3 KB	Display
Data in XML	8brr_validation.xml.gz	59.6 KB	Display
Data in CIF	8brr_validation.cif.gz	89 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/br/8brr ftp://data.pdbj.org/pub/pdb/validation_reports/br/8brr	HTTPS FTP

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Related structure data

Related structure data	8brqC 8brsC 8brtC 6nvxS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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	#166 - Oct 2013 Proteasome similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #176 - Aug 2014 Dynein similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: Penicillin G acylase

B: Penicillin G acylase

C: Penicillin G acylase

D: Penicillin G acylase

hetero molecules

173 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Penicillin G acylase

B: Penicillin G acylase

hetero molecules

defined by author&software
Evidence: gel filtration
86.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Penicillin G acylase

D: Penicillin G acylase

hetero molecules

defined by author&software
86.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.276, 139.227, 100.638
Angle α, β, γ (deg.)	90.00, 91.51, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Penicillin G ... , 2 types, 4 molecules ACBD

#1: Protein	Penicillin G acylase Mass: 24683.795 Da / Num. of mol.: 2 / Mutation: K201A, K202A, E203A Source method: isolated from a genetically manipulated source Details: penicillin G acylase, alpha-subunit, Surface entropy reduction variant (variant hypho_3) Source: (gene. exp.) Bacillus sp. FJAT-27231 (bacteria) / Gene: AC623_04440 / Production host: Priestia megaterium (bacteria) / References: UniProt: A0A0K9H482
#2: Protein	Penicillin G acylase Mass: 61372.836 Da / Num. of mol.: 2 / Mutation: K135A, E136A, K137A, K403A, E404A, E405A, K408V Source method: isolated from a genetically manipulated source Details: penicillin G acylase, beta-subunit, Surface entropy reduction variant (variant hypho_3) Source: (gene. exp.) Bacillus sp. FJAT-27231 (bacteria) / Gene: AC623_04440 / Production host: Priestia megaterium (bacteria) / References: UniProt: A0A0K9H482

#1: Protein

Penicillin G acylase

Mass: 24683.795 Da / Num. of mol.: 2 / Mutation: K201A, K202A, E203A
Source method: isolated from a genetically manipulated source
Details: penicillin G acylase, alpha-subunit, Surface entropy reduction variant (variant hypho_3)
Source: (gene. exp.)

Bacillus sp. FJAT-27231 (bacteria) / Gene: AC623_04440 / Production host:

Priestia megaterium (bacteria) / References: UniProt: A0A0K9H482

#2: Protein

Penicillin G acylase

Mass: 61372.836 Da / Num. of mol.: 2 / Mutation: K135A, E136A, K137A, K403A, E404A, E405A, K408V
Source method: isolated from a genetically manipulated source
Details: penicillin G acylase, beta-subunit, Surface entropy reduction variant (variant hypho_3)
Source: (gene. exp.)

Bacillus sp. FJAT-27231 (bacteria) / Gene: AC623_04440 / Production host:

Priestia megaterium (bacteria) / References: UniProt: A0A0K9H482

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Non-polymers , 4 types, 1117 molecules

#3: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#4: Chemical	ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₂
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1109 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES pH 7.5 40 mg/ml PEG 8000 Cryo-protection: 10 % (v/v) 2,3-(R,R)-butanediol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 8, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 1.95→100.6 Å / Num. obs: 109804 / % possible obs: 90.2 % / Redundancy: 3.7 % / CC_1/2: 0.994 / R_merge(I) obs: 0.104 / R_pim(I) all: 0.06 / R_rim(I) all: 0.121 / Χ²: 0.87 / Net I/σ(I): 8 / Num. measured all: 411100
Reflection shell	Resolution: 1.95→2.06 Å / % possible obs: 92.4 % / Redundancy: 3.8 % / R_merge(I) obs: 0.466 / Num. measured all: 62405 / Num. unique obs: 16432 / CC_1/2: 0.863 / R_pim(I) all: 0.27 / R_rim(I) all: 0.541 / Χ²: 0.78 / Net I/σ(I) obs: 3

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Processing

Software

Name	Version	Classification
PHENIX	1.20-4459	refinement
autoPROC		data processing
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6NVX

6nvx

Resolution: 1.95→50.3 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.25 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2322	5321	4.86 %
R_work	0.1907	-	-
obs	0.1928	109538	89.93 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.95→50.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11610	0	46	1109	12765

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11984
X-RAY DIFFRACTION	f_angle_d	0.666	16191
X-RAY DIFFRACTION	f_dihedral_angle_d	14.59	4403
X-RAY DIFFRACTION	f_chiral_restr	0.047	1651
X-RAY DIFFRACTION	f_plane_restr	0.006	2095

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 (%)
1.95-1.98	0.3555	194	0.2993	3845	X-RAY DIFFRACTION	99
1.98-2	0.3145	183	0.2662	3779	X-RAY DIFFRACTION	99
2-2.02	0.2731	187	0.2266	3801	X-RAY DIFFRACTION	99
2.02-2.05	0.3306	173	0.2189	3812	X-RAY DIFFRACTION	98
2.05-2.08	0.3208	22	0.3264	481	X-RAY DIFFRACTION	13
2.08-2.1	0.2794	204	0.2281	3808	X-RAY DIFFRACTION	98
2.1-2.13	0.2991	187	0.2066	3795	X-RAY DIFFRACTION	98
2.13-2.17	0.2776	176	0.2052	3837	X-RAY DIFFRACTION	99
2.17-2.2	0.2804	175	0.2138	3817	X-RAY DIFFRACTION	99
2.2-2.23	0.3639	172	0.3006	3108	X-RAY DIFFRACTION	89
2.25-2.27	0.2848	106	0.2509	1870	X-RAY DIFFRACTION	92
2.27-2.32	0.252	234	0.1891	3717	X-RAY DIFFRACTION	98
2.32-2.36	0.2416	177	0.1898	3840	X-RAY DIFFRACTION	98
2.36-2.41	0.2252	168	0.1925	3730	X-RAY DIFFRACTION	96
2.41-2.46	0.2071	183	0.1895	3607	X-RAY DIFFRACTION	93
2.46-2.52	0.2737	163	0.1904	3773	X-RAY DIFFRACTION	98
2.52-2.58	0.2301	195	0.183	3813	X-RAY DIFFRACTION	99
2.58-2.64	0.251	180	0.1944	3146	X-RAY DIFFRACTION	95
2.68-2.73	0.2296	145	0.1979	2502	X-RAY DIFFRACTION	96
2.73-2.82	0.2433	180	0.2017	3843	X-RAY DIFFRACTION	99
2.82-2.92	0.234	198	0.193	3839	X-RAY DIFFRACTION	99
2.92-3.03	0.2457	216	0.1919	3754	X-RAY DIFFRACTION	99
3.04-3.17	0.2356	219	0.1893	3801	X-RAY DIFFRACTION	99
3.17-3.34	0.2222	229	0.1867	3778	X-RAY DIFFRACTION	99
3.34-3.55	0.2671	135	0.1887	3126	X-RAY DIFFRACTION	80
3.55-3.82	0.2272	155	0.1781	3237	X-RAY DIFFRACTION	83
3.82-4.21	0.2062	155	0.16	3334	X-RAY DIFFRACTION	86
4.21-4.82	0.168	206	0.1515	3620	X-RAY DIFFRACTION	94
4.82-6.07	0.201	186	0.1678	3906	X-RAY DIFFRACTION	100
6.07-50.3	0.1827	218	0.1839	3898	X-RAY DIFFRACTION	99

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	7.045	3.1561	-5.1652	4.4203	0.2027	5.8934	0.1052	-0.1101	-1.4848	-0.9711	-0.3023	0.5258	2.4127	0.4146	0.0369	0.7782	0.0788	0.0833	0.4098	0.1475	0.6922	-2.1919	-50.8756	7.7053
2	1.2345	-0.1821	0.1091	0.3629	0.2543	0.6667	-0.0074	0.0173	-0.2186	0.0097	-0.0063	0.019	0.0368	0.0036	0.0097	0.2054	-0.0015	-0.0265	0.1562	0.0073	0.3187	17.1383	-46.0106	10.9163
3	0.5661	0.2016	0.0489	0.5618	0.03	-0.0437	0.0835	-0.0646	-0.2396	-0.0084	-0.0988	-0.3135	-0	0.0147	0.01	0.1953	-0.01	-0.0078	0.1919	-0.0029	0.2908	31.1927	-30.8801	14.9992
4	6.1544	1.7494	0.815	2.6242	-0.2431	1.6509	0.2291	-0.3646	0.6433	0.1393	-0.2276	0.1682	-0.0324	-0.132	-0.0137	0.2397	-0.0137	-0.0175	0.1622	-0.0494	0.287	29.2463	-6.2753	18.4806
5	0.2613	0.1751	0.2888	0.8801	0.1175	0.8743	0.0318	-0.0041	-0.0109	0.0326	0.0065	0.1131	-0.0538	-0.0916	-0.038	0.153	-0.0058	0.0095	0.1682	-0.0087	0.2465	11.1242	-27.069	12.0312
6	2.0811	1.5293	2.5923	4.1089	4.5742	5.9233	0.0987	0.1354	-0.5236	0.6584	0.5719	-0.317	0.8102	0.7935	-0.6667	0.2871	0.0562	-0.0698	0.3264	0.0049	0.387	43.1977	-40.2835	24.1771
7	3.0373	-0.035	0.9693	0.6103	-0.0086	0.746	0.0595	-0.1203	0.0136	0.1311	-0.0258	-0.0221	-0.0872	0.0148	-0.0434	0.2064	-0.005	0.0061	0.1992	-0.016	0.1966	21.6481	-24.8928	25.3404
8	0.5774	0.3968	-0.1419	0.4453	-0.2136	0.3826	0.0063	-0.0049	0.1454	0.0819	0.0227	0.0787	-0.1019	-0.0505	-0.037	0.2078	0.0227	-0.013	0.1904	-0.0198	0.2987	16.85	-8.8207	7.0752
9	1.2314	0.4623	0.9491	1.4811	0.1162	2.1393	-0.0822	0.0972	0.1633	-0.1455	0.0532	0.0058	0.0296	0.0437	0.0314	0.1539	-0.0114	0.025	0.157	0.0208	0.3212	30.5592	-5.4849	-3.3541
10	1.254	1.5248	0.2609	3.7081	-0.3124	0.5363	-0.1809	0.2533	0.0553	-0.5614	0.153	-0.1017	0.0276	0.0942	0.0369	0.3008	0.0086	0.0206	0.2594	0.0086	0.3428	31.5559	-7.3098	-13.3546
11	1.8945	-0.4546	0.1221	1.532	-0.1167	0.5824	0.0697	-0.0072	-0.2023	-0.0738	-0.0302	-0.0443	0.0368	0.1163	-0.0385	0.2041	-0.0068	-0.0042	0.196	-0.0103	0.2443	17.4583	-29.7565	-0.8403
12	1.4012	-0.6358	-0.3638	2.1476	0.856	1.429	-0.0019	0.1014	-0.2677	0.0142	0.0287	0.1541	0.0237	-0.0135	0.0188	0.1459	-0.0063	-0.0539	0.1786	-0.0115	0.2805	5.102	-34.4954	-2.4837
13	6.6316	2.6888	6.1225	1.4647	2.6373	8.3873	-0.0739	-0.0091	0.5549	-0.0994	0.051	-0.2764	-0.6826	0.1632	-0.0462	0.2631	-0.0777	0.0635	0.2104	0.0147	0.4558	32.5147	-29.6474	-43.9833
14	3.8523	-0.3415	0.431	1.631	-1.158	1.2042	-0.0832	-0.1228	0.6805	0.0332	-0.0222	-0.0545	-0.1595	-0.0789	0.1106	0.2483	0.0058	-0.0354	0.1611	-0.0305	0.3859	14.1813	-28.4363	-40.8268
15	3.6744	0.3097	2.4552	0.9736	-1.2239	3.8005	-0.0526	-0.3102	0.0644	0.0626	0.0746	0.1625	-0.176	-0.3276	0.0264	0.1934	0.026	0.012	0.2315	-0.0817	0.3636	3.5531	-33.1027	-30.5959
16	2.5995	-0.3187	1.0746	4.5177	-5.5563	9.0851	-0.0025	0.0642	0.4298	0.2773	-0.1968	-0.2068	-0.637	0.3163	0.2631	0.3086	-0.0336	-0.0012	0.2005	-0.0272	0.4622	20.2918	-22.3747	-37.3435
17	2.8	-0.7003	3.1498	0.328	-1.153	4.3593	-0.2095	-0.2116	0.2903	0.0307	0.052	-0.0451	-0.4694	-0.447	0.1749	0.2809	0.0279	-0.0213	0.1747	0.0334	0.4096	9.3363	-21.716	-46.6198
18	2.5329	1.4088	0.6078	4.5593	0.218	1.8378	0.0644	-0.1948	0.0175	-0.2222	-0.2605	0.0605	-0.1332	-0.1985	0.1896	0.1785	-0.0072	-0.0419	0.2198	-0.0008	0.2661	8.5101	-39.3874	-33.9175
19	6.2443	0.6069	0.8348	2.8505	1.7612	1.7197	-0.0246	0.0118	-0.2098	0.0077	-0.1401	0.583	0.009	-0.163	0.1403	0.1527	-0.023	-0.0134	0.1961	0.0331	0.2898	-11.292	-63.3344	-33.8476
20	5.5457	0.4129	-0.1287	3.5347	1.9324	4.9712	-0.0424	-0.246	-0.5123	0.1763	-0.0499	-0.4209	0.5774	0.2767	0.0362	0.178	0.0306	-0.0477	0.1717	0.0755	0.2578	10.4038	-67.4034	-33.0573
21	0.6738	0.3511	0.3222	1.5052	-0.092	0.7729	0.0579	0.0532	0.1075	0.0493	-0.0556	-0.0945	-0.0226	0.089	-0.0057	0.162	-0.005	-0.0217	0.1607	-0.004	0.2174	21.2614	-46.9851	-38.3717
22	2.4443	3.0748	-4.2326	5.4357	-5.4898	8.9089	0.2274	0.1353	0.8214	0.6124	0.5258	0.5962	-0.917	-0.7176	-0.7744	0.3005	0.1012	0.009	0.3903	-0.0468	0.5062	-10.7841	-34.3975	-25.5815
23	2.2267	0.2006	-0.3905	0.8765	0.0826	0.6261	0.0544	-0.2511	0.0091	0.0565	-0.0628	-0.0086	0.0225	-0.0394	0.0078	0.2036	-0.0221	-0.038	0.2078	0.0222	0.1995	11.8432	-52.7245	-27.3645
24	2.9136	1.6673	1.1855	2.0754	1.0708	1.199	0.0943	0.0753	-0.3702	-0.0256	-0.0195	-0.2245	0.1766	0.0559	-0.0823	0.2165	0.0262	-0.0224	0.1621	-0.0245	0.1917	16.8184	-66.9361	-51.013
25	1.4241	0.2737	-0.9478	1.0697	0.0148	1.6393	-0.0138	0.1269	-0.1541	-0.1654	-0.046	0.0919	0.0432	-0.1182	0.0577	0.2218	0.0082	-0.0609	0.2141	-0.0279	0.2871	1.7405	-68.6434	-54.1544
26	0.9846	1.2299	-0.7002	3.2924	-0.2714	0.69	-0.1668	0.3181	-0.1106	-0.4546	0.1557	0.0529	0.1223	-0.186	0.0091	0.3073	0.0101	-0.0838	0.3162	-0.0579	0.3898	0.7009	-66.6765	-64.3642
27	1.1392	-0.6508	0.587	1.8694	-0.3682	1.2402	0.0017	0.1162	0.2389	-0.1039	-0.1193	-0.1638	-0.1193	0.1335	0.1137	0.2186	-0.0147	0.0123	0.181	0.0464	0.2512	22.5134	-40.9302	-52.1997

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 9 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 10 through 125 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 126 through 168 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 169 through 197 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 81 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 82 through 124 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 125 through 229 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 230 through 313 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 314 through 402 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 403 through 442 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 443 through 473 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 474 through 527 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 7 through 25 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 26 through 61 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 62 through 89 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 90 through 117 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 118 through 133 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 134 through 152 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 153 through 180 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 181 through 194 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 1 through 81 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 82 through 124 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 125 through 265 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 266 through 312 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 313 through 402 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 403 through 441 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 442 through 527 )

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