PDB-4c75: Consensus (ALL-CON) beta-lactamase class A

ID or keywords:

Entry

Database: PDB / ID: 4c75

Title

Consensus (ALL-CON) beta-lactamase class A

Components

BETA-LACTAMASE

Keywords

HYDROLASE /

ANTIBIOTIC RESISTANCE

Function / homology

Beta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta /

ACETATE ION / DI(HYDROXYETHYL)ETHER

Function and homology information

Biological species

SYNTHETIC CONSTRUCT (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Gavira, J.A. / Risso, V.A. / Sanchez-Ruiz, J.M.

Citation

Journal: Proteins / Year: 2014
Title: Phenotypic Comparisons of Consensus Variants Versus Laboratory Resurrections of Precambrian Proteins.
Authors: Risso, V.A. / Gavira, J.A. / Gaucher, E.A. / Sanchez-Ruiz, J.M.

History

Deposition	Sep 19, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 16, 2014	Provider: repository / Type: Initial release
Revision 1.1	May 28, 2014	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4c75.cif.gz	421.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4c75.ent.gz	346.3 KB	Display	PDB format
PDBx/mmJSON format	4c75.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/c7/4c75 ftp://data.pdbj.org/pub/pdb/validation_reports/c7/4c75	HTTPS FTP

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Related structure data

Related structure data	4c6yC 4b88S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1pau-d 4pma-d 6afn-d 4de1-1 6ooh-1 3v50-d 4h8r-2 4l66-d 5fqm-d 4pm7-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) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

4c6yC

4b88S

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: BETA-LACTAMASE

B: BETA-LACTAMASE

C: BETA-LACTAMASE

D: BETA-LACTAMASE

hetero molecules

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

1

A: BETA-LACTAMASE

hetero molecules

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

2

B: BETA-LACTAMASE

hetero molecules

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

3

C: BETA-LACTAMASE

hetero molecules

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

4

D: BETA-LACTAMASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	80.715, 118.834, 118.939
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 4 molecules ABCD

#1: Protein	BETA-LACTAMASE / Mass: 27845.354 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Description: RESURRECTED SEQUENCE, ANCESTRAL RECONSTRUCTED / Plasmid: PET24 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: beta-lactamase

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Non-polymers , 5 types, 742 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 726 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	RESURRECTED SEQUENCE, ANCESTRAL RECONSTRUCTED

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.19 Å³/Da / Density % sol: 44 % / Description: NONE
Crystal grow	pH: 4.6 Details: COUNTERDIFFUSION CSK24KIT C18: 25% PEG 4K, 0.2M NH4 SULPHATE, 0.1M NA- ACETATE PH 4.60

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.954
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.954 Å / Relative weight: 1
Reflection	Resolution: 2.2→47.88 Å / Num. obs: 58758 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 7.4 % / B_iso Wilson estimate: 25.97 Å² / R_merge(I) obs: 0.13 / Net I/σ(I): 13.13
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.66 / Mean I/σ(I) obs: 3.15 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B88

4b88

Resolution: 2.2→47.85 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 22.67 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2276	2971	5.1 %
R_work	0.1788	-	-
obs	0.1813	58749	99.98 %

Solvent computation

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

Displacement parameters

B_iso mean: 37.2 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→47.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7811	0	77	726	8614

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	8120
X-RAY DIFFRACTION	f_angle_d	1	11065
X-RAY DIFFRACTION	f_dihedral_angle_d	12.372	2956
X-RAY DIFFRACTION	f_chiral_restr	0.063	1281
X-RAY DIFFRACTION	f_plane_restr	0.005	1457

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 (%)
2.2-2.2361	0.2901	141	0.2174	2635	X-RAY DIFFRACTION	100
2.2361-2.2747	0.2622	124	0.2118	2624	X-RAY DIFFRACTION	100
2.2747-2.316	0.2768	155	0.2094	2595	X-RAY DIFFRACTION	100
2.316-2.3606	0.2551	159	0.197	2602	X-RAY DIFFRACTION	100
2.3606-2.4087	0.2465	135	0.193	2614	X-RAY DIFFRACTION	100
2.4087-2.4611	0.2891	124	0.1875	2663	X-RAY DIFFRACTION	100
2.4611-2.5184	0.2382	137	0.1851	2647	X-RAY DIFFRACTION	100
2.5184-2.5813	0.2788	150	0.1844	2608	X-RAY DIFFRACTION	100
2.5813-2.6511	0.2403	135	0.1839	2621	X-RAY DIFFRACTION	100
2.6511-2.7291	0.2345	154	0.1828	2624	X-RAY DIFFRACTION	100
2.7291-2.8172	0.2387	144	0.1751	2633	X-RAY DIFFRACTION	100
2.8172-2.9179	0.2062	121	0.1751	2672	X-RAY DIFFRACTION	100
2.9179-3.0347	0.253	145	0.1812	2628	X-RAY DIFFRACTION	100
3.0347-3.1728	0.2299	121	0.1833	2672	X-RAY DIFFRACTION	100
3.1728-3.34	0.2455	119	0.1739	2692	X-RAY DIFFRACTION	100
3.34-3.5492	0.2136	158	0.1654	2631	X-RAY DIFFRACTION	100
3.5492-3.8232	0.2072	173	0.1668	2653	X-RAY DIFFRACTION	100
3.8232-4.2077	0.2085	139	0.1641	2683	X-RAY DIFFRACTION	100
4.2077-4.8161	0.2016	153	0.154	2687	X-RAY DIFFRACTION	100
4.8161-6.0658	0.2032	125	0.186	2743	X-RAY DIFFRACTION	100
6.0658-47.8615	0.2138	159	0.1901	2851	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	7.5185	-1.8046	-3.3632	2.6682	1.9801	4.0984	0.1185	-0.1366	0.3767	-0.0745	0.0193	0.0417	-0.2835	0.2782	-0.2653	0.3065	0.003	0.021	0.1494	0.0266	0.2431	12.0313	-1.8405	-29.0553
2	0.4097	-0.003	0.0992	1.6848	0.7657	0.3482	0.0423	0.0392	0.0232	0.2653	-0.0284	0.0584	0.1127	-0.1279	-0.0253	0.2339	-0.0151	0.004	0.1516	0.0139	0.1247	9.4953	-20.3611	-24.2161
3	5.6881	-3.9393	-1.8476	8.5653	2.4288	3.8878	-0.1177	-0.0958	-0.4722	0.4345	-0.1467	0.7516	0.2958	-0.6464	0.3153	0.345	-0.0991	0.0156	0.3504	0.014	0.2536	-10.1197	-33.2022	-15.0419
4	0.9479	-0.0842	-0.6619	2.2732	0.0602	1.2915	-0.0298	-0.0067	-0.1289	0.2242	-0.0382	0.2706	0.2826	-0.2853	0.0576	0.2743	-0.0556	0.0179	0.2338	0.0146	0.1826	0.7328	-27.4471	-19.0175
5	6.2125	0.1404	-2.1409	3.306	-2.1961	8.0241	0.1622	0.5115	-0.0422	-0.3887	-0.2006	0.3973	0.3238	-0.4035	0.0804	0.1966	0.0632	-0.0414	0.1855	-0.001	0.2403	-1.2608	-17.8223	-33.3371
6	2.1192	-1.9171	-1.3923	2.0298	1.3182	4.2288	0.0764	0.135	0.1174	-0.1231	-0.0051	-0.0021	-0.0727	-0.1416	-0.1388	0.1462	-0.0041	0.0076	0.1437	0.0167	0.1536	4.4874	-12.7557	-30.3688
7	2.2745	1.4999	1.4749	2.7484	1.5242	3.0934	-0.0374	-0.3478	0.1286	0.1389	-0.1482	0.0904	0.1634	-0.2975	0.1706	0.1604	-0.0036	0.0258	0.2318	0.0011	0.1494	6.8955	1.9081	12.424
8	3.5574	2.3376	-0.1119	2.2819	-0.269	0.4952	-0.31	0.5341	0.1488	-0.3784	0.1006	-0.3053	-0.4128	0.3218	0.1625	0.3607	-0.0823	0.0325	0.3197	0.0957	0.2922	22.7135	11.1428	-13.0291
9	6.0174	1.2281	-0.5799	3.2406	-0.1424	1.9298	0.0852	0.3332	0.2668	-0.2308	-0.1177	-0.6441	-0.3404	0.4889	0.0824	0.3417	-0.0996	0.0384	0.3379	0.0229	0.2886	26.9931	13.133	-6.8234
10	1.2857	0.3711	0.1595	3.1663	1.0812	3.8327	-0.1621	-0.0375	0.0886	-0.2284	0.142	-0.127	-0.4162	0.2612	0.0076	0.2069	-0.0252	-0.0221	0.1632	0.0102	0.216	14.0426	9.5587	-2.619
11	5.4635	0.4596	-1.1843	6.767	-2.4095	4.8195	0.0655	0.0584	-0.0737	-0.111	-0.0194	-0.3484	0.5463	0.4533	-0.0586	0.1781	0.0184	-0.0409	0.227	-0.0119	0.1487	21.2537	-3.9839	4.2767
12	1.6354	2.4477	2.1807	4.6977	2.9394	4.0813	0.0572	-0.0385	-0.0895	-0.0277	-0.008	-0.1607	0.1283	-0.0538	-0.1029	0.1265	0.0153	0.0037	0.136	0.0033	0.1325	15.5419	-1.0291	9.4604
13	4.7093	-4.5367	1.7871	4.5364	-0.8449	5.6374	0.3674	0.2848	0.1848	-0.3868	-0.4565	-0.1598	0.2591	-0.0948	0.1088	0.3146	0.0022	-0.0177	0.2124	-0.0141	0.2469	-8.1136	8.1652	-27.373
14	1.042	-1.5426	0.1875	3.551	-0.8609	2.491	0.0797	0.0044	0.0533	-0.1416	-0.1893	0.0163	0.1541	0.2439	0.1441	0.1436	-0	-0.0229	0.1518	0.0075	0.1478	-5.8054	10.5864	-14.9524
15	5.1023	-1.26	-0.3833	2.6438	-0.0859	2.5137	-0.4103	-0.8054	-0.2014	0.6318	0.2176	0.3908	-0.11	-0.2031	0.2615	0.3348	0.0679	0.0815	0.3088	-0.0301	0.3235	-21.6264	19.403	6.4043
16	7.6715	0.0925	-2.2825	5.1212	1.0886	6.0575	-0.072	-0.345	-0.1028	0.0417	0.1552	0.5425	-0.3115	-0.6932	-0.1068	0.2556	0.0668	0.0702	0.4807	0.0464	0.4123	-32.0881	19.3573	-0.7498
17	6.5442	-1.4767	0.7156	3.6711	0.7452	4.6007	-0.2611	-0.9753	0.3394	0.6558	0.3228	0.1991	-0.2844	-0.1385	0.0213	0.3669	0.0581	0.0355	0.2722	0.0197	0.203	-17.2203	24.5085	1.5306
18	1.8914	0.8761	-0.2625	4.6767	-1.7379	5.1243	-0.134	-0.1052	0.1324	0.3555	0.2063	0.3055	-0.2571	-0.3164	0.0152	0.2156	0.0269	0.0188	0.2012	-0.0145	0.205	-14.8652	26.9263	-10.0092
19	2.1048	2.4271	-1.8391	4.1271	-2.9017	7.5656	-0.0124	-0.4191	-0.1717	0.2459	-0.0748	-0.2209	0.5157	0.3382	0.1932	0.2562	0.056	-0.0452	0.278	0.0134	0.2104	-8.4045	13.4356	-5.4105
20	1.8837	-0.4232	-0.5043	2.4891	-0.1808	2.3039	-0.1956	-0.2237	-0.3731	0.1588	0.086	0.2265	0.3686	-0.0927	0.0427	0.2441	0.0048	0.0215	0.1977	0.0582	0.2686	-17.2375	6.7362	-8.2567
21	5.5714	-6.8157	3.7153	9.0453	-3.3511	4.2965	-0.1617	0.1211	-0.718	-0.0579	0.1126	0.4968	0.1024	0.0653	-0.0586	0.2113	-0.03	0.0563	0.1681	0.0148	0.3001	-16.0087	4.7418	-20.9812
22	2.8841	2.8369	-2.5326	4.8458	-0.9086	3.4233	-0.11	0.3281	1.0369	0.0791	0.4655	0.2998	-0.245	-0.1203	-0.2596	0.3593	-0.0252	-0.0102	0.3282	0.0262	0.3225	-12.2328	-9.8531	22.0134
23	1.0398	0.8893	0.2734	1.1833	-0.5873	1.2994	-0.487	0.8567	-1.0947	-0.3236	0.2918	-0.8387	0.3724	0.2667	0.1037	0.4818	-0.1433	0.3475	0.6604	-0.3822	0.9686	-0.2002	-34.9553	11.3077
24	2.4364	1.0735	-0.2195	1.2497	0.6184	0.6897	-0.5338	0.7182	-1.4353	-0.5301	0.4021	-0.6427	0.1932	-0.0362	0.2902	0.517	-0.246	0.256	0.5418	-0.3419	0.7884	-7.2729	-32.7539	12.3152
25	5.0398	1.7547	-0.9008	2.8099	0.499	1.107	-0.3757	-0.0249	-0.7467	0.0334	0.1172	-0.4566	0.1183	0.2618	0.2543	0.2632	-0.0271	0.0409	0.2507	0.0195	0.269	-3.0826	-22.4625	23.7554

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 26 THROUGH 40 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 41 THROUGH 85 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 86 THROUGH 105 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 106 THROUGH 212 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 213 THROUGH 238 )
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 240 THROUGH 290 )
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 26 THROUGH 68 )
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESID 69 THROUGH 98 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 99 THROUGH 154 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 155 THROUGH 212 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 213 THROUGH 238 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 240 THROUGH 290 )
13	X-RAY DIFFRACTION	13	CHAIN C AND (RESID 26 THROUGH 40 )
14	X-RAY DIFFRACTION	14	CHAIN C AND (RESID 41 THROUGH 68 )
15	X-RAY DIFFRACTION	15	CHAIN C AND (RESID 69 THROUGH 98 )
16	X-RAY DIFFRACTION	16	CHAIN C AND (RESID 99 THROUGH 131 )
17	X-RAY DIFFRACTION	17	CHAIN C AND (RESID 132 THROUGH 155 )
18	X-RAY DIFFRACTION	18	CHAIN C AND (RESID 156 THROUGH 179 )
19	X-RAY DIFFRACTION	19	CHAIN C AND (RESID 180 THROUGH 194 )
20	X-RAY DIFFRACTION	20	CHAIN C AND (RESID 195 THROUGH 271 )
21	X-RAY DIFFRACTION	21	CHAIN C AND (RESID 272 THROUGH 290 )
22	X-RAY DIFFRACTION	22	CHAIN D AND (RESID 26 THROUGH 40 )
23	X-RAY DIFFRACTION	23	CHAIN D AND (RESID 41 THROUGH 155 )
24	X-RAY DIFFRACTION	24	CHAIN D AND (RESID 156 THROUGH 212 )
25	X-RAY DIFFRACTION	25	CHAIN D AND (RESID 213 THROUGH 290 )

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