PDB-8z7m: The crystal structure of AFM-1

ID or keywords:

Entry

Database: PDB / ID: 8z7m

Title

The crystal structure of AFM-1

Components

Metallo-beta-lactamase type 2

Keywords

METAL BINDING PROTEIN / AFM-1 / Metallo-beta-lactamase

Function / homology

Function and homology information

antibiotic catabolic process / periplasmic space / hydrolase activity / response to antibiotic / metal ion binding
Similarity search - Function

Biological species

Alcaligenes faecalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.6 Å

Authors

Xiao, Y.J. / Wang, Z.F.

Funding support

China, 1items

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Structural insight into the subclass B1 metallo-beta-lactamase AFM-1.
Authors: Niu, W. / Ti, R. / Li, D. / Dong, R. / Dong, J. / Ye, Y. / Xiao, Y. / Wang, Z.

History

Deposition	Apr 20, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Feb 26, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8z7m.cif.gz	191.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8z7m.ent.gz	152.8 KB	Display	PDB format
PDBx/mmJSON format	8z7m.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/z7/8z7m ftp://data.pdbj.org/pub/pdb/validation_reports/z7/8z7m	HTTPS FTP

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Related structure data

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	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (3) #105 - Sep 2008 Ribonuclease A similarity (2)

Deposited unit

A: Metallo-beta-lactamase type 2

B: Metallo-beta-lactamase type 2

hetero molecules

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

1

A: Metallo-beta-lactamase type 2

hetero molecules

defined by author&software
Evidence: gel filtration
25.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Metallo-beta-lactamase type 2

hetero molecules

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

Unit cell

Length a, b, c (Å)	48.960, 105.459, 106.359
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Metallo-beta-lactamase type 2 / AFM-1 / B2 metallo-beta-lactamase / Metallo-beta-lactamase type II Mass: 25554.617 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: blaAFM / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G5BD68, beta-lactamase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.69 Å³/Da / Density % sol: 54.21 %
Crystal grow	Temperature: 289.15 K / Method: batch mode Details: 30% (w/v) PEG 8000, 100 mM imidazole/Hydrochloric acid pH 8.0, and 200 mM NaCl

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å
Detector	Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jan 16, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97891 Å / Relative weight: 1
Reflection	Resolution: 2.6→50 Å / Num. obs: 17530 / % possible obs: 99.8 % / Redundancy: 13 % / B_iso Wilson estimate: 53.26 Å² / CC_1/2: 0.99 / Net I/σ(I): 16.2
Reflection shell	Resolution: 2.6→2.69 Å / Num. unique obs: 1694 / CC_1/2: 0.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.19_4092: ???)	refinement
XDS		data scaling
PHENIX		model building
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

SAD / Resolution: 2.6→47.48 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.73 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2583	1745	9.95 %
R_work	0.2096	-	-
obs	0.2144	17530	99.86 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.6→47.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3436	0	4	129	3569

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3525
X-RAY DIFFRACTION	f_angle_d	0.444	4803
X-RAY DIFFRACTION	f_dihedral_angle_d	4.238	485
X-RAY DIFFRACTION	f_chiral_restr	0.041	539
X-RAY DIFFRACTION	f_plane_restr	0.003	637

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 (%)
2.6-2.68	0.3418	142	0.2674	1272	X-RAY DIFFRACTION	99
2.68-2.76	0.3337	140	0.2707	1296	X-RAY DIFFRACTION	100
2.76-2.86	0.3345	145	0.2793	1293	X-RAY DIFFRACTION	100
2.86-2.98	0.3378	143	0.2664	1282	X-RAY DIFFRACTION	100
2.98-3.11	0.3148	142	0.2428	1299	X-RAY DIFFRACTION	100
3.11-3.28	0.2806	146	0.2213	1324	X-RAY DIFFRACTION	100
3.28-3.48	0.2737	148	0.2259	1287	X-RAY DIFFRACTION	100
3.48-3.75	0.2835	139	0.2035	1325	X-RAY DIFFRACTION	100
3.75-4.13	0.2394	147	0.184	1301	X-RAY DIFFRACTION	100
4.13-4.72	0.2115	145	0.1768	1328	X-RAY DIFFRACTION	100
4.73-5.95	0.222	150	0.1961	1348	X-RAY DIFFRACTION	100
5.95-47.48	0.2307	158	0.1991	1430	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	2.9385	-0.0051	1.9917	5.0725	0.9881	4.795	-0.4755	-0.5007	-0.1302	1.1099	0.1344	0.7576	0.4061	0.6186	0.0284	0.4329	-0.023	-0.0096	0.5525	0.0892	0.5689	25.923	2.148	12.746
2	3.4337	-0.3663	1.0996	4.1737	0.5515	2.7944	0.1151	0.2851	-0.634	-0.2361	-0.1518	-0.0542	0.1298	0.5274	-0.1355	0.4206	0.0132	-0.0022	0.4433	0.026	0.4688	26.86	3.33	3.257
3	4.2505	-2.582	-1.4705	6.846	1.3503	4.7536	0.1274	-0.2909	-0.5405	0.2512	-0.2387	0.0025	0.2548	-0.0015	-0.1728	0.3783	-0.0933	0.0494	0.3888	0.0007	0.6057	16.632	6.127	4.685
4	2.4543	0.2871	0.498	3.6856	-1.0709	3.5201	0.027	-0.3596	-0.3292	0.3767	0.1978	0.3746	0.3664	-0.1695	-0.1711	0.3466	-0.0582	0.0416	0.3393	0.032	0.5179	15.273	0.556	7.673
5	1.3938	-0.247	2.1531	5.9485	-1.0343	3.3117	0.1367	0.3509	-0.2322	-0.7341	-0.0018	0.2594	0.5471	0.0143	-0.1343	0.4515	0.0163	-0.0565	0.4234	-0.0553	0.5028	16.215	6.257	-7.194
6	1.6292	-1.3063	1.1883	3.5424	-1.145	2.2345	-0.102	0.0793	-0.4642	-0.3046	0.0563	0.6103	0.164	-0.1856	-0.0946	0.2701	-0.0212	0.0431	0.4108	-0.0192	0.4664	16.015	17.684	-4.496
7	3.0528	0.5843	-0.2755	3.7708	-0.8407	3.5344	0.4325	0.1587	0.4223	-0.0673	-0.2177	-0.2574	-0.3812	0.1869	0.0559	0.3036	0.0284	0.0264	0.4393	-0.0299	0.4263	28.306	16.371	3.979
8	4.9881	0.6386	0.5578	4.0792	0.5887	3.9868	-0.0723	0.5443	0.1648	-0.4011	0.1871	-0.1335	0.3122	0.2626	-0.0663	0.2715	0.0137	0.0529	0.4625	-0.0294	0.5356	32.298	19.095	-8.239
9	4.6134	-0.1632	0.6206	1.6027	1.6742	2.8789	-0.0405	0.0995	-0.1031	-0.2156	0.1058	-0.2882	-0.1501	0.1878	-0.0566	0.2944	-0.0249	-0.0025	0.3816	-0.0741	0.5313	35.036	19.544	-0.955
10	2.6666	-1.4144	-0.1102	5.8032	0.8301	4.7639	-0.0136	0.2223	0.0374	-0.2646	-0.3716	-1.4972	-1.0251	1.156	0.6862	0.7491	-0.254	0.0215	0.8832	0.1115	0.4513	23.818	26.74	-36.696
11	3.2126	0.8546	1.0798	1.2443	-1.0316	4.6288	-0.5077	0.1618	0.1233	-0.357	0.0752	-0.5894	-0.53	0.4281	0.2272	0.6392	-0.0497	-0.0163	0.4714	0.0093	0.4627	15.655	27.074	-31.469
12	3.4381	-0.2877	0.2916	3.0386	-0.2768	3.5172	-0.6166	0.5428	0.6549	-0.5745	0.2755	-0.4146	-0.7461	0.1681	0.2998	0.9645	-0.1833	0.0162	0.475	0.0923	0.5669	16.519	35.588	-36.31
13	2.539	0.0976	-0.3892	2.5637	2.3866	4.2518	-0.2716	-0.3186	0.2091	-0.318	-0.3835	0.3076	-1.1296	-0.9541	0.4974	0.7028	0.1664	-0.222	0.5967	-0.1359	0.6816	2.011	30.892	-28.744
14	5.2162	-1.207	-0.73	2.9369	1.1374	2.4936	-0.2032	1.4456	0.3024	-0.9407	-0.1658	0.548	-1.4854	-1.3041	0.4698	0.9735	0.1157	-0.291	0.8066	-0.0571	0.508	-1.096	24.784	-42
15	3.5275	0.5602	0.8515	4.0858	0.5581	5.2763	-0.1425	-0.0138	-0.1967	-0.234	0.0985	0.5282	0.7423	-0.0028	0.0788	0.4565	-0.0229	-0.0205	0.5041	-0.1104	0.4524	5.955	17.558	-33.398
16	6.0015	-0.914	-0.8183	5.2562	0.4115	6.9925	-0.2409	-2.0131	1.1777	1.0836	0.3196	-0.1629	0.8288	0.0082	-0.0078	0.5016	-0.0392	-0.121	0.6943	-0.0719	0.6138	8.063	11.571	-21.516
17	3.9756	0.8163	2.0314	5.0903	0.6185	2.9757	0.494	0.2589	-0.3819	-0.4055	-0.3364	0.2687	0.1288	-0.1507	-0.1689	0.4785	-0.0143	0.0028	0.4841	-0.0452	0.5127	8.018	12.085	-34.678
18	1.9816	0.285	1.2772	5.3103	-2.0757	1.8224	0.6099	-0.758	0.308	0.437	-0.1761	-0.4939	1.791	0.5535	-0.1712	0.9369	-0.3163	-0.0502	0.6972	-0.069	0.6057	6.72	4.598	-26.279

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 42:57 )	A	42 - 57
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 58:82 )	A	58 - 82
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 83:94 )	A	83 - 94
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 95:118 )	A	95 - 118
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 119:152 )	A	119 - 152
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 153:194 )	A	153 - 194
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 195:215 )	A	195 - 215
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 216:239 )	A	216 - 239
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 240:270 )	A	240 - 270
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 43:57 )	B	43 - 57
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 58:94 )	B	58 - 94
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 95:118 )	B	95 - 118
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 119:166 )	B	119 - 166
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 167:183 )	B	167 - 183
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 184:212 )	B	184 - 212
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 213:227 )	B	213 - 227
17	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 228:255 )	B	228 - 255
18	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 256:269 )	B	256 - 269

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