PDB-9htz: M2-32, a new class A acid phosphatase

ID or keywords:

Entry

Database: PDB / ID: 9htz

Title

M2-32, a new class A acid phosphatase

Components

Phosphatase PAP2 family protein

Keywords

HYDROLASE / CLASS-A BACTERIAL / thermotolerant acid phosphatase

Function / homology

Function and homology information

acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space
Similarity search - Function

Biological species

metagenome (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Gavira, J.A. / Ramos, J.L. / Martinez-Rodriguez, S. / Recio, M.I. / de la Torre, J.

Funding support

Spain, 2items

Citation

Journal: Protein Sci. / Year: 2025
Title: Thermotolerant class A acid phosphatase active across broad pH range and diverse substrates.
Authors: Recio, M.I. / Gavira, J.A. / de La Torre, J. / Cano-Munoz, M. / Martinez-Rodriguez, S. / Daddaoua, A. / Duque, E. / Ramos, J.L.

History

Deposition	Dec 20, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 17, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9htz.cif.gz	369.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9htz.ent.gz	302.8 KB	Display	PDB format
PDBx/mmJSON format	9htz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9htz_validation.pdf.gz	516.4 KB	Display	wwPDB validaton report
Full document	9htz_full_validation.pdf.gz	523.9 KB	Display
Data in XML	9htz_validation.xml.gz	44.3 KB	Display
Data in CIF	9htz_validation.cif.gz	58 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ht/9htz ftp://data.pdbj.org/pub/pdb/validation_reports/ht/9htz	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	#225 - Sep 2018 Phytase similarity (1)

Deposited unit

A: Phosphatase PAP2 family protein

B: Phosphatase PAP2 family protein

C: Phosphatase PAP2 family protein

D: Phosphatase PAP2 family protein

hetero molecules

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

1

A: Phosphatase PAP2 family protein

C: Phosphatase PAP2 family protein

hetero molecules

defined by author
Evidence: equilibrium centrifugation, monomeric
59.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Phosphatase PAP2 family protein

D: Phosphatase PAP2 family protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	61.070, 123.637, 138.646
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Phosphatase PAP2 family protein Mass: 28876.768 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Gene: ABCR88_01690 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AAU7WWP3

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Non-polymers , 6 types, 400 molecules

#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 51.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% w/v PEG 8K

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.98 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.2→69.32 Å / Num. obs: 54038 / % possible obs: 99.8 % / Redundancy: 5 % / CC_1/2: 0.994 / R_merge(I) obs: 0.165 / R_pim(I) all: 0.082 / R_rim(I) all: 0.185 / Χ²: 0.95 / Net I/σ(I): 5.9 / Num. measured all: 272431
Reflection shell	Resolution: 2.2→2.26 Å / % possible obs: 100 % / Redundancy: 5.3 % / R_merge(I) obs: 1.105 / Num. measured all: 23216 / Num. unique obs: 4384 / CC_1/2: 0.629 / R_pim(I) all: 0.528 / R_rim(I) all: 1.227 / Χ²: 0.93 / Net I/σ(I) obs: 1.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.21.2_5419: ???)	refinement
Aimless		data scaling
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→69.32 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2426	2686	4.98 %
R_work	0.2036	-	-
obs	0.2055	53931	99.64 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.2→69.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6936	0	129	374	7439

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7263
X-RAY DIFFRACTION	f_angle_d	0.636	9849
X-RAY DIFFRACTION	f_dihedral_angle_d	14.442	2658
X-RAY DIFFRACTION	f_chiral_restr	0.037	1084
X-RAY DIFFRACTION	f_plane_restr	0.006	1294

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 (%)
2.2-2.24	0.336	139	0.2842	2641	X-RAY DIFFRACTION	100
2.24-2.28	0.348	137	0.2811	2660	X-RAY DIFFRACTION	100
2.28-2.33	0.3168	138	0.2714	2671	X-RAY DIFFRACTION	100
2.33-2.38	0.2851	131	0.2532	2682	X-RAY DIFFRACTION	100
2.38-2.44	0.2987	150	0.2419	2648	X-RAY DIFFRACTION	100
2.44-2.5	0.2533	134	0.2305	2653	X-RAY DIFFRACTION	100
2.5-2.56	0.2841	135	0.2263	2689	X-RAY DIFFRACTION	100
2.56-2.64	0.2654	158	0.2225	2665	X-RAY DIFFRACTION	100
2.64-2.72	0.2651	138	0.2235	2660	X-RAY DIFFRACTION	100
2.72-2.82	0.306	147	0.2225	2656	X-RAY DIFFRACTION	100
2.82-2.94	0.2963	146	0.2223	2696	X-RAY DIFFRACTION	100
2.94-3.07	0.2588	157	0.2095	2684	X-RAY DIFFRACTION	100
3.07-3.23	0.2534	140	0.2065	2702	X-RAY DIFFRACTION	100
3.23-3.43	0.2379	146	0.198	2692	X-RAY DIFFRACTION	100
3.43-3.7	0.2411	140	0.1879	2698	X-RAY DIFFRACTION	99
3.7-4.07	0.2062	129	0.167	2743	X-RAY DIFFRACTION	100
4.07-4.66	0.1835	136	0.1688	2732	X-RAY DIFFRACTION	99
4.66-5.87	0.2135	134	0.1962	2768	X-RAY DIFFRACTION	99
5.87-69.32	0.1999	151	0.1909	2905	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	1.2363	-0.9234	-0.1503	4.9202	-0.401	0.4452	-0.1945	0.0666	0.2521	0.4135	0.231	-0.9111	-0.1642	0.1934	-0.0867	0.2802	-0.0293	-0.0094	0.4241	-0.0064	0.3689	10.3097	-11.3045	53.1128
2	1.2975	-0.5748	0.2643	1.1244	-0.2012	1.0487	-0.0164	0.0904	-0.0667	-0.2082	0.128	0.1205	0.049	0.044	-0.1104	0.1902	-0.0247	0.0068	0.226	0.0039	0.198	-5.2937	-16.3229	44.3548
3	1.7618	-0.1103	0.6624	1.3434	-0.7512	1.6868	-0.2128	0.3294	0.2168	-0.0108	0.1091	-0.2514	-0.2145	0.457	0.0597	0.3605	-0.0041	0.0388	0.4426	-0.0214	0.3701	5.7228	-22.3968	37.8764
4	0.6375	0.4536	-0.1202	2.9502	0.4019	2.0887	0.0359	0.0551	-0.0253	0.0767	0.0801	0.088	0.003	0.011	-0.08	0.2266	0.0098	-0.0104	0.228	0.0019	0.2333	-4.3608	-17.335	51.475
5	1.6172	-1.039	0.813	1.9447	0.7019	2.6986	-0.2017	0.002	0.2063	0.1216	0.0315	0.4794	-0.2262	-0.1772	0.1201	0.2285	-0.0194	0.0471	0.2619	-0.0032	0.3149	-13.5396	-5.4186	52.6308
6	2.3062	0.3081	-0.2079	0.6922	-1.3895	2.9666	-0.0149	-0.0928	0.1505	-0.076	-0.0264	-0.2992	0.0572	0.0354	-0.095	0.3303	-0.0156	-0.025	0.3364	0.0356	0.4754	-16.8564	10.2885	37.1981
7	0.7338	0.1231	0.5471	0.4165	0.0456	1.4559	0.0318	0.2089	0.3671	-0.1212	0.039	-0.1445	-0.2832	-0.1204	-0.0083	0.2716	0.0004	0.0302	0.3065	0.0724	0.2873	-27.9039	31.1746	23.5576
8	4.0365	-1.7054	1.9012	5.4622	-0.569	3.5925	-0.1145	-0.8843	0.3465	-0.2447	-0.0545	-0.0055	-0.0808	-0.0905	0.1928	0.3156	0.1003	-0.0211	0.4627	0.0438	0.2965	-39.2718	28.8965	39.509
9	0.6813	-0.0687	0.1529	1.9385	-0.4927	0.6262	0.0644	-0.2136	0.0789	0.3951	0.0003	-0.2078	-0.0743	-0.1559	-0.0549	0.3416	-0.0269	-0.0633	0.3932	0.0734	0.2981	-32.8862	10.9273	46.4105
10	1.3573	0.0053	-0.2518	1.7373	-0.205	2.3178	-0.1306	-1.023	-0.4557	0.6291	-0.0834	-0.4977	0.3171	0.3784	0.1821	0.4067	-0.0461	-0.0204	0.5353	0.0207	0.5779	-15.9177	23.1678	33.3199
11	3.7917	0.4482	-1.4876	1.3392	0.8317	2.5185	0.2603	-0.3118	0.4058	0.0736	0.0197	0.0138	-0.5805	-0.1005	-0.1619	0.4183	-0.0165	-0.0388	0.3389	-0.0269	0.4526	-27.514	36.1618	36.5388
12	1.9734	0.5334	-0.5982	2.7798	1.3066	3.4882	-0.2839	-0.7174	0.0964	-0.3358	0.2971	-0.3904	-0.8786	0.8842	0.0583	0.4576	-0.0443	-0.0259	0.5489	-0.0304	0.475	-22.257	29.3713	39.7906
13	0.1606	-0.3239	0.2444	2.3885	0.3393	1.2785	-0.0436	0.0042	-0.0438	0.0501	0.1261	0.0205	0.0099	-0.166	-0.086	0.2459	-0.0068	-0.0104	0.3325	0.0544	0.302	-31.6342	15.1182	33.2941
14	5.3628	-1.4554	-2.5585	1.9842	1.1667	3.1489	-0.3105	0.1865	-0.3521	0.5284	0.1609	0.1711	0.6724	-0.3445	0.1591	0.4055	-0.0746	-0.0779	0.3729	0.0426	0.4253	-34.1842	-1.2212	43.344
15	0.6751	1.3053	0.0642	6.4129	-0.3811	1.1784	0.1994	0.289	0.5187	0.258	-0.27	0.7226	-0.1157	-0.4086	-0.0237	0.3942	0.0258	0.0397	0.4944	0.1494	0.5891	-46.9273	16.0559	43.9689
16	1.3539	-0.3758	-1.0895	1.6099	1.1393	1.2031	-0.0769	-0.0002	-0.1651	-0.2303	-0.0236	0.361	-0.0765	-0.0383	0.0834	0.3403	0.035	-0.0229	0.3271	-0.0169	0.3035	-7.4615	-31.7561	61.5906
17	0.872	-1.0766	-0.4874	2.2973	-0.0214	0.7907	-0.1486	-0.3224	0.0506	0.4412	0.2177	-0.0726	0.217	0.1319	-0.0656	0.3466	0.0808	-0.0254	0.3689	-0.0365	0.246	3.8314	-25.0853	77.0765
18	1.3509	0.5381	0.7131	0.7096	-0.4025	3.1257	-0.2351	-0.324	0.0268	0.4586	0.1129	0.3775	0.0766	-0.6272	0.1782	0.4109	0.0174	0.0753	0.4875	0.0556	0.4433	-8.8294	-39.1711	68.8981
19	1.7035	-0.4962	-0.253	2.0552	0.6947	1.9826	-0.1302	-0.0718	-0.0497	-0.0762	0.2057	-0.0445	0.1241	0.1302	-0.0829	0.2223	0.0168	-0.0057	0.2723	-0.0101	0.2174	1.0222	-24.722	65.5325
20	2.0761	-0.8987	0.1823	2.9038	-0.0276	0.6451	-0.0081	-0.1469	0.1475	0.1833	0.0986	-0.5433	0.0601	0.4318	-0.138	0.3386	0.0636	-0.037	0.403	-0.0922	0.3316	9.7436	-16.9906	74.8324
21	0.8986	0.2715	-0.3899	1.2641	-0.6405	1.6535	-0.1268	0.1754	-0.0936	-0.2992	0.2215	0.069	0.2671	-0.1885	-0.0944	0.3419	-0.0839	-0.0522	0.2903	0.0213	0.295	-29.3577	10.7287	12.834
22	2.239	0.0526	-0.1573	1.5401	0.0128	3.0702	0.036	0.4382	-0.8494	-0.4719	-0.0023	0.1287	1.633	-0.7041	-0.0137	0.7796	-0.0849	-0.0683	0.2673	-0.0386	0.5257	-26.6891	-7.647	16.9834
23	1.5985	-0.3706	-0.0486	1.4301	1.0568	1.6093	-0.2479	0.4794	-0.402	0.1113	0.1531	0.0568	0.2198	-0.6836	0.044	0.5275	-0.1298	-0.0627	0.6056	0.024	0.4191	-36.4337	13.356	6.0241
24	0.8172	0.6963	-0.2214	2.5436	-0.4776	2.7572	-0.0881	-0.0311	-0.1498	-0.1132	0.0479	-0.2147	0.2632	-0.0461	0.0033	0.2811	-0.0294	0.0011	0.2766	0.0126	0.3199	-26.2478	7.8046	19.3094
25	2.8996	-0.2746	-0.2962	1.1792	-0.1132	3.601	0.0635	0.0057	-0.2671	-0.237	0.0949	-0.2465	0.9799	0.2067	-0.0674	0.5787	0.0286	-0.0434	0.2637	0.0228	0.5115	-18.3289	-5.8636	20.3402
26	9.2452	1.9997	-5.111	1.9998	2	1.9998	2.1158	-0.4332	0.6141	-1.4706	-2.7415	-2.7112	-1.6209	2.9169	0.4976	0.8915	0.0974	0.3706	0.8815	0.1227	0.6769	-11.3103	11.7319	16.5846

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 38 through 55 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 56 through 131 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 132 through 172 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 173 through 234 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 235 through 274 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 38 through 55 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 56 through 80 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 81 through 92 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 93 through 131 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 132 through 146 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 147 through 157 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 158 through 172 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 173 through 234 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 235 through 254 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 255 through 271 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 38 through 80 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 81 through 131 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 132 through 172 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 173 through 234 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 235 through 274 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 38 through 108 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 109 through 131 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 132 through 172 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 173 through 234 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 235 through 271 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 272 through 272 )

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 6 types, 400 molecules

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 6 types, 400 molecules

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