PDB-5cx4: Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase

ID or keywords:

Entry

Database: PDB / ID: 5cx4

Title

Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase

Components

multiple inositol polyphosphate histidine phosphatase 1

Keywords

TRANSFERASE /

Phosphatase

Function / homology

Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) /

Phosphoglycerate mutase-like / Histidine phosphatase superfamily /

Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta /

PHOSPHATE ION / Multiple inositol polyphosphate histidine phosphatase 1

Function and homology information

Biological species

Bacteroides thetaiotaomicron (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.06 Å

Model details

A324D mutant

Authors

Li, A.W.H. / Hemmings, A.M.

Citation

Journal: To be published
Title: The Hydrolytic Positional Specificity Towards Phytic Acid of a Bacterial Multiple Inositol Polyphosphate Phosphatase
Authors: Li, A.W.H. / Brearley, C.A. / Hemmings, A.M.

History

Deposition	Jul 28, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Aug 17, 2016	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5cx4.cif.gz	342.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5cx4.ent.gz	279.7 KB	Display	PDB format
PDBx/mmJSON format	5cx4.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/cx/5cx4 ftp://data.pdbj.org/pub/pdb/validation_reports/cx/5cx4	HTTPS FTP

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Related structure data

Related structure data	5cu7C C: citing same article (ref.)
Similar structure data	5cu7-1 5cu7-2 4fdu-2 4fdt-2 5a2a-d 6wni-1 2ps1-d 5a2c-d 1vhe-d 1l0p-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) Similarity search - Function & homologyF&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 (3) #257 - May 2021 Fetal Hemoglobin similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

A: multiple inositol polyphosphate histidine phosphatase 1

B: multiple inositol polyphosphate histidine phosphatase 1

hetero molecules

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

1

A: multiple inositol polyphosphate histidine phosphatase 1

hetero molecules

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

2

B: multiple inositol polyphosphate histidine phosphatase 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	52.800, 119.640, 76.080
Angle α, β, γ (deg.)	90.000, 108.080, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	multiple inositol polyphosphate histidine phosphatase 1 / MINPP Mass: 49188.414 Da / Num. of mol.: 2 / Mutation: E325N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria) Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_4744 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 plysS / References: UniProt: Q89YI8
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.32 Å³/Da / Density % sol: 47.03 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.2M Ammonium acetate, pH5.0, 18% PEG 3350, Protein 1mg/ml PH range: 5

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I24 / Wavelength: 0.969 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2012

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.969 Å / Relative weight: 1

Reflection

Resolution: 2.06→50.193 Å / Num. all: 55128 / Num. obs: 55128 / % possible obs: 99.4 % / Redundancy: 3.4 % / R_pim(I) all: 0.061 / R_rim(I) all: 0.114 / R_sym value: 0.078 / Net I/av σ(I): 6.405 / Net I/σ(I): 7.9 / Num. measured all: 187172

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_pim(I) all	R_sym value	Net I/σ(I) obs	% possible all
2.06-2.11	3.4	0.748	0.9	13893	4084	0.553	0.748	2.2	99.1
2.11-2.17	3.4	0.596	1.2	13358	3911	0.442	0.596	2.7	99.3
2.17-2.23	3.3	0.473	1.5	12582	3856	0.371	0.473	3	99.4
2.23-2.3	3.4	0.422	1.7	12848	3756	0.314	0.422	3.5	99.1
2.3-2.38	3.5	0.328	2.1	12561	3630	0.242	0.328	4.2	99.5
2.38-2.46	3.4	0.275	2.5	11998	3490	0.205	0.275	4.8	99.7
2.46-2.56	3.4	0.235	2.9	11468	3389	0.176	0.235	5.3	99.5
2.56-2.66	3.2	0.172	4	10672	3286	0.134	0.172	6.2	99.5
2.66-2.78	3.5	0.141	4.9	10813	3120	0.105	0.141	7.4	99.5
2.78-2.91	3.3	0.115	6	9852	2993	0.088	0.115	8.2	99.6
2.91-3.07	3.5	0.098	7	9889	2862	0.075	0.098	9.5	99.5
3.07-3.26	3.5	0.079	8.4	9486	2696	0.058	0.079	11.1	99.7
3.26-3.48	3.5	0.069	9	8737	2526	0.051	0.069	12.8	99.8
3.48-3.76	3.3	0.06	9.6	7815	2396	0.045	0.06	14	99.7
3.76-4.12	3.5	0.054	10.5	7596	2163	0.041	0.054	15.8	99.6
4.12-4.61	3.3	0.049	10.8	6521	1966	0.038	0.049	16.5	99.5
4.61-5.32	3.6	0.044	11.8	6278	1757	0.036	0.044	17.3	99.5
5.32-6.51	3.4	0.044	13.7	4972	1479	0.039	0.044	16.3	99.8
6.51-9.21	3.3	0.035	17.2	3742	1134	0.029	0.035	17.1	99.2
9.21-50.193	3.3	0.03	18.9	2091	634	0.022	0.03	17.9	95.8

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Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction

Refinement

Resolution: 2.06→36.295 Å / FOM work R set: 0.8655 / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.93 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2006	2796	5.08 %
R_work	0.1575	52282	-
obs	0.1597	55078	99.37 %

Solvent computation

Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 114.59 Å² / B_iso mean: 39.08 Å² / B_iso min: 16.96 Å²

Refinement step

Cycle: final / Resolution: 2.06→36.295 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6468	0	10	319	6797
B_iso mean	-	-	48.4	45.12	-
Num. residues	-	-	-	-	792

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6763
X-RAY DIFFRACTION	f_angle_d	1.056	9169
X-RAY DIFFRACTION	f_chiral_restr	0.074	973
X-RAY DIFFRACTION	f_plane_restr	0.005	1174
X-RAY DIFFRACTION	f_dihedral_angle_d	15.04	2549

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.06-2.0955	0.2748	140	0.2435	2604	2744	99
2.0955-2.1336	0.31	141	0.2287	2596	2737	99
2.1336-2.1747	0.2575	126	0.2196	2613	2739	99
2.1747-2.2191	0.2737	134	0.2085	2597	2731	99
2.2191-2.2673	0.2562	154	0.1981	2573	2727	99
2.2673-2.32	0.2532	146	0.1919	2590	2736	99
2.32-2.378	0.2225	133	0.1808	2644	2777	99
2.378-2.4423	0.2603	142	0.1804	2599	2741	100
2.4423-2.5142	0.2225	140	0.1755	2637	2777	100
2.5142-2.5953	0.2367	145	0.1733	2559	2704	99
2.5953-2.688	0.2259	130	0.1667	2645	2775	100
2.688-2.7956	0.2087	131	0.159	2636	2767	99
2.7956-2.9228	0.1991	150	0.1495	2601	2751	100
2.9228-3.0768	0.1946	149	0.1575	2589	2738	99
3.0768-3.2695	0.1931	150	0.1576	2621	2771	100
3.2695-3.5217	0.1928	134	0.1472	2649	2783	100
3.5217-3.8758	0.1905	125	0.144	2611	2736	100
3.8758-4.4358	0.1533	145	0.1287	2643	2788	100
4.4358-5.5853	0.1678	140	0.1304	2627	2767	99
5.5853-36.3011	0.1825	141	0.1527	2648	2789	98

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	1.0643	0.9111	-0.5662	1.9985	-1.0234	1.4617	-0.0393	-0.0371	-0.056	0.0447	0.079	0.2334	0.0188	-0.1928	-0.0104	0.1871	0.0018	0.0095	0.2821	0.0305	0.2859	-3.9858	-5.8294	38.9778
2	0.6732	0.3457	0.0554	0.9011	-0.3422	0.8986	0.0445	-0.0823	-0.0932	-0.0288	0.042	0.2045	0.0729	-0.1643	-0.0182	0.2378	0.0126	-0.0103	0.2562	0.0046	0.2619	-1.3669	-5.7363	34.9716
3	0.8712	0.1247	0.0401	0.852	-0.2153	0.6827	0.0602	-0.0227	0.0171	-0.0336	-0.0383	-0.0008	-0.0111	0.1283	-0.0129	0.2114	0.0091	0.0009	0.2125	-0.0066	0.1923	13.0527	1.6844	36.3074
4	1.1819	-0.0277	0.2972	1.5367	-0.416	1.5801	0.0449	0.0128	0.0365	0.0095	-0.1103	-0.0792	-0.1966	0.1742	-0.0008	0.2141	-0.0194	0.0045	0.1951	-0.0067	0.1784	16.341	11.216	37.5469
5	2.5197	-1.0287	0.2849	0.8787	0.1679	1.0063	-0.0365	-0.0272	0.0421	0.05	-0.0802	0.2414	-0.0583	-0.1427	0.0299	0.2528	-0.0392	0.0086	0.2341	0.0136	0.2955	6.2225	20.8066	72.4762
6	1.758	-0.4253	2.052	0.7827	-0.9846	2.7041	-0.3184	-0.3004	0.3939	0.257	0.0952	0.382	-0.3038	-0.5197	0.0894	0.3722	0.0485	0.0107	0.3953	-0.0747	0.3998	-9.9721	29.6556	81.2656
7	0.995	-0.8831	-0.3389	3.1059	1.4709	1.1194	-0.2385	-0.3019	-0.0165	0.4637	0.3324	0.0109	0.1855	0.0282	0.0263	0.31	-0.0092	0.0273	0.2463	0.005	0.2567	12.1431	11.3501	79.2415
8	1.3575	-0.7643	0.2185	2.4068	0.0382	1.2683	-0.0388	0.0486	-0.0208	0.0129	0.0626	0.0179	0.0323	0.1458	-0.0074	0.2724	0.0134	-0.012	0.2406	0.0049	0.2087	23.5007	7.9391	79.69
9	0.716	0.169	-0.1066	0.6533	0.0278	1.009	-0.0238	0.1315	0.3155	0.0335	-0.0309	0.0706	-0.296	-0.0163	0.0984	0.3464	-0.0275	-0.0407	0.2351	0.0081	0.303	11.1856	30.2934	67.4966
10	2.8416	-1.2581	1.1676	1.7254	-0.3545	3.2037	-0.1372	0.0799	-0.016	-0.1747	0.0833	0.1128	-0.2103	-0.4491	0.0323	0.2603	0.0326	0.0013	0.3586	-0.0191	0.3554	-3.2694	27.263	71.5222
11	0.9183	-0.3094	-0.1196	0.752	0.1058	1.4544	0.022	0.2788	0.0234	-0.0866	-0.0694	-0.0264	-0.1763	0.2677	0.0119	0.2439	-0.0615	-0.0131	0.2398	0.0022	0.2166	20.1558	19.7089	61.7925
12	0.4459	0.0783	0.3148	0.8796	-0.049	1.6243	0.0246	0.1159	-0.0271	-0.0297	-0.0158	-0.0291	0.1219	0.0923	-0.0188	0.1894	-0.0099	0.0045	0.2139	-0.0152	0.2042	20.2158	8.0594	58.868
13	0.739	-0.1046	0.1802	4.8087	0.9988	1.0428	-0.0039	0.2514	0.2295	-0.1839	0.0936	-0.4347	-0.3327	0.4612	-0.0532	0.3548	-0.1458	0.0392	0.5084	0.0286	0.2693	31.5532	18.3978	54.8306

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 21 through 87 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 88 through 261 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 262 through 345 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 346 through 425 )	A
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 21 through 83 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 84 through 104 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 105 through 129 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 130 through 164 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 165 through 229 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 230 through 261 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 262 through 345 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 346 through 398 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 399 through 425 )	B

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