PDB-5cu7: Bacteroides Thetaiotaomicron Multiple Inositol Polyphosphate Phos...

ID or keywords:

Entry

Database: PDB / ID: 5cu7

Title

Bacteroides Thetaiotaomicron Multiple Inositol Polyphosphate Phosphatase A324D Mutant

Components

multiple inositol polyphosphate histidine phosphatase 1

Keywords

HYDROLASE / Phosphatase

Function / homology

Function and homology information

inositol phosphate phosphatase activity / acid phosphatase activity
Similarity search - Function

Biological species

Bacteroides thetaiotaomicron VPI-5482 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.73 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 24, 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	5cu7.cif.gz	353.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5cu7.ent.gz	288.4 KB	Display	PDB format
PDBx/mmJSON format	5cu7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5cu7_validation.pdf.gz	451.5 KB	Display	wwPDB validaton report
Full document	5cu7_full_validation.pdf.gz	456.2 KB	Display
Data in XML	5cu7_validation.xml.gz	34.8 KB	Display
Data in CIF	5cu7_validation.cif.gz	51.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cu/5cu7 ftp://data.pdbj.org/pub/pdb/validation_reports/cu/5cu7	HTTPS FTP

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Related structure data

Related structure data	5cx4C 4fdt C: citing same article (ref.)
Similar structure data	4fdt-1 5i5r-4 5cx4-1 7mc5-d 3sms-d 2efw-2 4fdu-2 6pe6-d 4fdt-2 5l9p-1 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 - 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 (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

98.7 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)	52.960, 119.680, 75.910
Angle α, β, γ (deg.)	90.000, 108.180, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	multiple inositol polyphosphate histidine phosphatase 1 / MINPP Mass: 49247.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) 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 Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 571 / 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: 2.49 Å³/Da / Density % sol: 50.53 %
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

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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 15, 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: 1.73→59.84 Å / Num. all: 92472 / Num. obs: 92472 / % possible obs: 99.4 % / Redundancy: 3.4 % / R_pim(I) all: 0.04 / R_rim(I) all: 0.075 / R_sym value: 0.052 / Net I/av σ(I): 8.268 / Net I/σ(I): 10.4 / Num. measured all: 313887

Reflection shell

Diffraction-ID: 1 / Rejects: _

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
1.73-1.78	3.5	0.683	1.1	23949	6856	0.47	0.683	2	99.9
1.78-1.83	3.5	0.531	1.4	23230	6725	0.374	0.531	2.5	100
1.83-1.88	3.4	0.391	1.8	21994	6481	0.283	0.391	3.2	99.9
1.88-1.94	3.2	0.302	2.4	20307	6264	0.225	0.302	3.9	99.7
1.94-2	3.4	0.236	3	21138	6129	0.172	0.236	4.8	99.8
2-2.07	3.3	0.179	4.1	19378	5916	0.136	0.179	5.9	99.7
2.07-2.15	3.4	0.128	5.7	19367	5687	0.1	0.128	7.4	99.5
2.15-2.24	3.5	0.102	7.1	18832	5449	0.08	0.102	9	99.2
2.24-2.34	3.4	0.082	8.8	17727	5236	0.067	0.082	10.3	99.2
2.34-2.45	3.3	0.068	10.6	16397	5026	0.057	0.068	11.6	99.1
2.45-2.58	3.5	0.061	11.5	16561	4758	0.049	0.061	13.4	99.3
2.58-2.74	3.3	0.053	13.3	15029	4530	0.043	0.053	15	99.6
2.74-2.93	3.6	0.048	14	15263	4272	0.036	0.048	17.2	99.7
2.93-3.16	3.5	0.045	14.5	13925	3968	0.035	0.045	18.7	99.7
3.16-3.47	3.3	0.044	13.2	12036	3646	0.036	0.044	20	99.7
3.47-3.87	3.5	0.043	13.9	11459	3306	0.032	0.043	22.2	99.8
3.87-4.47	3.3	0.036	16.2	9719	2917	0.026	0.036	22.8	99.2
4.47-5.48	3.4	0.033	16.9	8354	2452	0.023	0.033	23.5	98.1
5.48-7.75	3.2	0.031	18.7	6065	1869	0.022	0.031	22.5	96.9
7.75-59.84	3.2	0.025	22.8	3157	985	0.019	0.025	23.3	90.7

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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: 1.73→38.511 Å / FOM work R set: 0.8818 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.17 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1814	4646	5 %
R_work	0.1561	88196	-
obs	0.1574	92472	99.36 %

Solvent computation

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

Displacement parameters

B_iso max: 95.58 Å² / B_iso mean: 31.29 Å² / B_iso min: 13.85 Å²

Refinement step

Cycle: final / Resolution: 1.73→38.511 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6476	0	10	571	7057
B_iso mean	-	-	29.33	42.34	-
Num. residues	-	-	-	-	792

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6916
X-RAY DIFFRACTION	f_angle_d	1.02	9399
X-RAY DIFFRACTION	f_chiral_restr	0.077	994
X-RAY DIFFRACTION	f_plane_restr	0.005	1214
X-RAY DIFFRACTION	f_dihedral_angle_d	14.065	2635

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.73-1.7497	0.3061	154	0.2713	2913	3067	100
1.7497-1.7702	0.2754	142	0.2518	3026	3168	100
1.7702-1.7918	0.2917	148	0.2337	2889	3037	100
1.7918-1.8145	0.2752	164	0.225	2972	3136	100
1.8145-1.8384	0.2756	159	0.2142	2923	3082	100
1.8384-1.8636	0.2245	170	0.201	2920	3090	100
1.8636-1.8902	0.2395	166	0.1915	2991	3157	100
1.8902-1.9184	0.2269	158	0.1868	2886	3044	100
1.9184-1.9484	0.197	148	0.1824	3004	3152	100
1.9484-1.9803	0.2116	151	0.1692	2888	3039	100
1.9803-2.0145	0.2115	164	0.1688	2919	3083	100
2.0145-2.0511	0.1894	148	0.1675	3001	3149	100
2.0511-2.0905	0.1786	138	0.1607	2907	3045	100
2.0905-2.1332	0.1921	151	0.1489	2959	3110	99
2.1332-2.1796	0.1699	157	0.1497	2928	3085	99
2.1796-2.2303	0.178	138	0.1472	2964	3102	99
2.2303-2.2861	0.1836	155	0.1518	2949	3104	99
2.2861-2.3479	0.1951	160	0.1469	2873	3033	99
2.3479-2.4169	0.1889	163	0.15	2941	3104	99
2.4169-2.4949	0.1764	147	0.1454	2938	3085	99
2.4949-2.5841	0.1671	167	0.15	2912	3079	99
2.5841-2.6875	0.1929	151	0.1525	2960	3111	100
2.6875-2.8098	0.1862	141	0.1523	2962	3103	100
2.8098-2.9579	0.1803	156	0.1573	2955	3111	100
2.9579-3.1431	0.21	145	0.1607	2970	3115	100
3.1431-3.3857	0.1699	167	0.1588	2933	3100	100
3.3857-3.7262	0.1667	161	0.1483	2968	3129	100
3.7262-4.2647	0.154	152	0.1365	2943	3095	99
4.2647-5.3708	0.1489	155	0.13	2937	3092	98
5.3708-38.5209	0.1658	170	0.1612	2865	3035	95

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	1.4073	0.2084	-0.6343	1.5149	-0.9683	1.8872	0.1419	-0.2542	0.1352	0.5329	0.0256	0.5328	-0.4806	-0.153	-0.1322	0.2853	0.0185	0.044	0.2479	-0.0107	0.2359	-0.8853	7.3942	41.7885
2	1.1515	0.5667	-0.3391	1.5277	-0.6142	1.1483	-0.0382	-0.128	-0.1292	-0.1316	0.0654	0.2445	0.1583	-0.2687	-0.0054	0.1374	-0.0101	-0.0065	0.2453	0.0375	0.2286	-8.6167	-8.6981	35.2692
3	0.8577	0.0887	0.6135	1.0954	-0.2903	1.3311	0.0578	0.0618	-0.0182	-0.2047	-0.0179	0.1691	-0.0154	0.0004	0.0027	0.1888	0.0161	0.003	0.1749	0.0059	0.1548	3.7583	7.2471	21.3465
4	1.4655	0.3854	0.0275	1.0835	-0.3021	0.9416	0.0773	-0.2089	-0.4465	0.1249	-0.08	0.0154	0.1201	-0.2372	0.0112	0.235	-0.0188	-0.016	0.2322	0.0643	0.2637	4.6532	-19.4359	47.5254
5	0.6991	0.37	0.5826	1.2196	-0.8636	2.3208	-0.0431	-0.2966	-0.0822	0.1681	0.0027	-0.1084	-0.0198	-0.1469	-0.0124	0.189	-0.0403	-0.0097	0.292	0.072	0.2877	-7.2788	-13.2344	44.7019
6	3.0615	0.3027	-0.9978	0.9766	-0.1819	1.513	0.0208	-0.1926	-0.1367	0.0571	-0.0216	0.0384	0.0531	-0.0527	-0.0167	0.2	-0.0013	-0.0131	0.2157	0.0247	0.1907	8.2358	-7.9851	47.0513
7	1.1141	-0.5248	0.2307	1.2813	-0.4797	0.8218	0.0035	-0.0129	0.0114	0.009	-0.015	-0.0132	-0.0534	0.1441	0.0085	0.1794	0.003	0.0016	0.1825	0.0007	0.1537	15.4434	6.2352	31.2663
8	0.6529	-0.3812	0.5161	0.6123	-0.1592	1.1415	0.0052	-0.0694	0.0941	0.0691	-0.0351	0.0358	-0.1923	0.0577	0.0015	0.197	-0.0116	0.0153	0.1825	-0.0102	0.1582	11.7673	13.0887	39.5184
9	2.1495	-1.782	-0.4812	4.725	0.3199	1.6956	0.0388	0.1016	-0.0762	-0.1361	-0.1208	-0.2383	-0.0134	0.2416	-0.0216	0.1445	-0.0171	-0.0076	0.236	0.0104	0.1572	24.976	7.0139	33.6966
10	2.2712	-0.8953	0.282	0.9962	0.0903	0.7723	-0.0495	-0.0164	0.0682	0.0418	-0.0221	0.1789	-0.095	-0.0289	0.0305	0.186	-0.0367	0.0067	0.1453	0.0191	0.2007	5.1009	21.3045	72.3532
11	0.9548	0.2775	0.02	0.5451	0.2046	0.9593	-0.1132	-0.22	0.0763	0.197	0.109	0.1074	-0.0509	-0.0762	0.0347	0.2695	-0.0141	0.0315	0.1796	0.0179	0.1912	3.3969	18.6426	80.3881
12	0.7103	-0.1385	0.6008	1.2776	-0.2773	1.4436	-0.0579	-0.0043	0.0519	0.0661	0.0572	-0.0392	-0.0256	0.1505	-0.0096	0.2226	-0.0095	-0.0169	0.2166	0.0089	0.1855	25.4093	12.6704	78.2786
13	1.4213	-0.1599	-0.5803	0.4295	-0.018	1.3166	0.0225	0.0738	0.2634	-0.0286	0.0046	0.2108	-0.3217	-0.2587	0.0199	0.2709	0.0282	-0.0331	0.1881	0.0251	0.2493	-0.4287	32.6137	65.9342
14	0.7552	-0.3636	-0.1497	0.694	0.0828	1.2116	-0.0219	0.1544	0.0452	-0.0389	-0.026	-0.0424	-0.1618	0.1868	0.0052	0.204	-0.0623	-0.007	0.2115	0.0165	0.172	20.2022	19.6602	61.5465
15	0.8909	-0.5248	-0.0275	0.9302	0.2682	1.7073	-0.0152	0.1278	0.0114	-0.0471	0.0162	-0.0659	-0.0396	0.3363	-0.0163	0.1772	-0.0392	0.0101	0.2605	-0.0055	0.1743	24.9312	11.0794	57.2724

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 51 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 52 through 129 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 130 through 188 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 189 through 229 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 230 through 261 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 262 through 288 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 289 through 345 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 346 through 398 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 399 through 425 )	A
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 21 through 87 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 88 through 129 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 130 through 188 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 189 through 261 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 262 through 345 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 346 through 425 )	B

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