PDB-7zgf: Crystal Structure of Amycolatopsis jejuensis Multiple Inositol Po...

ID or keywords:

Entry

Database: PDB / ID: 7zgf

Title

Crystal Structure of Amycolatopsis jejuensis Multiple Inositol Polyphosphate Phosphatase, apo-protein

Components

Multiple inositol-polyphosphate phosphatase

Keywords

HYDROLASE / phytase / histidine phosphatase / MINPP / Amycolatopsis

Function / homology

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

Function and homology information

Biological species

Amycolatopsis jejuensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Acquistapace, I.M. / Brearley, C.A. / Hemmings, A.M.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of Amycolatopsis jejuensis Multiple Inositol Polyphosphate Phosphatase, apo-protein
Authors: Acquistapace, I.M. / Brearley, C.A. / Hemmings, A.M.

History

Deposition	Apr 3, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 18, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7zgf.cif.gz	412.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7zgf.ent.gz	277.5 KB	Display	PDB format
PDBx/mmJSON format	7zgf.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/zg/7zgf ftp://data.pdbj.org/pub/pdb/validation_reports/zg/7zgf	HTTPS FTP

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Related structure data

Related structure data	7zggC 6rxdS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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 (1)

Deposited unit

A: Multiple inositol-polyphosphate phosphatase

B: Multiple inositol-polyphosphate phosphatase

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

1

A: Multiple inositol-polyphosphate phosphatase

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

2

B: Multiple inositol-polyphosphate phosphatase

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

Unit cell

Length a, b, c (Å)	68.848, 87.137, 70.358
Angle α, β, γ (deg.)	90.000, 97.402, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb

#1: Protein	Multiple inositol-polyphosphate phosphatase Mass: 46871.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amycolatopsis jejuensis (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle Express T7 / References: multiple inositol-polyphosphate phosphatase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 850 / Source method: isolated from a natural source / Formula: H₂O
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: 2.23 Å³/Da / Density % sol: 44.9 % / Description: plate clusters
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M NaCitrate, 20% PEG 3000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04-1 / Wavelength: 0.91587 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 5, 2017

Radiation

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

Radiation wavelength

Wavelength: 0.91587 Å / Relative weight: 1

Reflection

Resolution: 2.05→69.771 Å / Num. obs: 51333 / % possible obs: 99.11 % / Redundancy: 2.8 % / B_iso Wilson estimate: 15.71 Å² / R_merge(I) obs: 0.182 / R_pim(I) all: 0.133 / Net I/σ(I): 4.3

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	% possible all
2.05-2.09	2.86	0.733	1.4	2541	0.586	0.528	98.45
2.09-2.12	2.9	0.68	1.5	2528	0.589	0.488	98.48
2.12-2.16	2.91	0.606	1.7	2524	0.633	0.438	98.4
2.16-2.21	2.88	0.532	1.9	2557	0.696	0.387	98.84
2.21-2.26	2.82	0.485	2	2548	0.721	0.354	99.14
2.26-2.31	2.77	0.454	2.1	2586	0.734	0.337	99.46
2.31-2.37	2.69	0.413	2.3	2557	0.763	0.309	99.19
2.37-2.43	2.57	0.373	2.4	2578	0.815	0.283	99.96
2.43-2.5	2.7	0.348	2.7	2520	0.806	0.26	98.59
2.5-2.58	2.88	0.323	3	2552	0.86	0.234	99.22
2.58-2.68	2.9	0.29	3.3	2547	0.869	0.209	98.72
2.68-2.78	2.88	0.262	3.4	2566	0.893	0.189	98.88
2.78-2.91	2.87	0.219	4.1	2577	0.92	0.158	99.42
2.91-3.06	2.72	0.201	4.3	2565	0.928	0.149	99.73
3.06-3.25	2.62	0.151	5.3	2560	0.953	0.113	98.92
3.25-3.51	2.93	0.124	6.9	2572	0.969	0.09	99.5
3.51-3.86	2.93	0.101	8.6	2572	0.978	0.073	99.5
3.86-4.42	2.79	0.076	10.2	2590	0.984	0.055	99.58
4.42-5.56	2.7	0.07	9.6	2603	0.986	0.052	99.54

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Processing

Software

Name	Version	Classification
GDA		data collection
PHENIX	1.19.2_4158	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6RXD

6rxd

Resolution: 2.05→69.77 Å / SU ML: 0.2954 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3851
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2619	2465	4.83 %
R_work	0.2074	48608	-
obs	0.2101	51073	98.61 %

Solvent computation

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

Displacement parameters

B_iso mean: 19.12 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→69.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6525	0	0	850	7375

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0075	6683
X-RAY DIFFRACTION	f_angle_d	0.8584	9063
X-RAY DIFFRACTION	f_chiral_restr	0.0493	966
X-RAY DIFFRACTION	f_plane_restr	0.0088	1202
X-RAY DIFFRACTION	f_dihedral_angle_d	5.8142	914

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 (%)
2.05-2.09	0.3502	137	0.2953	2663	X-RAY DIFFRACTION	97.05
2.09-2.13	0.3679	134	0.2989	2648	X-RAY DIFFRACTION	97.51
2.13-2.18	0.3417	148	0.2826	2658	X-RAY DIFFRACTION	97.94
2.18-2.23	0.3348	132	0.2634	2672	X-RAY DIFFRACTION	98.28
2.23-2.28	0.3094	117	0.2678	2712	X-RAY DIFFRACTION	98.74
2.28-2.35	0.3397	124	0.2527	2708	X-RAY DIFFRACTION	98.64
2.35-2.42	0.3096	139	0.2475	2660	X-RAY DIFFRACTION	98.28
2.42-2.49	0.2845	124	0.241	2695	X-RAY DIFFRACTION	98.19
2.49-2.58	0.3487	134	0.235	2704	X-RAY DIFFRACTION	98.92
2.58-2.69	0.3058	132	0.2262	2673	X-RAY DIFFRACTION	98.32
2.69-2.81	0.3046	123	0.224	2732	X-RAY DIFFRACTION	98.72
2.81-2.96	0.2507	161	0.2072	2682	X-RAY DIFFRACTION	99.27
2.96-3.14	0.2733	127	0.1966	2717	X-RAY DIFFRACTION	99.13
3.14-3.38	0.2375	119	0.1765	2752	X-RAY DIFFRACTION	99.1
3.38-3.72	0.237	147	0.1615	2715	X-RAY DIFFRACTION	99.34
3.72-4.26	0.1875	153	0.1442	2725	X-RAY DIFFRACTION	99.55
4.26-5.37	0.1707	138	0.1496	2738	X-RAY DIFFRACTION	99.14
5.37-69.77	0.2144	176	0.1922	2754	X-RAY DIFFRACTION	98.95

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	0.128872426265	0.0105731288258	0.13620288179	0.088247559381	0.0572254942452	0.161494375429	0.107011661206	-0.0290084105153	-0.134459731789	0.0256009649385	-0.074382617093	-0.0242511424748	-0.0315623332687	-0.000474968338016	0.000223241759423	0.168284029854	-0.0216006110303	-0.00417028045123	0.121112752548	-0.00610556874019	0.113445306047	63.5913481083	-2.86655539964	17.1865005637
2	0.213908801638	-0.0350782670167	0.0156260385814	0.129707045772	0.052804654481	0.123561397993	0.0605242488771	-0.0177229583945	0.111294634872	-0.062133505604	0.0276441334896	-0.0427522379485	-0.0413729806667	-0.0194936980462	0.00922128195289	0.0616736556361	-0.0126808027193	0.0115530316105	0.0641418532645	-0.00827209664476	0.0852915313351	80.4787843633	-9.67928457667	-1.33247000659
3	0.091059529992	0.0936500754371	-0.0544877955533	0.233196801536	-0.0361793896484	0.087213065388	0.0444746244177	0.0685975044179	-0.0834726072725	-0.0524931151282	-0.0153593528502	0.0644295939082	0.0412651040155	-0.0471154230433	0.103968698625	0.0661624626203	-0.00290872344705	-0.0103288508489	0.0761899745356	0.00607612036659	0.0780795166259	71.0976041572	-13.7828868737	1.80388105126
4	0.172402996898	0.0172534182045	0.0958907246876	0.195247296084	0.121178976662	0.303544350636	0.0179278768293	0.0868158194546	-0.0338452443555	-0.0708415436737	-0.03081830726	-0.00609330685726	-0.0136151950109	-0.0483556536007	-0.00871301066424	0.082863515573	0.00934803717753	0.00473303866913	0.0822422100113	-0.00691613274352	0.0937381468679	61.6209093242	3.82711519372	-0.742745719331
5	0.0765860177388	0.000457822847341	-0.0296493782468	0.0254769417866	-0.0230725215054	0.0557278160224	-0.0768787854912	0.136007672923	0.0246687026467	-0.0262664791124	0.167408917498	-0.085464619708	0.000689816423251	0.0273693260224	0.0127262151598	0.060015180497	0.00703607087352	0.00217233852279	0.130779492128	-0.0168014826415	0.135800375898	99.3441033762	-6.62470826119	3.38368771133
6	0.0713355047818	0.0185048460541	0.0925755312176	0.00459253699852	0.0245524461837	0.113894105958	0.0297665435556	0.00881316451253	-0.00304801956105	-0.0236484103251	-0.050563232335	0.0210881064946	0.0190615776468	0.0326555902643	-0.0533347175064	0.072114892639	-0.0246205722938	-0.00053366735044	0.0787873364368	0.00556964848787	0.094224309191	83.2139689137	-2.01949188667	5.28480284418
7	0.234362898307	-0.0696136333409	0.0639884497564	0.0722536800192	-0.0812640754488	0.194601647848	0.00587125033678	0.0552908210509	0.0973789376076	0.019354567338	-0.0343671277833	-0.0234580217011	-0.0584760807513	0.0219723149606	-0.020318085806	0.0929072750653	-0.00740856538163	-0.00678329659065	0.0759544058675	-0.00127093995249	0.0830482665075	64.3226135754	9.1623832886	8.83072438797
8	0.0809294625614	0.0734465213104	-0.0723773268625	0.0589476188531	-0.0553179158396	0.0979903387371	-0.0326629681707	0.0551457208455	-0.0203287456558	0.0435201556864	0.0177106345322	0.0411880906495	0.00352449147024	-0.0835473803985	-0.00846935932875	0.0981934629236	0.0156913550519	-0.0038062993015	0.0740628599476	-0.00120217994364	0.0823315513124	55.1994402444	13.0203751054	18.2259639934
9	0.0735663087142	-0.00957715079991	0.060184671026	0.0483994651925	0.00875130942446	0.255258906009	0.025301547606	-0.0102519361413	-0.0971441427861	-0.133844457507	-0.0655706535557	0.0723302052923	0.0316579799113	0.0149283473075	-0.00112959432734	0.158359564002	0.00140430815517	0.0132305161319	0.142512086691	0.00718441088106	0.118688205274	79.3276568128	-7.56828506016	27.6811331001
10	0.262611604898	-0.11168258473	0.0256320994539	0.246206224803	-0.244092552158	0.523050166994	-0.0965533218705	-0.115591984537	-0.0595510307981	0.104834686814	0.118210636666	-0.081606524033	0.0748907484101	-0.114055047069	0.0965340709788	0.131200509485	-0.00609312808802	0.0166983130363	0.167493214723	0.0236453133729	0.0829886939921	64.4821411192	-6.73028208344	44.8123939395
11	0.450087575816	0.226850339491	-0.100846802089	0.267754879463	-0.202153105253	0.663193000747	-0.0534638955629	-0.186204380476	0.0267379486115	0.0524398362901	-0.0730561549456	-0.0111031271084	0.0423420955043	0.108783979897	-0.13873855485	0.110402287084	0.015639773623	0.00537287061701	0.124288334904	0.0287136189019	0.0805230606697	84.9867348587	-2.81980054541	45.3323703416
12	0.217349637697	0.10408156096	0.0672874815013	0.114505500224	-0.136234778166	0.401791087948	0.0336690122876	-0.0242106786573	0.0543330435776	0.0763486241834	0.0264804150075	-0.0261486401253	-0.0994346353544	-0.107760304343	0.0700674115008	0.15518636055	0.0212299990737	-0.000111855065252	0.148799964727	0.0151680662369	0.0933695791245	59.5527573348	7.20346577637	39.997028614
13	0.235317466665	0.0522366236919	-0.0401875417084	0.162560764665	0.0191391065021	0.425962713911	-0.0393695009631	-0.0492158045062	0.0253220314114	0.0399458571998	-0.0136756655691	-0.0088339057245	-0.0249109640929	0.120198907048	-0.0299077682622	0.0842470483891	0.000366943936529	-0.0109854838265	0.122672960399	0.0233450221951	0.0926639560504	89.0896664053	1.67175341165	32.1679132494

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 5 through 31 )	A	A	5 - 31	1 - 27
2	2	chain 'A' and (resid 32 through 71 )	A	A	32 - 71	28 - 67
3	3	chain 'A' and (resid 72 through 113 )	A	A	72 - 113	68 - 109
4	4	chain 'A' and (resid 114 through 200 )	A	A	114 - 200	110 - 196
5	5	chain 'A' and (resid 201 through 226 )	A	A	201 - 226	197 - 222
6	6	chain 'A' and (resid 227 through 290 )	A	A	227 - 290	223 - 286
7	7	chain 'A' and (resid 291 through 372 )	A	A	291 - 372	287 - 368
8	8	chain 'A' and (resid 373 through 417 )	A	A	373 - 417	369 - 413
9	9	chain 'B' and (resid 5 through 31 )	B	B	5 - 31	1 - 27
10	10	chain 'B' and (resid 32 through 113 )	B	B	32 - 113	28 - 109
11	11	chain 'B' and (resid 114 through 200 )	B	B	114 - 200	110 - 196
12	12	chain 'B' and (resid 201 through 290 )	B	B	201 - 290	197 - 286
13	13	chain 'B' and (resid 291 through 414 )	B	B	291 - 414	287 - 410

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