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

ID or keywords:

Entry

Database: PDB / ID: 7zgg

Title

Crystal Structure of Amycolatopsis jejuensis Multiple Inositol Polyphosphate Phosphatase, phosphate-bound

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 / PHOSPHATE ION

Function and homology information

Biological species

Amycolatopsis jejuensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.66 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	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7zgg.cif.gz	418.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7zgg.ent.gz	282.9 KB	Display	PDB format
PDBx/mmJSON format	7zgg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7zgg_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	7zgg_full_validation.pdf.gz	1.2 MB	Display
Data in XML	7zgg_validation.xml.gz	38.8 KB	Display
Data in CIF	7zgg_validation.cif.gz	60 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zg/7zgg ftp://data.pdbj.org/pub/pdb/validation_reports/zg/7zgg	HTTPS FTP

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Related structure data

Related structure data	7zgfC 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

hetero molecules

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

1

A: Multiple inositol-polyphosphate phosphatase

hetero molecules

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

2

B: Multiple inositol-polyphosphate phosphatase

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.887, 86.910, 70.540
Angle α, β, γ (deg.)	90.000, 97.928, 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: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 859 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.25 Å³/Da / Density % sol: 45.28 % / Description: plate clusters
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.2 M NaThiocyanate, 20 % PEG 3350

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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: 1.659→69.93 Å / Num. obs: 97117 / % possible obs: 99.9 % / Redundancy: 2 % / B_iso Wilson estimate: 13.12 Å² / R_rim(I) all: 0.19 / Net I/σ(I): 6.4

Reflection shell

Diffraction-ID: 1 / Redundancy: 2 %

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.66-1.72	1.151	1	9679	0.215	1.627	99.5
1.72-1.79	0.904	1.3	9642	0.312	1.279	99.9
1.79-1.87	0.637	1.8	9700	0.469	0.901	100
1.87-1.97	0.435	2.5	9711	0.65	0.615	100
1.97-2.09	0.309	3.4	9676	0.78	0.437	99.9
2.09-2.25	0.217	4.6	9670	0.874	0.307	99.9
2.25-2.48	0.155	6.2	9722	0.931	0.219	100
2.48-2.84	0.11	8	9738	0.963	0.156	100
2.84-3.57	0.059	13.2	9747	0.99	0.083	100
3.57-69.93	0.027	21.8	9892	0.998	0.039	100

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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: 1.66→69.87 Å / SU ML: 0.2629 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.4488
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2263	4698	4.85 %
R_work	0.1801	92217	-
obs	0.1824	96915	99.64 %

Solvent computation

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

Displacement parameters

B_iso mean: 18.76 Å²

Refinement step

Cycle: LAST / Resolution: 1.66→69.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6534	0	16	859	7409

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0073	6720
X-RAY DIFFRACTION	f_angle_d	0.8755	9117
X-RAY DIFFRACTION	f_chiral_restr	0.0516	970
X-RAY DIFFRACTION	f_plane_restr	0.0082	1208
X-RAY DIFFRACTION	f_dihedral_angle_d	5.6302	923

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 (%)
1.66-1.68	0.3771	179	0.3364	3012	X-RAY DIFFRACTION	97.67
1.68-1.7	0.3452	138	0.3253	3044	X-RAY DIFFRACTION	99.13
1.7-1.72	0.3651	150	0.3021	3073	X-RAY DIFFRACTION	99.17
1.72-1.74	0.4188	140	0.3092	3022	X-RAY DIFFRACTION	99.4
1.74-1.76	0.3903	159	0.2843	3097	X-RAY DIFFRACTION	99.51
1.76-1.79	0.3702	146	0.274	3032	X-RAY DIFFRACTION	99.41
1.79-1.81	0.3292	160	0.2676	3093	X-RAY DIFFRACTION	99.36
1.81-1.84	0.3064	170	0.2514	2989	X-RAY DIFFRACTION	99.81
1.84-1.87	0.2796	164	0.2205	3084	X-RAY DIFFRACTION	99.57
1.87-1.9	0.3042	141	0.2152	3074	X-RAY DIFFRACTION	99.78
1.9-1.93	0.2832	150	0.2072	3047	X-RAY DIFFRACTION	99.47
1.93-1.97	0.2798	136	0.2	3136	X-RAY DIFFRACTION	99.79
1.97-2.01	0.2619	164	0.1953	3030	X-RAY DIFFRACTION	99.87
2.01-2.05	0.2501	170	0.1974	3053	X-RAY DIFFRACTION	99.75
2.05-2.09	0.2578	164	0.1957	3078	X-RAY DIFFRACTION	99.63
2.09-2.14	0.245	145	0.1711	3073	X-RAY DIFFRACTION	99.69
2.14-2.19	0.2041	155	0.1657	3052	X-RAY DIFFRACTION	99.84
2.19-2.25	0.1993	161	0.1562	3072	X-RAY DIFFRACTION	99.91
2.25-2.32	0.216	166	0.156	3053	X-RAY DIFFRACTION	99.94
2.32-2.39	0.2124	149	0.1557	3131	X-RAY DIFFRACTION	99.88
2.39-2.48	0.2215	139	0.1539	3072	X-RAY DIFFRACTION	99.84
2.48-2.58	0.2365	155	0.1509	3092	X-RAY DIFFRACTION	99.91
2.58-2.7	0.186	171	0.1506	3068	X-RAY DIFFRACTION	99.78
2.7-2.84	0.213	126	0.1483	3116	X-RAY DIFFRACTION	99.88
2.84-3.02	0.1787	138	0.1526	3105	X-RAY DIFFRACTION	99.94
3.02-3.25	0.18	172	0.1482	3093	X-RAY DIFFRACTION	99.97
3.25-3.57	0.1661	154	0.147	3079	X-RAY DIFFRACTION	99.91
3.57-4.09	0.161	194	0.1413	3080	X-RAY DIFFRACTION	99.94
4.09-5.16	0.1947	167	0.1549	3104	X-RAY DIFFRACTION	99.97
5.16-69.87	0.2119	175	0.1888	3163	X-RAY DIFFRACTION	99.76

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