PDB-7u1v: Structure of SPAC806.04c protein from fission yeast covalently bo...

ID or keywords:

Entry

Database: PDB / ID: 7u1v

Title

Structure of SPAC806.04c protein from fission yeast covalently bound to BeF3

Components

Damage-control phosphatase SPAC806.04c

Keywords

HYDROLASE / metal-dependent phosphatase / Domain of Unknown Function 89 (DUF89)

Function / homology

Function and homology information

fructose-1-phosphatase activity / fructose 6-phosphate aldolase activity / inorganic diphosphate phosphatase activity /

Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / cellular detoxification /

phosphatase activity /

metal ion binding /

nucleus /

cytosol
Similarity search - Function

Biological species

Schizosaccharomyces pombe (fission yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Jacewicz, A. / Sanchez, A.M. / Shuman, S.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2022
Title: Fission yeast Duf89 and Duf8901 are cobalt/nickel-dependent phosphatase-pyrophosphatases that act via a covalent aspartyl-phosphate intermediate.
Authors: Sanchez, A.M. / Jacewicz, A. / Shuman, S.

History

Deposition	Feb 22, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 1, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7u1v.cif.gz	442.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7u1v.ent.gz	302.5 KB	Display	PDB format
PDBx/mmJSON format	7u1v.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/u1/7u1v ftp://data.pdbj.org/pub/pdb/validation_reports/u1/7u1v	HTTPS FTP

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Related structure data

Related structure data	7t7kSC 7t7nC 7t7oC 7u1xC 7u1yC S: Starting model for refinement C: citing same article (ref.)
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

Deposited unit

A: Damage-control phosphatase SPAC806.04c

B: Damage-control phosphatase SPAC806.04c

hetero molecules

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

1

A: Damage-control phosphatase SPAC806.04c

hetero molecules

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

2

B: Damage-control phosphatase SPAC806.04c

hetero molecules

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

Unit cell

Length a, b, c (Å)	59.495, 115.864, 161.674
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁
Space group name Hall	P22ab(z,x,y)
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y+1/2,-z+1/2 #4: -x,-y+1/2,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	B-502- NI

#1: Protein	Damage-control phosphatase SPAC806.04c / Sugar phosphate phosphatase SPAC806.04c Mass: 50101.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9UT55, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical	ChemComp-NI / NICKEL (II) ION / Nickel Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.78 Å³/Da / Density % sol: 55.76 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 1.8 M sodium/potassium phosphate (pH 7.8), cryoprotected in crystallization buffer supplemented with 25% sucrose

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.4857 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.4857 Å / Relative weight: 1
Reflection	Resolution: 2.1→161.67 Å / Num. obs: 66303 / % possible obs: 99.7 % / Redundancy: 12.8 % / B_iso Wilson estimate: 35.2 Å² / CC_1/2: 0.999 / R_pim(I) all: 0.027 / Net I/σ(I): 19.2
Reflection shell	Resolution: 2.1→2.15 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4219 / CC_1/2: 0.793 / R_pim(I) all: 0.323 / % possible all: 96.1

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Processing

Software

Name	Version	Classification
PHENIX	1.20_4459	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7T7K

7t7k

Resolution: 2.1→59.49 Å / SU ML: 0.2415 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.2253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2087	6296	4.99 %
R_work	0.1791	119913	-
obs	0.1806	66303	99.66 %

Solvent computation

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

Displacement parameters

B_iso mean: 46.53 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→59.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7022	0	9	368	7399

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0072	7243
X-RAY DIFFRACTION	f_angle_d	0.9081	9843
X-RAY DIFFRACTION	f_chiral_restr	0.0493	1073
X-RAY DIFFRACTION	f_plane_restr	0.0074	1257
X-RAY DIFFRACTION	f_dihedral_angle_d	6.3745	963

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 (%)
2.1-2.12	0.2841	197	0.2719	3657	X-RAY DIFFRACTION	91.35
2.12-2.15	0.3412	221	0.2602	3959	X-RAY DIFFRACTION	99.88
2.15-2.17	0.2913	202	0.2455	4043	X-RAY DIFFRACTION	99.93
2.17-2.2	0.3047	189	0.2428	4023	X-RAY DIFFRACTION	99.95
2.2-2.23	0.3067	205	0.2464	3992	X-RAY DIFFRACTION	99.93
2.23-2.26	0.2648	211	0.2316	4009	X-RAY DIFFRACTION	99.91
2.26-2.29	0.285	205	0.2251	4050	X-RAY DIFFRACTION	100
2.29-2.32	0.2592	221	0.2242	3976	X-RAY DIFFRACTION	100
2.32-2.36	0.2858	198	0.2169	4081	X-RAY DIFFRACTION	99.95
2.36-2.4	0.2508	183	0.2201	3986	X-RAY DIFFRACTION	99.98
2.4-2.44	0.2899	205	0.206	4022	X-RAY DIFFRACTION	99.93
2.44-2.49	0.2037	183	0.203	4037	X-RAY DIFFRACTION	99.93
2.49-2.53	0.2745	217	0.2038	3984	X-RAY DIFFRACTION	99.9
2.53-2.59	0.2369	230	0.1979	4018	X-RAY DIFFRACTION	99.98
2.59-2.64	0.2749	243	0.2167	3967	X-RAY DIFFRACTION	100
2.64-2.7	0.2572	204	0.2099	4041	X-RAY DIFFRACTION	99.93
2.7-2.77	0.2409	211	0.216	3973	X-RAY DIFFRACTION	99.81
2.77-2.85	0.2912	164	0.2283	4070	X-RAY DIFFRACTION	99.98
2.85-2.93	0.243	210	0.2235	3986	X-RAY DIFFRACTION	100
2.93-3.02	0.2305	244	0.2302	3974	X-RAY DIFFRACTION	99.98
3.02-3.13	0.2638	202	0.1981	4107	X-RAY DIFFRACTION	100
3.13-3.26	0.2208	243	0.1911	3920	X-RAY DIFFRACTION	100
3.26-3.41	0.2128	228	0.1827	3976	X-RAY DIFFRACTION	99.95
3.41-3.58	0.2138	199	0.1748	4017	X-RAY DIFFRACTION	100
3.58-3.81	0.1566	202	0.1501	4012	X-RAY DIFFRACTION	100
3.81-4.1	0.1621	211	0.1382	4003	X-RAY DIFFRACTION	100
4.1-4.52	0.1533	224	0.1249	4039	X-RAY DIFFRACTION	100
4.52-5.17	0.1442	209	0.1228	3970	X-RAY DIFFRACTION	99.95
5.17-6.51	0.1712	235	0.1563	4016	X-RAY DIFFRACTION	99.95
6.51-59.49	0.1705	200	0.158	4005	X-RAY DIFFRACTION	99.6

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	3.11995605901	-1.22388088507	-1.18004153207	2.26865055047	1.09100665314	1.30858170662	-0.0715004844395	0.171065050804	-0.158080206722	-0.329615991802	-0.0109719047558	0.245289196243	-0.0024004588046	-0.171748264086	0.0563717406198	0.329559807732	-0.0568607899605	-0.0673476064374	0.3516932127	0.0895642932361	0.226709266947	-16.6922144479	48.5692137318	15.962626616
2	5.52569977969	-1.99161568035	2.27385747832	3.2935276094	-1.11553042292	6.57056231616	-0.402405463242	-1.45626540787	0.345660145226	0.434602234039	0.124676250686	-0.456805951169	-0.199910469062	-0.209841261646	0.239012413586	0.37434591751	0.107540975966	-0.0181965670948	0.472249186626	0.0152143041969	0.302701288902	2.87994380022	51.356153654	42.4159872432
3	2.98376276852	1.66047260025	-0.483568804729	4.64834839262	0.0599057180751	3.30854488272	0.0682611244714	-0.907024404905	-0.596057328179	0.509902901867	0.103167525747	-0.452767586646	0.0359426685775	-0.156016225836	-0.185986756717	0.351290363929	0.0313914063695	-0.0191507242127	0.396454078742	0.0893499086527	0.404751034999	8.63769008018	41.9679835595	36.8750589465
4	2.73306430653	-0.155535554448	0.616185211321	2.00139994673	0.198966926523	1.0052469726	-0.13023212218	-0.0803175674955	-0.0139308724967	-0.149790691309	0.148375429228	-0.356112226632	-0.0122777834146	0.034481079285	-0.0119990874025	0.246971957769	-0.0174219169753	0.0532939214956	0.270915590173	0.0698701402909	0.307798536944	6.10592007868	48.6946623344	24.4340567892
5	1.66591619354	0.594394739098	-1.31261755533	2.60416743062	-2.13857512372	3.7894949027	-0.0452298610463	-0.0513623480775	0.500734050043	0.159994132684	0.101760415288	0.0190827690434	-0.343880739819	-0.0228503051547	-0.0954950889159	0.274579985508	-0.0207253649963	-0.0853729067835	0.258878405933	-0.0350595893163	0.527718197044	23.5097331029	24.3471073996	37.049795771
6	6.94867465471	0.979129477764	0.0278186822781	2.93492931852	2.6421487748	4.49545849655	-0.214448699913	-0.378637237585	1.16639579234	0.309904174089	0.412643986655	-1.01845192702	-0.355499245302	0.631859426941	-0.23337333069	0.35119425412	-0.0445617891273	-0.0855844924512	0.395273426821	-0.110509539482	0.797408779161	36.8724444692	29.7056801815	35.1665652733
7	2.61519984516	0.320518087485	-0.00455649923447	1.52629419085	1.04003127184	4.08130267633	-0.0249900320774	0.0817784894833	0.080950025466	0.150417108853	-0.0490546528466	0.0360053181329	0.495340794005	-0.169282753819	0.0562766867132	0.261274782699	0.00946016613508	-0.0481465094255	0.251905149275	0.0263553833515	0.335431261552	22.4539208525	9.24979321757	31.0140205458
8	6.73248828689	-4.94062801622	-4.61049397658	5.01511340763	5.5243386634	6.74580347818	-0.373978970677	0.25358641687	-0.40946795717	0.369796437526	0.0153300609093	0.230660617267	0.66920258805	-0.0828808566492	0.37129285338	0.471529978193	-0.0712095646426	0.00932905543798	0.483805250314	0.0620708104425	0.296863407076	23.7494644328	-2.70768826704	7.80915679494
9	3.82954273644	-0.427989026103	-2.76816073668	2.93424357661	3.70789726513	6.57176875105	-0.0342766183295	0.780409027318	-0.141945695054	-0.499470513099	-0.304981662001	0.715125872269	0.21133637608	-0.564219623592	0.350988030352	0.513499386201	-0.0167431054822	-0.161747043698	0.495016298588	0.0748709388575	0.580293248282	14.8749165181	11.9401194359	15.8085328466
10	2.60139621783	0.441201086493	-0.394381972485	1.74732526362	0.193992968981	2.01484728893	-0.104694501818	0.133965012961	0.0973946608021	-0.10469470883	0.00654192831008	-0.176521870847	0.262170577838	0.194722781953	0.101736752104	0.293340450247	0.00320883673744	-0.00916539978912	0.240621402127	0.0414376229503	0.2890123093	31.8758832209	5.2703957766	21.8593713424
11	1.77456969772	0.098268382325	0.520664641209	2.24464679238	1.86134958064	2.32521052562	-0.0669901851816	0.658578740175	0.58106532268	-0.558839894035	-0.27928315119	0.115705797316	-0.381217587164	-0.00350048885744	0.329404908742	0.435916576454	-0.0589629244407	-0.0333328963083	0.414104250742	0.187977733602	0.469908898528	27.2221267624	18.6766332939	10.1344798108

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 'B' and (resid 1 through 136 )	B	B	1 - 136	1 - 136
2	2	chain 'B' and (resid 137 through 166 )	B	B	137 - 166	137 - 166
3	3	chain 'B' and (resid 167 through 222 )	B	B	167 - 222	167 - 218
4	4	chain 'B' and (resid 223 through 438 )	B	B	223 - 438	219 - 434
5	5	chain 'A' and (resid 1 through 74 )	A	A	1 - 74	1 - 74
6	6	chain 'A' and (resid 75 through 108 )	A	A	75 - 108	75 - 108
7	7	chain 'A' and (resid 109 through 166 )	A	A	109 - 166	109 - 166
8	8	chain 'A' and (resid 167 through 193 )	A	A	167 - 193	167 - 193
9	9	chain 'A' and (resid 194 through 226 )	A	A	194 - 226	194 - 226
10	10	chain 'A' and (resid 227 through 388 )	A	A	227 - 388	227 - 388
11	11	chain 'A' and (resid 389 through 438 )	A	A	389 - 438	389 - 438

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