PDB-7u1x: Structure of SPAC806.04c protein from fission yeast covalently bo...

ID or keywords:

Entry

Database: PDB / ID: 7u1x

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 6-phosphate aldolase activity / fructose-1-phosphatase activity / inorganic diphosphate phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / intracellular phosphate ion homeostasis / cellular detoxification / phosphatase activity / DNA damage response / metal ion binding / nucleus / cytosol
Similarity search - Function

Biological species

Schizosaccharomyces pombe (fission yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.12 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
Revision 1.2	Nov 13, 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	7u1x.cif.gz	434.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7u1x.ent.gz	294.7 KB	Display	PDB format
PDBx/mmJSON format	7u1x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7u1x_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	7u1x_full_validation.pdf.gz	1.5 MB	Display
Data in XML	7u1x_validation.xml.gz	32.5 KB	Display
Data in CIF	7u1x_validation.cif.gz	46.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u1/7u1x ftp://data.pdbj.org/pub/pdb/validation_reports/u1/7u1x	HTTPS FTP

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Related structure data

Related structure data	7t7kSC 7t7nC 7t7oC 7u1vC 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

100 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
50.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	59.300, 117.533, 153.435
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	A-729- HOH

#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-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.67 Å³/Da / Density % sol: 53.9 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.8 M Sodium/potassium phosphate (pH 8.0), cryoprotected in crystallization solution 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: 1.2822 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 17, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.2822 Å / Relative weight: 1
Reflection	Resolution: 2.11→46.92 Å / Num. obs: 61347 / % possible obs: 98.6 % / Redundancy: 10 % / B_iso Wilson estimate: 28.8 Å² / CC_1/2: 0.997 / R_pim(I) all: 0.057 / Net I/σ(I): 13
Reflection shell	Resolution: 2.11→2.17 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3701 / CC_1/2: 0.592 / R_pim(I) all: 0.378 / % possible all: 82

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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: 2.12→46.92 Å / SU ML: 0.2533 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.663
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2157	3104	5.07 %
R_work	0.1763	58063	-
obs	0.1783	61167	98.59 %

Solvent computation

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

Displacement parameters

B_iso mean: 35.87 Å²

Refinement step

Cycle: LAST / Resolution: 2.12→46.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7033	0	7	268	7308

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0076	7224
X-RAY DIFFRACTION	f_angle_d	0.8728	9810
X-RAY DIFFRACTION	f_chiral_restr	0.0501	1066
X-RAY DIFFRACTION	f_plane_restr	0.008	1254
X-RAY DIFFRACTION	f_dihedral_angle_d	6.2777	952

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 (%)
2.12-2.15	0.3841	88	0.3112	1888	X-RAY DIFFRACTION	71.67
2.15-2.18	0.3389	148	0.254	2628	X-RAY DIFFRACTION	99.71
2.18-2.22	0.2965	143	0.2402	2675	X-RAY DIFFRACTION	99.89
2.22-2.26	0.2533	135	0.2302	2613	X-RAY DIFFRACTION	99.85
2.26-2.31	0.2793	158	0.2207	2617	X-RAY DIFFRACTION	100
2.31-2.35	0.2783	143	0.2144	2676	X-RAY DIFFRACTION	99.96
2.35-2.4	0.2634	146	0.2079	2612	X-RAY DIFFRACTION	100
2.4-2.46	0.2704	147	0.2029	2646	X-RAY DIFFRACTION	99.75
2.46-2.52	0.2626	126	0.204	2648	X-RAY DIFFRACTION	99.93
2.52-2.59	0.238	133	0.1975	2669	X-RAY DIFFRACTION	99.86
2.59-2.67	0.2539	150	0.1972	2633	X-RAY DIFFRACTION	99.93
2.67-2.75	0.2667	147	0.2	2642	X-RAY DIFFRACTION	99.71
2.75-2.85	0.247	154	0.2057	2673	X-RAY DIFFRACTION	100
2.85-2.96	0.2576	138	0.2088	2652	X-RAY DIFFRACTION	99.71
2.96-3.1	0.29	135	0.1948	2682	X-RAY DIFFRACTION	99.93
3.1-3.26	0.2309	137	0.1882	2681	X-RAY DIFFRACTION	99.93
3.26-3.47	0.2032	176	0.1663	2661	X-RAY DIFFRACTION	99.86
3.47-3.73	0.1946	133	0.1546	2691	X-RAY DIFFRACTION	99.61
3.73-4.11	0.1667	140	0.1327	2695	X-RAY DIFFRACTION	99.86
4.11-4.7	0.1422	130	0.1189	2747	X-RAY DIFFRACTION	99.9
4.7-5.93	0.1689	155	0.14	2749	X-RAY DIFFRACTION	99.93
5.93-46.92	0.1778	142	0.1802	2885	X-RAY DIFFRACTION	99.38

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	0.347142770574	0.277415607933	-1.2130940451	4.82429402043	0.0974713994338	4.49186066639	0.0900238128864	-0.00744924232802	0.108127257449	-0.13728813659	-0.0101530829633	-0.060440891643	-0.227846064572	0.0925202234857	-0.0981123959283	0.180305361351	-0.0505438083591	-0.0448559227117	0.23833547397	-0.0126612105935	0.198247944716	31.3119757154	30.7376768642	22.2773407903
2	0.7879988644	0.528688635391	0.185179005159	6.85520443134	-7.43664677957	9.45648734064	0.0449098853961	-0.129648395845	0.072727665026	0.507980592402	0.0881434840953	0.162385909258	-0.296607335609	-0.161966800332	-0.148821941325	0.236070824543	0.0462478678729	0.0525610042419	0.266991834871	-0.0610783098238	0.270823327176	18.3162462184	21.2157543742	45.5964203594
3	7.25896779632	-4.00758286555	-0.531792895289	4.92757434346	1.41071319515	6.74410617968	0.0389892839236	-0.122432064629	0.167685225806	0.177819487951	-0.00858712966398	-0.184899649445	-0.123041192598	0.245302869717	-0.0629552240971	0.251471640741	-0.0618646003398	-0.0256768789364	0.252500868566	-0.0603969065937	0.267446926924	36.2724575865	30.5203376707	34.6442714901
4	1.18072045452	1.95373166264	-2.57744955828	4.27949618684	-5.85223355031	8.02882999639	-0.025212038671	-0.0518849815312	-0.0305209460478	-0.0884519566571	-0.125078674907	-0.0356720039613	0.209753929815	0.200172112425	0.132686792786	0.193237094998	0.0227732807936	-0.0154072851656	0.199827121796	-0.0335000324546	0.21940641577	27.9159328079	20.5217641513	38.7465526849
5	5.52370755173	0.521631070907	0.683702269867	6.00061841497	2.73697890934	8.27465012828	-0.348070976563	0.411087696602	-0.400416421617	-0.116617385535	0.0432230442951	0.535206175633	0.538971637494	-0.138471409536	0.36164546985	0.221629835034	-0.0441628931353	0.048377340312	0.230885001296	0.0691234240191	0.234210332508	15.4675584388	-2.68616930848	22.3938488782
6	1.44969966062	-2.41173456107	-1.8125473959	6.20650106878	4.1945085988	4.56188754332	-0.107758367386	0.0577783850235	-0.153270957651	0.126649568548	-0.120909026907	0.460559743611	0.1770411594	-0.199823482141	0.285368171405	0.182355382474	-0.0264201980016	-0.0233498429332	0.232175953071	0.0208815847053	0.246058306738	19.8536943635	5.28457302092	11.704499373
7	0.695285455705	0.0703985080494	-0.145210575114	1.5002347504	0.102904981483	1.11646130879	-0.0520615906263	-0.0173798055267	-0.0605926643226	0.0566333360736	0.0491293789532	-0.0535905655374	0.10370039736	0.111457177373	-0.000176610283288	0.213599822903	0.0264721839881	-0.00201630089627	0.218337307892	-0.0175138815217	0.188981929576	30.1229915792	8.80599736877	19.881054119
8	2.37272412846	-2.24292326178	-1.17438295822	2.50072725366	1.29188493875	1.26485099458	0.00613564978443	0.00435035103061	-0.0563769812751	-0.0791102103575	0.00372452227201	0.148588638509	0.0288154670615	-0.00651175214128	0.000741939120288	0.185327227093	-0.0501398294909	-0.0141844451589	0.222219757196	-0.0107779155874	0.213287628319	-18.4798210237	47.2141674601	16.8481164828
9	4.51307242833	0.0042939088449	-1.38816836389	5.04015975123	-0.805565702828	2.54834856059	0.036426326338	0.356051755278	0.121023487661	-0.752224150143	-0.131895967172	0.323632321627	-0.0975473605649	-0.0116423782358	0.0726935791487	0.271433444786	0.0146720616973	-0.0739460668572	0.339739833669	-0.0449782209531	0.198831887056	-13.7270782097	47.01161105	3.35745441906
10	2.74155823171	-3.03335564469	-1.45964135094	3.40151592304	1.5390201932	1.1779897269	0.0667442061823	0.0013974588276	0.0289766233974	-0.158845587776	-0.0256002531977	-0.0093146610437	-0.0817059201573	0.0240323887196	-0.0878673378684	0.214187548582	-0.0257687120322	0.00832983689868	0.237336906863	-0.00325308421453	0.236410285923	-15.8006028265	53.4820643886	15.1677979687
11	3.8380277385	-0.941025104183	0.998505383398	1.55255630172	0.375505951829	2.7472397369	-0.224483067947	-0.498662638528	0.144151027196	0.0845897350573	0.0889979307723	-0.0995005351563	-0.26627264532	0.0155769659718	0.0889452328178	0.351986607105	-0.0591279848778	0.0481388193962	0.318689521628	-0.0229359285138	0.236278643419	2.5149176114	54.0582362573	39.7266989182
12	3.11065524991	2.10344358294	1.88570866161	5.51670986497	2.33226341781	5.3683647701	0.125580017877	-0.209010455511	-0.297538913598	0.106716783952	0.102638909445	-0.609733924544	-0.253021042077	0.44071173037	-0.160173647931	0.321061520085	-0.038198896068	0.0281146985025	0.322752844377	-0.0110570311347	0.279279203584	15.0193091778	45.7124944727	34.1026754027
13	2.3543767883	-2.11550056246	0.391685741666	2.17825836563	0.438694447704	2.56401037823	-0.0907610713123	-0.619074760968	-0.173992811134	0.300685386325	0.203829194634	0.216775899551	-0.0212355153115	-0.304899677218	-0.0970828353045	0.403992065182	-0.00607715408183	0.0132621294851	0.362828301618	0.038881661648	0.353200963913	-0.495381046445	39.2633728213	33.8133024825
14	1.47280326948	0.17710613669	0.225995398858	0.958508751741	0.435864979352	1.48470717993	0.0731409659951	-0.127582289122	0.22762588503	0.048443084176	-0.0250115099835	-0.0374956438084	-0.131517938079	0.0180647072137	-0.0368201046862	0.211540088673	-0.00478403499433	0.0265411684345	0.183653933423	-0.0121577632461	0.244687302741	5.53962858817	55.8084130968	23.787489384
15	1.69850999753	-0.439566251216	0.154708999031	2.49832413837	-0.204928656934	1.48352390823	0.00908632660177	0.0068519966787	-0.197973402402	-0.223517263084	0.00156028197695	0.120798870522	0.131151869643	-0.0802134924215	-0.0141791966295	0.214267050761	0.031861203434	-0.00476648635899	0.211914524622	-0.0129090460127	0.187106531674	6.602700268	35.7268189927	18.1512681134

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 0 through 26 )	A	A	0 - 26	1 - 27
2	2	chain 'A' and (resid 27 through 74 )	A	A	27 - 74	28 - 75
3	3	chain 'A' and (resid 75 through 108 )	A	A	75 - 108	76 - 109
4	4	chain 'A' and (resid 109 through 136 )	A	A	109 - 136	110 - 137
5	5	chain 'A' and (resid 137 through 166 )	A	A	137 - 166	138 - 167
6	6	chain 'A' and (resid 167 through 235 )	A	A	167 - 235	168 - 236
7	7	chain 'A' and (resid 236 through 438 )	A	A	236 - 438	237 - 439
8	8	chain 'B' and (resid 0 through 74 )	B	B	0 - 74	1 - 75
9	9	chain 'B' and (resid 75 through 108 )	B	B	75 - 108	76 - 109
10	10	chain 'B' and (resid 109 through 136 )	B	B	109 - 136	110 - 137
11	11	chain 'B' and (resid 137 through 166 )	B	B	137 - 166	138 - 167
12	12	chain 'B' and (resid 167 through 193 )	B	B	167 - 193	168 - 189
13	13	chain 'B' and (resid 194 through 226 )	B	B	194 - 226	190 - 222
14	14	chain 'B' and (resid 227 through 370 )	B	B	227 - 370	223 - 366
15	15	chain 'B' and (resid 371 through 438 )	B	B	371 - 438	367 - 434

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Jul 12, 2017. Major update of PDB

-
Yorodumi