PDB-7erm: Crystal structure of D-allulose 3-epimerase from Agrobacterium sp...

ID or keywords:

Entry

Database: PDB / ID: 7erm

Title

Crystal structure of D-allulose 3-epimerase from Agrobacterium sp. SUL3

Components

D-tagatose 3-epimerase

Keywords

ISOMERASE / D-allulose / rare sugar / Agrobacterium sp. SUL3 / D-allulose 3-epimerase

Function / homology

Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / D-tagatose 3-epimerase

Function and homology information

Biological species

Agrobacterium sp. SUL3 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.32 Å

Authors

Zhu, Z.L. / Miyakawa, T. / Tanokura, M. / Lu, F.P. / Qin, H.-M.

Citation

Journal: Adv Sci / Year: 2024
Title: Growth-Coupled Evolutionary Pressure Improving Epimerases for D-Allulose Biosynthesis Using a Biosensor-Assisted In Vivo Selection Platform
Authors: Li, C. / Gao, H. / Li, H. / Wang, T. / Lu, F.P. / Qin, H.-M.

History

Deposition	May 6, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 11, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Feb 7, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7erm.cif.gz	521 KB	Display	PDBx/mmCIF format
PDB format	pdb7erm.ent.gz	358.2 KB	Display	PDB format
PDBx/mmJSON format	7erm.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/er/7erm ftp://data.pdbj.org/pub/pdb/validation_reports/er/7erm	HTTPS FTP

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Related structure data

Related structure data	7ernC 7eroC 7dz2S 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	#74 - Feb 2006 alpha-Amylase similarity (3)

Deposited unit

A: D-tagatose 3-epimerase

B: D-tagatose 3-epimerase

C: D-tagatose 3-epimerase

D: D-tagatose 3-epimerase

hetero molecules

122 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	67.381, 98.711, 161.003
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	D-tagatose 3-epimerase Mass: 30471.295 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium sp. SUL3 (bacteria) / Gene: AKG12_23230 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: A0A0L6K0Q2
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.23 Å³/Da / Density % sol: 44.9 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M Magnesium chloride, 0.1M Tris pH=8.5, 30% PEG 4000

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Data collection

Diffraction	Mean temperature: 95 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 16, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.32→47.19 Å / Num. obs: 89663 / % possible obs: 100 % / Redundancy: 13.1 % / B_iso Wilson estimate: 39.07 Å² / CC_1/2: 0.998 / R_pim(I) all: 0.051 / R_rim(I) all: 0.184 / Net I/σ(I): 11.1
Reflection shell	Resolution: 2.32→2.4 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4570 / R_pim(I) all: 0.437

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7DZ2

7dz2

Resolution: 2.32→47.19 Å / SU ML: 0.2926 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 26.197
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2476	4315	4.81 %
R_work	0.1791	85348	-
obs	0.1823	89663	99.87 %

Solvent computation

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

Displacement parameters

B_iso mean: 46.11 Å²

Refinement step

Cycle: LAST / Resolution: 2.32→47.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8572	0	25	171	8768

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0077	8784
X-RAY DIFFRACTION	f_angle_d	0.8686	11928
X-RAY DIFFRACTION	f_chiral_restr	0.0496	1300
X-RAY DIFFRACTION	f_plane_restr	0.0047	1568
X-RAY DIFFRACTION	f_dihedral_angle_d	13.9647	1212

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 (%)
2.32-2.35	0.3031	152	0.2446	2816	X-RAY DIFFRACTION	99.93
2.35-2.37	0.3994	151	0.2582	2818	X-RAY DIFFRACTION	100
2.37-2.4	0.3407	154	0.2644	2867	X-RAY DIFFRACTION	100
2.4-2.43	0.3226	153	0.2476	2791	X-RAY DIFFRACTION	99.93
2.43-2.47	0.321	117	0.2389	2913	X-RAY DIFFRACTION	100
2.47-2.5	0.3369	148	0.2454	2858	X-RAY DIFFRACTION	100
2.5-2.53	0.3151	177	0.2362	2807	X-RAY DIFFRACTION	100
2.53-2.57	0.292	167	0.2373	2819	X-RAY DIFFRACTION	99.93
2.57-2.61	0.2958	130	0.2229	2877	X-RAY DIFFRACTION	100
2.61-2.66	0.2643	161	0.2133	2804	X-RAY DIFFRACTION	99.9
2.66-2.7	0.3149	148	0.2182	2844	X-RAY DIFFRACTION	100
2.7-2.75	0.2569	126	0.207	2872	X-RAY DIFFRACTION	100
2.75-2.8	0.2705	155	0.209	2849	X-RAY DIFFRACTION	99.93
2.8-2.86	0.2777	106	0.201	2880	X-RAY DIFFRACTION	100
2.86-2.92	0.281	156	0.2048	2833	X-RAY DIFFRACTION	100
2.92-2.99	0.3163	127	0.2103	2915	X-RAY DIFFRACTION	100
2.99-3.07	0.3144	152	0.2043	2840	X-RAY DIFFRACTION	99.9
3.07-3.15	0.3114	142	0.2198	2826	X-RAY DIFFRACTION	100
3.15-3.24	0.326	152	0.2027	2827	X-RAY DIFFRACTION	100
3.24-3.35	0.3188	138	0.2023	2843	X-RAY DIFFRACTION	99.93
3.35-3.47	0.2778	160	0.1841	2836	X-RAY DIFFRACTION	99.9
3.47-3.6	0.282	139	0.1647	2843	X-RAY DIFFRACTION	99.67
3.6-3.77	0.1922	137	0.1592	2841	X-RAY DIFFRACTION	99.73
3.77-3.97	0.2246	155	0.148	2882	X-RAY DIFFRACTION	99.74
3.97-4.21	0.2193	124	0.1372	2838	X-RAY DIFFRACTION	99.76
4.22-4.54	0.2172	139	0.133	2826	X-RAY DIFFRACTION	99.56
4.54-5	0.1611	136	0.1356	2844	X-RAY DIFFRACTION	99.77
5-5.72	0.1987	126	0.159	2873	X-RAY DIFFRACTION	99.9
5.72-7.2	0.199	148	0.1734	2832	X-RAY DIFFRACTION	99.9
7.2-47.19	0.1686	139	0.1525	2834	X-RAY DIFFRACTION	98.97

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	2.61167688452	1.27390789017	0.773329742492	2.3806642452	0.501057659823	1.1094888623	0.13836685109	-0.0469212551941	0.254030277001	0.0435021941703	-0.0649058255374	0.319810002387	-0.0638983615118	-0.333968414303	-0.0559548669473	0.319733946111	-0.0168810291681	0.0215054582947	0.405232482164	0.0383273963291	0.319623931339	-47.9174669799	-3.58954550164	6.77031540364
2	1.27897227914	0.482786873358	-0.214348054724	1.62931162905	-0.633285269304	2.6496457542	-0.00106964514932	0.0649454288091	-0.05006058944	-0.171572821193	-0.0571908323335	-0.0396319159697	0.390529828648	-0.0903228633377	0.0625371004132	0.365304972374	-0.0288034824852	-0.00462726810249	0.283887042073	0.00163457601708	0.302827187695	-35.8504823413	-8.35793146525	9.75788377803
3	2.55700146239	-0.350103441783	-0.296090233537	3.81199390284	1.6874960514	3.3113325224	-0.0459519506922	-0.325203930868	-0.269514780989	0.516696339424	0.0981637946235	-0.273928695837	0.669582899426	0.540228638118	0.088889226851	0.403767020885	0.00340074979756	0.00835508498857	0.340148051996	0.0696202169245	0.35540969068	-30.763600466	-13.090713414	19.9269910779
4	3.76710182002	0.496980830091	1.05574953375	2.30638393765	0.479261682703	1.02979569535	0.204548172602	-0.550271429085	-1.11779182784	0.243748835599	-0.258140875309	-0.714302134078	0.346661539505	0.0162606228922	0.0779579331905	0.428465184162	0.0609947417956	-0.00339248234387	0.463394456754	0.179992121466	0.622554131783	-1.73594078089	-14.1762308277	32.6141981129
5	2.41037647659	0.0555780380301	-0.0181654317958	0.779210598917	-0.237853178967	1.49490080852	0.00966376223248	-0.220213956149	-0.096203910427	0.203561849882	-0.140458277033	-0.237048167217	-0.136360023929	0.370444364985	0.128053711892	0.300445919594	-0.0597414467472	-0.0295132273063	0.349028221668	0.0686324225262	0.322282917417	-1.73223067919	6.13438899704	29.308282758
6	0.688632479163	-0.480976183569	0.674648834246	1.27531864428	0.20248169204	2.2410797397	0.0138960222006	-0.226030953292	-0.0278048998965	0.240220927652	0.0291016195272	0.0808166799201	0.361566062137	-0.209065657451	0.0216407881088	0.302866345283	-0.0190087725139	-0.0144615999169	0.358790419109	0.0315695582838	0.31461505181	-14.1797081452	-2.85878687016	29.1407723469
7	1.87313443352	-0.720337167797	1.08513105646	3.02471848105	-1.70859595178	6.27878286132	0.0864982344738	0.0818664563849	-0.167995233837	-0.423753940763	-0.0897169717696	0.0306510007075	1.19754218011	-0.125769467072	-0.0516849318148	0.378435794524	0.011791035088	0.00279888707839	0.216790084149	0.00171087935953	0.3044487818	-15.6499260887	-10.4083230746	18.5515702282
8	2.79315409437	0.0321374863266	0.288773324741	2.75386271297	0.821719493884	3.46254221212	-0.0333123535476	-0.30378552123	0.533727833394	-0.057713479821	-0.0849876768541	-0.412439896666	-0.714021025672	0.312029218899	0.0269419728985	0.53355857837	-0.0133368959697	0.0357423669579	0.296608111772	-0.0393105032782	0.499756023614	-31.6754689336	31.797098534	32.2244726194
9	1.1662753571	-0.117696559364	-0.415541251418	1.75439675069	-0.140994699233	0.909870655503	-0.0288885532577	-0.29279549848	0.35462367024	0.274449561657	0.107179985	-0.0965913196415	-0.381328234115	-0.0742886488275	-0.067032389942	0.500006246367	0.039562713208	-0.00749864261852	0.3840844073	-0.104655010044	0.395299262797	-32.5368487129	23.5530646468	44.0445583456
10	3.17406768723	-2.20436439421	0.485247231415	3.45067458514	-0.519218043267	1.21204584707	-0.224723696986	-0.704748616978	-0.295854632427	0.788496604236	0.184298838676	0.532244187519	-0.0281258420332	-0.357043371609	0.0284247945872	0.404078569184	0.0576730707017	0.0610810277006	0.565894506695	0.0299485387513	0.355195803848	-36.7584184898	11.1240997578	52.9007273921
11	1.20343848089	-0.369194511003	0.213395911977	1.10356221518	-0.227173306144	1.48531834739	0.0278257387348	-0.0502528551452	0.104301157861	-0.0295562884611	-0.0838206084762	0.0266888651913	-0.102979808102	0.00883809242572	0.0688350725185	0.29137983178	0.0165724285101	0.00089322598951	0.285958882825	-0.020599802258	0.260456026183	-33.0144149795	10.2413255206	33.751533601
12	3.2511934967	-0.53878089264	0.587420107907	1.40780461707	-0.0377317160928	0.155902582835	-0.0590839659636	-0.148693369956	1.05372614518	-0.393442704513	-0.181612804772	-0.524803150767	-0.078149556458	0.32785803177	0.265030552768	0.662471878889	-0.0768181949564	0.0129531035467	0.661102267772	0.0391654443517	0.691855331459	-16.4356494108	23.4933403687	31.749841986
13	2.61707357569	1.95296039264	1.37627313991	4.50169229713	2.00587443053	2.67162389777	-0.412517948662	0.313372989195	0.4805352627	-0.823205328599	0.14632123437	0.426345953309	-0.443907959062	0.0303047189783	0.138849590581	0.346558658061	0.0882930692308	-0.0591120382	0.320934396744	0.0222286573745	0.317381523922	-34.2697069672	19.7191881728	18.526074469
14	0.934970637786	-0.352692547502	-0.21401161839	2.57885817734	-0.636840100864	3.05944419101	0.0270419609936	0.183353666418	0.030303463752	0.00278086184664	-0.101097371423	0.30407848064	-0.0746784922543	-0.399045636444	0.118969734108	0.336561521763	0.0102006408696	-0.032729792691	0.274143767911	0.0159105675432	0.322592953224	-28.4728750059	23.7816278554	-12.3138930747
15	1.1126927534	-0.149248997624	-0.132120488767	0.718921908229	-0.471946225452	2.64285772273	0.00176069587775	0.193495140679	-0.0488140860752	-0.042332408136	-0.0346360397028	0.0169965380058	0.18018328424	0.0760895830771	0.0362775627637	0.264146764047	0.020100729747	0.0222272506996	0.293263015532	-0.00998906523074	0.261105480445	-21.5465165181	3.76951512932	-12.9550759606
16	2.10367014737	0.127322882382	-0.139659495238	2.46183478447	-0.422020033503	2.16314960383	-0.0116167897679	0.0821237143312	0.165144500639	-0.136860585288	0.0992532778648	0.537231276844	-0.0492346908616	-0.466190777283	-0.0357202881278	0.329302876593	-0.0120551882813	-0.0222519877446	0.334027819804	0.0286054429529	0.34438881718	-31.3033962248	11.0949283502	0.821001941104
17	3.31427063728	-1.00419925489	1.48103056606	2.77267551705	-0.657900573538	3.87230793488	-0.402327646104	0.0791087963133	0.560836264638	0.293817596048	-0.0643867111448	-0.135274026634	-0.480109255184	0.18421641775	0.428584851453	0.339568738812	-0.0382254630893	-0.020590401825	0.216843112212	0.0279800174146	0.289260836151	-24.4974367261	19.4377858094	7.33216732696
18	2.93718202681	0.705566953654	0.839206928413	3.11132511846	0.380418818905	1.84116947144	0.00467156449007	0.177774218536	-0.6104827954	-0.170395959798	0.0770567921441	-0.149306206009	0.393895701594	0.197274700399	-0.0337741592384	0.533867286678	-0.0419218322128	-0.00157758958491	0.373532303766	0.0282187536584	0.448689312787	-38.3191884734	-25.2256269172	9.00433273928
19	1.54168217091	-0.642198495502	0.172591556782	0.602022637757	0.279039361161	1.01789667129	0.0748116531833	0.0153191940564	-0.486955072025	-0.268840581194	0.0233672742128	0.393316690967	0.513687126967	-0.153163971942	-0.0779327841288	0.549048126808	-0.147540599436	-0.094326454277	0.380093190873	0.0586953213296	0.488907252627	-47.0199052623	-22.5498644395	5.93887945861
20	2.83179692416	-0.495940031348	0.326990847874	0.884865605267	0.541062528969	0.604549149057	0.0828814419288	0.225234958225	-0.125234995991	-0.429701139029	0.0719784966061	0.542862258909	0.359907196829	-0.43280018088	-0.16288021732	0.424133415981	-0.0918206613194	-0.0829909230094	0.517604985087	0.00287732560815	0.468244705136	-53.0735030739	-12.6811350557	0.301507718017
21	1.04355575703	0.0938380703568	-0.104848861175	3.53210722145	-0.55872565704	2.15959613869	0.362334799604	0.25236353879	0.177263489623	0.240410214042	-0.119698926627	1.33801779316	0.102444809444	-0.511638869101	-0.23965745747	0.341824342643	-0.0756664110911	-0.104046766119	0.588009064251	0.0328690438886	0.682333767963	-60.9499198208	-7.08517863972	2.75784676889

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 137 through 187 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 188 through 260 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 261 through 283 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 1 through 57 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 58 through 218 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 219 through 260 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 261 through 283 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 1 through 29 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 30 through 116 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 117 through 136 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 137 through 237 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 238 through 260 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 261 through 283 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 1 through 57 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 58 through 204 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 205 through 260 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 261 through 283 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 1 through 29 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 30 through 76 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 77 through 116 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 117 through 136 )

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