PDB-7tem: Crystal Structure of the Putative Exported Protein YPO2471 from Y...

ID or keywords:

Entry

Database: PDB / ID: 7tem

Title

Crystal Structure of the Putative Exported Protein YPO2471 from Yersinia pestis

Components

Putative exported protein YPO2471

Keywords

UNKNOWN FUNCTION / protein of unkown function / glycoside hydrolase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Metal binding protein

Function / homology

sucrose / ACETIC ACID / Exported protein

Function and homology information

Biological species

Yersinia pestis CO92 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.65 Å

Authors

Kim, Y. / Chhor, G. / Endres, M. / Babnigg, G. / Schneewind, O. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of the Putative Exported Protein YPO2471 from Yersinia pestis
Authors: Kim, Y. / Chhor, G. / Endres, M. / Babnigg, G. / Schneewind, O. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jan 5, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 19, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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	7tem.cif.gz	434.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7tem.ent.gz	295.1 KB	Display	PDB format
PDBx/mmJSON format	7tem.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/te/7tem ftp://data.pdbj.org/pub/pdb/validation_reports/te/7tem	HTTPS FTP

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Related structure data

Similar structure data	2j79-2 4n6r-d 7tem-2 3wh7-d 5knt-d 3hwo-2 5ebe-1 3qhb-d 2e40-1 6m6m-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: IDP96002

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: Putative exported protein YPO2471

B: Putative exported protein YPO2471

hetero molecules

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

1

A: Putative exported protein YPO2471

hetero molecules

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

2

B: Putative exported protein YPO2471

hetero molecules

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

Unit cell

Length a, b, c (Å)	54.774, 90.016, 181.301
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

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein

Putative exported protein YPO2471

Mass: 48810.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Yersinia pestis CO92 (bacteria) / Gene: y1718, YP_2290, EGX46_13440, ypo2471 / Plasmid: pMCSG68 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A5P8YGV9

#2: Polysaccharide

beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose

Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose

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Non-polymers , 5 types, 690 molecules

#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₄O₂
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 680 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 2.31 Å³/Da / Density % sol: 46.79 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Sodium acetate trihydrate pH 7.0, 20 % (w/v) Polyethylene glycol 3,350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97916 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 12, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97916 Å / Relative weight: 1
Reflection	Resolution: 1.65→50 Å / Num. obs: 106782 / % possible obs: 97.6 % / Redundancy: 7 % / B_iso Wilson estimate: 19.59 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.1 / Net I/σ(I): 25.9
Reflection shell	Resolution: 1.65→1.68 Å / R_merge(I) obs: 0.921 / Mean I/σ(I) obs: 1.43 / Num. unique obs: 4253 / CC_1/2: 0.538

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Processing

Software

Name	Version	Classification
PHENIX	1.19_4092	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MLPHARE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.65→23.44 Å / SU ML: 0.1532 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.8622
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1887	5299	4.97 %
R_work	0.1589	101367	-
obs	0.1604	106666	97.43 %

Solvent computation

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

Displacement parameters

B_iso mean: 25.35 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→23.44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6501	0	82	680	7263

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	7000
X-RAY DIFFRACTION	f_angle_d	0.9898	9535
X-RAY DIFFRACTION	f_chiral_restr	0.0604	1039
X-RAY DIFFRACTION	f_plane_restr	0.0078	1234
X-RAY DIFFRACTION	f_dihedral_angle_d	14.1438	2587

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 (%)
1.65-1.66	0.2779	135	0.2664	2526	X-RAY DIFFRACTION	73.51
1.66-1.68	0.3102	158	0.2525	2761	X-RAY DIFFRACTION	82.43
1.68-1.7	0.2991	145	0.2375	3021	X-RAY DIFFRACTION	86.27
1.7-1.73	0.266	142	0.229	3104	X-RAY DIFFRACTION	90.67
1.73-1.75	0.2437	156	0.2181	3230	X-RAY DIFFRACTION	94.63
1.75-1.77	0.2704	168	0.2085	3371	X-RAY DIFFRACTION	97.36
1.77-1.8	0.2362	168	0.1986	3417	X-RAY DIFFRACTION	99.78
1.8-1.82	0.2451	173	0.1897	3475	X-RAY DIFFRACTION	99.89
1.82-1.85	0.2079	189	0.1794	3386	X-RAY DIFFRACTION	99.97
1.85-1.88	0.2198	177	0.19	3458	X-RAY DIFFRACTION	99.95
1.88-1.92	0.2367	175	0.1822	3431	X-RAY DIFFRACTION	99.92
1.92-1.95	0.2217	153	0.1711	3494	X-RAY DIFFRACTION	99.95
1.95-1.99	0.2224	155	0.1627	3426	X-RAY DIFFRACTION	100
1.99-2.03	0.1935	196	0.1584	3448	X-RAY DIFFRACTION	100
2.03-2.07	0.1991	175	0.1528	3422	X-RAY DIFFRACTION	100
2.07-2.12	0.2016	172	0.1548	3452	X-RAY DIFFRACTION	100
2.12-2.17	0.2008	199	0.1535	3439	X-RAY DIFFRACTION	100
2.17-2.23	0.1849	163	0.1483	3465	X-RAY DIFFRACTION	100
2.23-2.3	0.1921	164	0.1475	3497	X-RAY DIFFRACTION	100
2.3-2.37	0.1842	187	0.1477	3458	X-RAY DIFFRACTION	100
2.37-2.46	0.1782	184	0.1508	3430	X-RAY DIFFRACTION	100
2.46-2.56	0.1855	181	0.1568	3491	X-RAY DIFFRACTION	100
2.56-2.67	0.1866	187	0.1626	3458	X-RAY DIFFRACTION	100
2.67-2.81	0.2029	220	0.1667	3459	X-RAY DIFFRACTION	99.97
2.81-2.99	0.2142	192	0.1681	3477	X-RAY DIFFRACTION	100
2.99-3.22	0.2125	181	0.1736	3531	X-RAY DIFFRACTION	100
3.22-3.54	0.1873	207	0.1608	3478	X-RAY DIFFRACTION	100
3.54-4.05	0.1521	203	0.1426	3529	X-RAY DIFFRACTION	100
4.05-5.09	0.1259	186	0.1176	3582	X-RAY DIFFRACTION	99.92
5.1-23.44	0.1567	208	0.1442	3651	X-RAY DIFFRACTION	97.87

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	3.29082186869	0.0292928912581	0.0254770991444	1.46840399946	0.338397453076	1.69640834162	0.035577386603	-0.114001827906	0.308016686127	0.11056350719	0.0194626257009	-0.0201562285817	-0.347678862174	-0.0540869375927	-0.0306641708645	0.196315126672	0.0208867198285	0.0259464294043	0.101623849722	-0.00394112707842	0.130697301825	47.0760883286	93.8588766228	38.3322439012
2	5.32309803619	0.719285664426	0.324125824561	2.55551702967	-0.232055018669	2.79227422794	-0.130778897576	-0.28604220659	-0.304976023765	0.447980052818	0.0309462308713	0.0279192550801	-0.039636091733	-0.102600363937	0.1095846851	0.180825460438	0.0374404938057	0.053484136566	0.147161099624	1.75750701141E-5	0.134486738941	43.3974490038	83.4426035558	44.3855187427
3	1.80241981927	-1.78578339581	-1.76666165055	3.88201038551	2.4663138665	1.97803596742	-0.0843828322806	0.235922470332	-0.0889351811958	0.095131470179	-0.0934991192168	0.79796123889	-0.199627106507	-0.793778200112	0.268359029398	0.179233228664	0.130759075418	-0.00221516646106	0.357119882445	0.00658805301391	0.287945650657	30.9072313569	88.2186265081	30.9604270651
4	0.859662638668	-0.110725553153	-0.502432781659	1.14103308513	0.367335986714	1.71051973512	-0.0425193141795	0.101671878918	-0.0885771369696	0.0258672868829	0.0351035718763	0.154805047706	0.255300717752	-0.214130550915	-0.0160406153881	0.113545432158	-0.0270702942649	0.00448549920343	0.143814571804	-0.0152040324838	0.160535184218	42.1048530177	71.2454956971	30.5960914371
5	2.11549206921	1.0243766996	-0.133867457418	1.44403964245	0.000376865359548	1.32199146626	0.00612705704439	-0.062265674261	-0.380969642622	0.0691811449608	0.000663664448049	-0.0850775702432	0.3422487892	-0.179170175012	-0.0163359936861	0.183531031291	-0.0279058495083	-0.00393690353499	0.124911066979	-0.0101494664296	0.184517102762	46.4650273489	64.2819462949	31.8302427893
6	1.82413985357	-1.18100077741	0.316080745671	2.30148668937	-0.172170522951	1.54321029425	0.0830408656109	0.0770293065172	-0.283991089073	-0.150174247925	-0.107939573956	0.119005886445	0.14318982259	0.0236070900243	0.0356003043264	0.113989123405	0.00894393560977	-0.0043835755859	0.0975532934614	-0.0123735376725	0.139004156162	28.37008832	73.7292657942	61.0137561315
7	1.1694968926	-0.5564660695	-0.0825645706515	1.29496772466	0.192520781707	1.94995054231	-0.0350907733084	-0.0301651649389	-0.174116176178	0.0525557216947	0.00812400230669	0.11397577018	0.256859661253	-0.0409637388981	0.0162149353082	0.182194773298	0.000381803808708	0.0137398284245	0.117177241014	0.0162127010683	0.18118164041	31.5183865965	71.5076881494	69.9750038716
8	3.13957448391	0.319320918656	2.24525916469	1.63443570709	1.22774572483	4.88506009293	0.0373160200689	0.168881369608	-0.230080560045	-0.0427038619053	0.106403483616	-0.180121000405	0.256181084778	0.552938911069	-0.120571638523	0.180434346165	0.0738688844868	0.0276902921552	0.224842631274	0.0117681634819	0.180393280973	47.6426452053	71.1618096909	66.6933828289
9	3.99061446771	1.53093428816	-1.61750774286	2.52499507053	-1.04688234394	3.39586977755	-0.086756895407	-0.0309789284448	0.0270699303469	-0.00773324598899	0.0926583621782	0.119249417796	0.463361915993	-0.00804639383102	0.000613254765113	0.184096003733	0.0246248193791	0.000757074065044	0.150220535738	0.0291129920591	0.137452237051	36.2784177029	71.384600457	79.320125463
10	2.83195794282	1.33267191765	1.046662247	2.54873851601	0.792076471965	2.67147020624	0.171711792318	-0.0661900930673	-0.677820746803	0.114993672743	0.0437619984215	-0.320183105522	0.71674264881	0.309321163531	-0.0448479278967	0.316358012293	0.0849867506657	-0.0128833014758	0.169627546937	0.0520605973005	0.186557891293	43.7104474978	65.0725810923	83.2089302374
11	1.23278821625	-0.174598610336	0.23855786763	1.66412533575	-0.181444046621	2.13920184582	-0.0681972305239	-0.023150758391	0.109164151619	0.0906963928025	-0.0138491618558	-0.0927512622474	-0.174768636808	0.363560437946	0.0634773610596	0.13581372097	-0.0357128743096	-0.0196740605617	0.166998020799	0.0188120963653	0.136407758388	43.315913969	89.1723819835	86.400593111
12	1.38525685761	0.526730143561	0.505188006308	1.19552999107	0.236672477251	1.124777764	0.00899206806237	-0.0366590458742	0.14671640419	0.148257208495	-0.197163460439	-0.148879061167	-0.507190612211	0.353620934588	0.123944949624	0.26079288948	-0.075168266701	-0.0512384845788	0.142599329921	0.0420908793016	0.203526092297	37.3717751901	97.4089630024	78.462278152
13	0.765079473671	0.355532497132	1.02931836387	0.595596014594	0.0969891481957	2.29196717347	-0.0916772605713	-0.0444205230306	0.141668789508	0.0187534784123	-0.0730441088562	0.0158123775278	-0.388830880861	-0.227177782823	0.134585332229	0.173250766606	0.0511763021783	-0.0146294339326	0.12187509751	0.00713386964368	0.153582392328	24.5499202568	93.605107334	70.5366956299
14	1.4452274765	-0.732078293307	0.45500455943	2.17624225729	-0.582183035878	1.4294712874	-0.148458305399	-0.269397345096	0.08127931854	0.263682525441	0.226237169916	0.3522550624	-0.28656882243	-0.425199392627	-0.0560047314713	0.190883687256	0.0759002603311	0.0333626010679	0.230127037762	0.0284272791125	0.215321690635	18.2572292985	88.6745251854	75.2818132328
15	3.19024978255	0.974642386773	0.277778358395	2.96515338925	0.248465579894	2.5056531681	-0.14192240879	0.486531747834	-0.126744321612	-0.392391618722	0.173322079423	-0.367922389721	0.0467097153573	0.308819613767	0.0336212800396	0.15255939489	-0.00293598684991	0.0566085657912	0.193937591502	-0.0536953280683	0.169128487103	59.0680140798	73.7478932547	15.5114121335
16	1.27294675642	0.238406097176	-0.107063561409	1.69401361899	-0.620771114788	2.28112840287	-0.0145354984581	0.0840094326819	-0.0606821675839	-0.108369770139	-0.0191205815704	-0.205786476271	0.0527021601206	0.185746455198	0.0502349950014	0.131197482905	-0.0095641533119	0.016697937155	0.162668012615	-0.0256610118429	0.188336653744	62.0439705857	77.7613329145	22.9021395341
17	1.57162849483	0.0597664063306	0.0465409813548	2.25067593966	1.1903509198	3.92501636504	0.112199328896	0.209209499511	0.146978225497	-0.0783346326835	-0.036525795093	-0.21313324224	-0.359831332608	0.0502424804395	-0.0749543128356	0.235649115053	-0.0358415266924	0.0468253532299	0.151026766131	0.0283623364391	0.200147942563	60.767769319	93.2283179502	17.8436776045
18	2.3553182379	-0.808698865535	0.0579996574667	2.32064383446	-0.336105065279	1.71249020804	0.0472042778515	-0.102536347817	0.0981602442562	0.108925025072	0.0443393571566	-0.420940993606	-0.231796473621	0.36967138408	-0.0766958013797	0.153915496491	-0.0656265065914	-0.00895078160444	0.192697678681	-0.0404789153034	0.206683490901	66.032724268	87.3237430541	32.8989168257

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 176 through 261 )	B	H	176 - 261	157 - 242
2	2	chain 'B' and (resid 262 through 295 )	B	H	262 - 295	243 - 276
3	3	chain 'B' and (resid 296 through 322 )	B	H	296 - 322	277 - 303
4	4	chain 'B' and (resid 323 through 389 )	B	H	323 - 389	304 - 370
5	5	chain 'B' and (resid 390 through 424 )	B	H	390 - 424	371 - 405
6	6	chain 'A' and (resid 21 through 56 )	A	A	21 - 56	1 - 36
7	7	chain 'A' and (resid 57 through 103 )	A	A	57 - 103	37 - 83
8	8	chain 'A' and (resid 104 through 133 )	A	A	104 - 133	84 - 113
9	9	chain 'A' and (resid 134 through 154 )	A	A	134 - 154	114 - 134
10	10	chain 'A' and (resid 155 through 175 )	A	A	155 - 175	135 - 155
11	11	chain 'A' and (resid 176 through 296 )	A	A	176 - 296	156 - 276
12	12	chain 'A' and (resid 297 through 340 )	A	A	297 - 340	277 - 320
13	13	chain 'A' and (resid 341 through 389 )	A	A	341 - 389	321 - 369
14	14	chain 'A' and (resid 390 through 424 )	A	A	390 - 424	370 - 404
15	15	chain 'B' and (resid 20 through 56 )	B	H	20 - 56	1 - 37
16	16	chain 'B' and (resid 57 through 103 )	B	H	57 - 103	38 - 84
17	17	chain 'B' and (resid 104 through 133 )	B	H	104 - 133	85 - 114
18	18	chain 'B' and (resid 134 through 175 )	B	H	134 - 175	115 - 156

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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