PDB-6yc6: Structure of C. glutamicum GlnK

ID or keywords:

Entry

Database: PDB / ID: 6yc6

Title

Structure of C. glutamicum GlnK

Components

PII protein

Keywords

SIGNALING PROTEIN / PII / Corynebacteria / Nitrogen regulation

Function / homology

Function and homology information

regulation of nitrogen utilization / enzyme regulator activity / ATP binding / cytosol
Similarity search - Function

Biological species

Corynebacterium glutamicum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Grau, F.C. / Muller, Y.A.

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Crystal structures of adenylylated and unadenylylated P II protein GlnK from Corynebacterium glutamicum.
Authors: Grau, F.C. / Burkovski, A. / Muller, Y.A.

History

Deposition	Mar 18, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 24, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6yc6.cif.gz	236.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6yc6.ent.gz	161.6 KB	Display	PDB format
PDBx/mmJSON format	6yc6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6yc6_validation.pdf.gz	458.5 KB	Display	wwPDB validaton report
Full document	6yc6_full_validation.pdf.gz	459.4 KB	Display
Data in XML	6yc6_validation.xml.gz	14.1 KB	Display
Data in CIF	6yc6_validation.cif.gz	18.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yc/6yc6 ftp://data.pdbj.org/pub/pdb/validation_reports/yc/6yc6	HTTPS FTP

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Related structure data

Related structure data	6yc7C 3bzqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4co5-1 2fa8-d 1p18-d 1tc2-d 1p19-1 6who-2 6whn-2 2e40-2 7bop-4 5mqv-5 Search similar-shape structures by Omokage search (details) 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: PII protein

B: PII protein

C: PII protein

hetero molecules

40 kDa, 3 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)	82.511, 82.511, 170.587
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2
Space group name Hall	P4nw2abw
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z+3/4 #3: y+1/2,-x+1/2,z+1/4 #4: x+1/2,-y+1/2,-z+1/4 #5: -x+1/2,y+1/2,-z+3/4 #6: -x,-y,z+1/2 #7: y,x,-z #8: -y,-x,-z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	C-308- HOH

#1: Protein	PII protein Mass: 13063.007 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: glnB / Production host: Escherichia coli (E. coli) / References: UniProt: H7C694
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.7 Å³/Da / Density % sol: 66.8 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2:0M ammonium sulfate, 5% (v/v) 2-propanol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 16, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.2→48.16 Å / Num. obs: 30720 / % possible obs: 99.93 % / Redundancy: 8.6 % / B_iso Wilson estimate: 48.27 Å² / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.1015 / Net I/σ(I): 15.34
Reflection shell	Resolution: 2.2→2.279 Å / Redundancy: 8.2 % / R_merge(I) obs: 1.75 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 2999 / CC_1/2: 0.458 / CC star: 0.793 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3BZQ

3bzq

Resolution: 2.2→48.16 Å / SU ML: 0.242 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.3382

	R_factor	Num. reflection	% reflection
R_free	0.2342	1540	5.01 %
R_work	0.2078	-	-
obs	0.2092	30714	99.94 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 59.02 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→48.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2480	0	47	54	2581

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0041	2538
X-RAY DIFFRACTION	f_angle_d	0.567	3414
X-RAY DIFFRACTION	f_chiral_restr	0.0496	415
X-RAY DIFFRACTION	f_plane_restr	0.003	430
X-RAY DIFFRACTION	f_dihedral_angle_d	17.1652	1518

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 (%)
2.2-2.27	0.3279	136	0.3098	2570	X-RAY DIFFRACTION	100
2.27-2.35	0.2921	130	0.2892	2626	X-RAY DIFFRACTION	99.96
2.35-2.45	0.2989	129	0.2729	2606	X-RAY DIFFRACTION	99.96
2.45-2.56	0.2701	145	0.2575	2601	X-RAY DIFFRACTION	100
2.56-2.69	0.2837	125	0.2474	2622	X-RAY DIFFRACTION	99.89
2.69-2.86	0.2623	152	0.2362	2627	X-RAY DIFFRACTION	99.93
2.86-3.08	0.2451	133	0.2373	2636	X-RAY DIFFRACTION	99.96
3.08-3.39	0.263	144	0.2233	2642	X-RAY DIFFRACTION	100
3.39-3.88	0.2106	137	0.1938	2675	X-RAY DIFFRACTION	99.93
3.88-4.89	0.2099	164	0.1621	2690	X-RAY DIFFRACTION	100

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	0.2513342733	-0.0687119995238	-0.151682573974	0.135191959968	0.118419658869	0.151413544168	0.0405330118095	0.326239251566	0.231578034632	-0.0297510204857	0.110242889078	-0.687149371605	0.0707722888561	0.21061316818	2.65872671779E-5	0.603554340613	-0.0484152155043	0.10714859321	0.455192953238	0.0410325419177	0.56486343254	-7.09898815384	-13.9058694756	-24.0446296761
2	0.0140414589139	0.0140013832029	0.0216559526873	0.00745072519186	-0.00318851487378	0.0355221516431	-0.43498835434	0.0196701556497	0.132880589619	0.17865995114	-0.510935218516	-0.852695006367	0.528135351612	0.355770909889	0.00093699251373	0.617964741808	-0.0193119714247	0.236483504051	0.929147275976	0.0592859593482	0.95021932599	-0.0708369199589	-15.2181018866	-23.0925063336
3	1.30593484168	0.396299414647	-0.694268404869	1.34727728695	-0.989081578169	1.56790591537	-0.0221093552745	0.00565326070796	-0.00651232807011	-0.0188220490904	0.0249823983064	0.264067987694	0.0539251461302	-0.0881844163568	6.3481038619E-6	0.529467106823	-0.0290124645165	0.0215465902753	0.380003116006	0.00840086085587	0.467381337819	-20.4689443842	-16.6916034795	-17.7440931228
4	0.32505364155	0.273069927319	0.0972188732203	0.666874501411	0.565658454489	0.467781092406	-0.344787688373	-0.827334424966	0.302439855723	0.380512154237	-0.414748954919	-1.2578406924	-0.65280733024	0.220327951988	0.000378931532565	0.643723231823	0.0956615300276	-0.0743383858006	0.847487528614	0.0828251101933	0.815538300267	-0.993690430718	-16.159957241	7.36189264169
5	1.08851657319	0.219701763524	-0.821423005023	0.807257819282	-0.0179244545948	0.681020778769	0.0321186782509	0.0779369863752	0.0610936977003	-0.145899628549	0.0237824599219	-0.0476840939734	0.0991368225096	0.192186327025	3.89167801937E-6	0.623282425754	-0.0295118022674	0.00910116741739	0.362580572125	0.0140648661691	0.402526319242	-17.2869162695	-16.2960015501	-21.5143454699
6	0.733836166349	-0.388564455996	-0.312283624346	0.243913058193	-0.0706556980535	0.295731289471	-0.0457579882016	-0.0958459767224	0.0334896533666	-0.243295475955	-0.244821012517	-0.375424298615	-0.027694013179	0.0206735485855	6.36605977082E-6	0.636154826373	-0.0225318890592	0.0637549596604	0.390193223435	0.0381370574685	0.400233398621	-11.4052597787	-14.5243336972	-19.5966922529
7	0.404762048839	0.353920485361	0.143252340233	0.286745345854	-0.0608696593911	0.393806055316	-0.214327996542	0.586835355566	-0.247857067481	-0.563371440497	0.0176116923227	0.168466838124	-0.107096885295	-0.327701355421	5.72345285988E-5	0.671225936078	-0.0167307356642	-0.0732791958501	0.460743975168	-0.0275871351205	0.495366609043	-27.2978966464	-33.9803841773	-24.3519266794
8	0.812047532019	0.716049904036	-0.402482123249	1.52091701928	0.961836720516	2.33311801174	0.190444818503	-0.075276443211	0.00353750726685	0.0315270204322	-0.178507974111	0.0348821614536	-0.110246710987	-0.0288802286618	0.000527949867674	0.518727255924	-0.0103718422877	0.0388280673068	0.381248511249	0.0193516156131	0.400152163704	-24.655554571	-28.123939561	-9.21162545124
9	-0.00861752314568	-0.493552268343	-0.0569178250965	0.236192676022	0.220614080191	-0.0349738707231	-0.208826957798	-0.262261837613	-0.347515425226	-0.127462114331	0.268962411833	0.157191124765	0.0672562995574	0.0153653939469	8.18605788834E-5	0.519473996057	-0.00465933779747	0.0111601740855	0.339258700713	-0.0291811353729	0.48738211769	-21.0714274794	-30.9867780845	-10.3109637447
10	0.287692590854	0.94631143608	0.455277285898	1.28307644864	0.594982422823	0.560848398591	0.0255491171407	0.00397716744851	-0.0597879383342	-0.559815738488	0.0207573928511	-0.0898024408129	0.199779124072	0.00153060262463	-4.43260880896E-5	0.590877092068	-0.000262736510742	0.0171433694845	0.349298988532	-0.00432748359855	0.464607999175	-24.3776153373	-38.3953008013	-16.6340113648
11	0.222415079614	-0.273814987691	0.10998015131	0.685694657518	0.248232935634	0.267027598316	0.124134950755	-0.0277265087164	-0.737670427685	-0.386749682983	-0.0462574832473	-0.216219877958	0.885407228226	0.48542048772	-9.2378658698E-8	0.56299742977	0.156961462922	0.0362972558696	0.600267965967	0.0349895839736	0.746680774939	-1.60904286975	-39.6741322341	-10.6560126318
12	0.34487925152	-0.363603765864	-0.125451872117	0.457738615672	0.252105786655	0.130700259508	-0.245529490727	-0.420798797033	-0.16174182705	-0.178127049725	0.00417851068533	-0.455072291042	-0.00568189360976	0.812597717075	0.000155174623459	0.560245139809	0.0169773053497	0.0670681525157	0.503575566462	0.00331081924632	0.527095128765	-4.72412658831	-27.7427734391	-11.5896209963
13	0.154814426308	-0.0629145719529	-0.0219365570595	0.188827298994	0.145969893991	0.124004185535	0.0419231605354	-1.25919023974	0.535826197287	0.994212594906	-0.254312500551	-0.611243924259	-0.400021748981	0.527088917061	0.000173354504546	0.549882343044	-0.0407742418939	-0.0479228455207	0.856286008996	-0.11475463191	0.701602310758	1.07928479861	-21.4530589168	-1.53983767205
14	-0.000724856169514	0.00879668822856	-0.00607033593248	0.0893328547531	0.00773637140453	-0.00821609316161	0.17837508199	-0.516578616106	0.740220348891	0.550511118444	0.281183169272	-0.627357758058	-0.538492647389	-0.338716047959	-0.000289605033468	0.543212487176	-0.088501173259	-0.00473054471218	0.51786377252	-0.0368064558462	0.695422871731	1.33696495481	-17.4727885968	-10.6241597358
15	0.188809240668	-0.0261915795349	-0.0924772866533	0.169796422784	0.0493144440849	-0.0241580019422	-0.0490853902515	-0.445688314721	0.273694393535	0.259441099642	0.203611420135	0.079600099929	-0.121084576877	0.299843647078	-0.00014645895753	0.6739016546	0.0343941741682	0.0176650337087	0.51254461988	-0.0638128608181	0.499287627823	-14.0653943507	-27.1820821418	-2.77161924546
16	0.166307803443	-0.0617028306598	-0.195566114853	0.148563721838	0.0919327411272	0.0964153719249	0.437177285519	0.237855540883	-0.859970688724	0.708195000595	-0.583774315678	0.724519434532	0.0556566485138	0.279674209183	8.79127952612E-5	0.906393624782	-0.0106344928765	0.0139945234813	0.811075004444	-0.0509940867866	0.880526526982	-28.3382925665	-38.8283778255	4.43916969443
17	0.200502688643	-0.105747369297	-0.145860755533	0.336654209766	0.2157766516	0.370692334405	-0.576994028229	0.139014367957	-0.497422860488	-0.435213292713	-0.079093477647	-0.777368119619	0.445837850563	-0.334263767674	-0.00013576066532	0.540139781529	0.0256978748937	0.0465107408233	0.49091684745	0.0295361061146	0.543823243003	-8.31636698385	-26.6357191233	-6.86411210941
18	0.460425598752	-0.0894363595936	-0.0884079941298	0.414706976424	0.128197076796	0.128736964589	-0.341932715393	-0.424016238203	-0.221381624039	-0.381479437243	-0.13073791895	-1.37563202005	0.0795202432529	0.189659976809	8.86992790109E-5	0.539597526745	-0.00299086328753	0.0838264820344	0.688303479069	-0.00623595958956	0.78018875755	4.57058149718	-28.2109393773	-11.3205131747
19	0.533618213967	-0.245841714451	0.0158073732507	0.409838923234	0.328532243797	0.25052453801	-0.0800890016294	0.0304652640859	-0.263524701238	-0.338952440566	-0.0631687545617	-0.317926227621	1.23228667078	0.136027216746	-0.00464232978936	0.441340066106	0.0920799432673	0.0473253440255	0.497696186627	0.0685372234084	0.606237299087	-3.1247326625	-34.0662480567	-6.47320194256

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 96 through 107 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 108 through 112 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid -1 through 36 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 37 through 54 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 55 through 81 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 82 through 96 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 97 through 112 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 54 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 55 through 66 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 67 through 95 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 96 through 112 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1 through 9 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 10 through 22 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 23 through 28 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 29 through 36 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 37 through 54 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 55 through 66 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 67 through 81 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 82 through 95 )

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