PDB-8cil: Crystal structure of Coxiella burnetii Fic protein 2

ID or keywords:

Entry

Database: PDB / ID: 8cil

Title

Crystal structure of Coxiella burnetii Fic protein 2

Components

Fic family protein

Keywords

LIGASE / Post-translational modification / AMPylation / Fic enzyme / bacterial infection

Function / homology

Domain of unknown function DUF4172 / Domain of unknown function (DUF4172) / Fido domain-containing protein / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / ATP binding / Fic family protein

Function and homology information

Biological species

Coxiella burnetii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.98 Å

Authors

Hoepfner, D. / Itzen, A. / Pogenberg, V.

Funding support

1items

Citation

Journal: Commun Biol / Year: 2023
Title: The DNA-binding induced (de)AMPylation activity of a Coxiella burnetii Fic enzyme targets Histone H3.
Authors: Hopfner, D. / Cichy, A. / Pogenberg, V. / Krisp, C. / Mezouar, S. / Bach, N.C. / Grotheer, J. / Zarza, S.M. / Martinez, E. / Bonazzi, M. / Feige, M.J. / Sieber, S.A. / Schluter, H. / Itzen, A.

History

Deposition	Feb 10, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 15, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8cil.cif.gz	324.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8cil.ent.gz	251.6 KB	Display	PDB format
PDBx/mmJSON format	8cil.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8cil_validation.pdf.gz	432.3 KB	Display	wwPDB validaton report
Full document	8cil_full_validation.pdf.gz	441.2 KB	Display
Data in XML	8cil_validation.xml.gz	27.8 KB	Display
Data in CIF	8cil_validation.cif.gz	39.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ci/8cil ftp://data.pdbj.org/pub/pdb/validation_reports/ci/8cil	HTTPS FTP

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Related structure data

Related structure data	4rglS S: Starting model for refinement
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: Fic family protein

B: Fic family protein

88 kDa, 2 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)	69.621, 124.378, 71.636
Angle α, β, γ (deg.)	90.000, 98.134, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	SER	SER	(chain 'A' and (resid 4 or resid 6 through 46...	A	A	4	4
1	2	TRP	TRP	GLN	GLN	(chain 'A' and (resid 4 or resid 6 through 46...	A	A	6 - 46	6 - 46
1	3	THR	THR	ASN	ASN	(chain 'A' and (resid 4 or resid 6 through 46...	A	A	48 - 53	48 - 53
1	4	VAL	VAL	LEU	LEU	(chain 'A' and (resid 4 or resid 6 through 46...	A	A	56 - 87	56 - 87
1	5	LYS	LYS	ARG	ARG	(chain 'A' and (resid 4 or resid 6 through 46...	A	A	94 - 98	94 - 98
1	6	ILE	ILE	PRO	PRO	(chain 'A' and (resid 4 or resid 6 through 46...	A	A	100 - 151	100 - 151
1	7	TYR	TYR	LYS	LYS	(chain 'A' and (resid 4 or resid 6 through 46...	A	A	166 - 172	166 - 172
1	8	VAL	VAL	MET	MET	(chain 'A' and (resid 4 or resid 6 through 46...	A	A	174 - 178	174 - 178
1	9	ILE	ILE	ARG	ARG	(chain 'A' and (resid 4 or resid 6 through 46...	A	A	180 - 246	180 - 246
1	10	ASN	ASN	LEU	LEU	(chain 'A' and (resid 4 or resid 6 through 46...	A	A	248 - 253	248 - 253
1	11	GLY	GLY	ASN	ASN	(chain 'A' and (resid 4 or resid 6 through 46...	A	A	259 - 312	259 - 312
1	12	LEU	LEU	THR	THR	(chain 'A' and (resid 4 or resid 6 through 46...	A	A	314 - 328	314 - 328
1	13	LYS	LYS	SER	SER	(chain 'A' and (resid 4 or resid 6 through 46...	A	A	330 - 338	330 - 338
1	14	THR	THR	THR	THR	(chain 'A' and (resid 4 or resid 6 through 46...	A	A	341	341
1	15	GLU	GLU	THR	THR	(chain 'A' and (resid 4 or resid 6 through 46...	A	A	345 - 359	345 - 359
1	16	SER	SER	ASN	ASN	(chain 'A' and (resid 4 or resid 6 through 46...	A	A	364 - 373	364 - 373
2	17	SER	SER	SER	SER	(chain 'B' and (resid 4 or resid 6 through 46...	B	B	4	4
2	18	TRP	TRP	GLN	GLN	(chain 'B' and (resid 4 or resid 6 through 46...	B	B	6 - 46	6 - 46
2	19	THR	THR	ASN	ASN	(chain 'B' and (resid 4 or resid 6 through 46...	B	B	48 - 53	48 - 53
2	20	VAL	VAL	LEU	LEU	(chain 'B' and (resid 4 or resid 6 through 46...	B	B	56 - 87	56 - 87
2	21	LYS	LYS	ARG	ARG	(chain 'B' and (resid 4 or resid 6 through 46...	B	B	94 - 98	94 - 98
2	22	ILE	ILE	PRO	PRO	(chain 'B' and (resid 4 or resid 6 through 46...	B	B	100 - 151	100 - 151
2	23	TYR	TYR	LYS	LYS	(chain 'B' and (resid 4 or resid 6 through 46...	B	B	166 - 172	166 - 172
2	24	VAL	VAL	MET	MET	(chain 'B' and (resid 4 or resid 6 through 46...	B	B	174 - 178	174 - 178
2	25	ILE	ILE	ARG	ARG	(chain 'B' and (resid 4 or resid 6 through 46...	B	B	180 - 246	180 - 246
2	26	ASN	ASN	LEU	LEU	(chain 'B' and (resid 4 or resid 6 through 46...	B	B	248 - 253	248 - 253
2	27	GLY	GLY	ASN	ASN	(chain 'B' and (resid 4 or resid 6 through 46...	B	B	259 - 312	259 - 312
2	28	LEU	LEU	THR	THR	(chain 'B' and (resid 4 or resid 6 through 46...	B	B	314 - 328	314 - 328
2	29	LYS	LYS	SER	SER	(chain 'B' and (resid 4 or resid 6 through 46...	B	B	330 - 338	330 - 338
2	30	THR	THR	THR	THR	(chain 'B' and (resid 4 or resid 6 through 46...	B	B	341	341
2	31	GLU	GLU	THR	THR	(chain 'B' and (resid 4 or resid 6 through 46...	B	B	345 - 359	345 - 359
2	32	SER	SER	ASN	ASN	(chain 'B' and (resid 4 or resid 6 through 46...	B	B	364 - 373	364 - 373

#1: Protein	Fic family protein Mass: 43978.742 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxiella burnetii (bacteria) / Gene: CBU_0822 / Production host: Escherichia coli (E. coli) / References: UniProt: Q83DB6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.49 Å³/Da / Density % sol: 64.76 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion / Details: 0.1M Tris pH8.5 20% PEG 1000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976247 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2021
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976247 Å / Relative weight: 1
Reflection	Resolution: 1.98→49.02 Å / Num. obs: 83795 / % possible obs: 99.9 % / Redundancy: 4.3 % / B_iso Wilson estimate: 42.55 Å² / CC_1/2: 0.98 / R_merge(I) obs: 0.135 / Net I/σ(I): 5.3
Reflection shell	Resolution: 1.98→2.05 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.894 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4586 / CC_1/2: 0.65 / % possible all: 100

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Processing

Software

Name	Version	Classification
XDS		data reduction
Aimless		data scaling
Auto-Rickshaw		phasing
MoRDa	1.5.07	phasing
Coot	0.9.8.2	model building
PHENIX	1.19.2_4158	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4rgl

4rgl

Resolution: 1.98→46.76 Å / SU ML: 0.2596 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4913
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2077	4044	4.83 %
R_work	0.1869	79657	-
obs	0.1878	83701	99.85 %

Solvent computation

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

Displacement parameters

B_iso mean: 56.89 Å²

Refinement step

Cycle: LAST / Resolution: 1.98→46.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5838	0	0	225	6063

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0168	5972
X-RAY DIFFRACTION	f_angle_d	1.4021	8072
X-RAY DIFFRACTION	f_chiral_restr	0.3588	885
X-RAY DIFFRACTION	f_plane_restr	0.0116	1013
X-RAY DIFFRACTION	f_dihedral_angle_d	17.6701	2193

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 (%)
1.98-2	0.3501	150	0.317	2722	X-RAY DIFFRACTION	99.79
2-2.03	0.3195	147	0.3076	2730	X-RAY DIFFRACTION	99.86
2.03-2.05	0.3047	137	0.2833	2764	X-RAY DIFFRACTION	99.86
2.05-2.08	0.3242	140	0.2535	2675	X-RAY DIFFRACTION	99.72
2.08-2.11	0.2756	133	0.2475	2802	X-RAY DIFFRACTION	99.66
2.11-2.14	0.2607	132	0.2301	2691	X-RAY DIFFRACTION	99.75
2.14-2.17	0.223	124	0.2129	2815	X-RAY DIFFRACTION	100
2.17-2.2	0.2884	126	0.2142	2710	X-RAY DIFFRACTION	99.93
2.2-2.24	0.2067	119	0.2144	2772	X-RAY DIFFRACTION	99.66
2.24-2.28	0.2179	123	0.1974	2719	X-RAY DIFFRACTION	99.89
2.28-2.32	0.2368	137	0.1977	2796	X-RAY DIFFRACTION	99.69
2.32-2.37	0.2246	146	0.1978	2682	X-RAY DIFFRACTION	99.89
2.37-2.41	0.207	137	0.1956	2747	X-RAY DIFFRACTION	99.9
2.41-2.47	0.2292	134	0.2018	2755	X-RAY DIFFRACTION	99.86
2.47-2.52	0.2368	132	0.2009	2731	X-RAY DIFFRACTION	99.93
2.52-2.59	0.2277	153	0.2002	2769	X-RAY DIFFRACTION	99.9
2.59-2.66	0.2164	150	0.1927	2720	X-RAY DIFFRACTION	99.9
2.66-2.74	0.2345	164	0.2007	2710	X-RAY DIFFRACTION	99.93
2.74-2.82	0.2233	172	0.1956	2718	X-RAY DIFFRACTION	99.9
2.82-2.92	0.2395	137	0.1926	2755	X-RAY DIFFRACTION	99.97
2.92-3.04	0.2091	136	0.1858	2752	X-RAY DIFFRACTION	99.76
3.04-3.18	0.208	145	0.1995	2742	X-RAY DIFFRACTION	100
3.18-3.35	0.2245	146	0.1947	2749	X-RAY DIFFRACTION	99.97
3.35-3.56	0.1815	163	0.1741	2736	X-RAY DIFFRACTION	100
3.56-3.83	0.1856	148	0.1787	2738	X-RAY DIFFRACTION	99.97
3.83-4.22	0.1943	115	0.1623	2813	X-RAY DIFFRACTION	100
4.22-4.83	0.1757	146	0.1544	2742	X-RAY DIFFRACTION	99.97
4.83-6.08	0.1928	132	0.1926	2773	X-RAY DIFFRACTION	99.62
6.08-46.76	0.1904	120	0.1724	2829	X-RAY DIFFRACTION	99.43

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	2.09373306868	0.880066855518	0.252259106608	2.99160768486	-0.617774847562	1.0639506164	-0.034293212823	-0.000948061495142	0.0561895845091	0.272277596889	0.0312391593703	-0.0330353603058	-0.122869332255	0.00138100843858	0.0102200075405	0.35793007483	0.0155774981611	0.00621083045785	0.36915512785	0.00219982793347	0.425906533029	47.1484665191	81.3817342005	-7.36637773129
2	7.7395885005	-1.2713568365	-1.34304316297	4.02591556882	0.292210300699	2.84247079371	-0.247957862584	0.634154413944	-0.936964541319	-0.0222999585604	0.213747973316	0.481007025325	0.0367990313737	-0.0276567262682	0.0254549247689	0.346475728519	-0.0962775584796	0.0170145352596	0.604340167772	0.0380083546903	0.814435636219	11.4229014531	69.070676828	-9.24482545089
3	5.89368628408	-1.81494426933	-0.716468212406	5.7349581394	-0.23264590952	3.32240835204	-0.560370654901	-0.306637333171	-1.1927203258	0.560080546066	0.221210346871	0.761318836543	0.342717546992	-0.0294647352227	0.386704995084	0.536248276962	-0.0518880585147	0.174147634962	0.652037872944	0.196277407289	1.10944023585	7.28846770387	64.8742686504	-3.61198065901
4	1.90298054871	0.472845010083	0.883465624883	2.8150419055	0.0921383254748	1.71280215563	-0.0210642562617	0.106753875159	0.0623349445722	-0.268896464212	-0.0467547461153	-0.0905027368017	0.191975046307	-0.0863931089882	0.0592536746101	0.303057923245	-0.0132251843084	0.11771957148	0.315781967747	-0.047391418072	0.334561063872	49.5794430642	46.2680069936	-1.99869128961
5	3.34121623361	-0.374331850543	1.3338704484	4.5878786542	-0.239910541221	4.50984170318	0.0874777294306	-0.00321979162132	-0.2361928429	-0.00557429108829	0.0674100450324	-0.105605898555	0.325028106923	-0.249781959524	-0.152538327917	0.267530791216	-0.0434270314867	0.0416087031652	0.328325941612	-0.00133611107699	0.339846496036	45.3669216137	32.7165449236	7.2771643229
6	3.49158498748	3.6495728099	-1.17655579923	4.10173694058	-1.17585750346	0.510143576818	-0.51689356643	-1.01597868059	-1.69529844874	1.42896564966	1.60452077188	0.191831606971	-0.104035984958	0.514759578776	-0.704530073578	0.837452640669	0.349640594307	-0.0711496917048	0.94287144456	0.0693025307265	1.04062668642	65.2471548084	32.0637015626	4.84205857532
7	5.51142318675	-0.371595356464	1.86713965132	4.48936186463	-2.32578948738	5.95140853098	0.0730699476933	-0.350067150929	-0.158899471241	0.471892482719	-0.0494033112514	-0.19515694694	0.00315888433438	-0.0405908676319	0.000818333034933	0.344049343796	-0.0229593805217	-0.0633527413057	0.321553949266	-0.0860972217423	0.432191083878	56.8183323043	46.468929413	13.9738476493
8	0.55129640668	0.689040247901	0.177240250408	3.57457437646	-1.59889878066	3.4303398458	-0.0287324067773	0.103685217692	-0.00228044983474	-0.455316393044	-0.216536138477	-0.868716408532	0.168279936348	0.452469110493	0.151364214685	0.361830146038	0.0169766310415	0.0965957929424	0.419108784789	-0.0242932081648	0.578444956095	53.8921228543	44.1655390434	1.07061382596
9	6.86538477322	1.17638024922	4.65464725969	2.4144175813	1.48793079571	5.87763547396	-0.0530533001681	0.880812577314	0.0263317031015	-0.396216004128	0.0292904530747	-0.376160052813	0.0319676120243	0.773228776335	-0.00710343353688	0.406432646783	0.0108242458278	0.0926514750961	0.315382825911	0.0132099546054	0.482729989855	52.6840495095	51.4580285315	-7.49550393536
10	4.57357390201	0.0011639188631	-0.82228348674	6.81540996136	3.99844483608	8.4958563647	-0.224286821289	-0.180020654045	0.0937920581407	0.0244503227694	-0.155769676236	0.0621593874327	-0.112735904005	-0.43862094333	0.3237150214	0.533636615083	0.0400241433763	0.0136796268228	0.388176695537	-0.0637623751156	0.303728023777	37.2280161366	38.0106038021	-33.5252118023
11	5.28125922107	0.566834868824	1.65496284184	6.61024886712	-3.18939704993	3.11337574845	0.0797540662834	-0.206763235147	0.301780828201	1.31063148959	-0.509415891426	-1.36607315491	-0.552829122132	0.159314486683	0.348964199496	0.573936584617	-0.102031982473	-0.164460475361	0.457444174728	0.0111364979451	0.589798349115	61.5960426824	89.6464818133	0.592471181145
12	2.88184955322	-1.21831993095	1.15945359546	2.70408515682	-0.742841251264	1.44478069698	0.0782772559636	0.143374621686	-0.159688769134	-0.119437039028	-0.0638239104582	0.206141537598	0.0896517305185	-0.0984766629258	-1.8811929092E-5	0.318327756219	-0.00833456123506	0.0489455997153	0.363817552379	0.0040331531376	0.397490454921	36.8545306988	75.1289142811	-12.0498495335
13	6.54146284186	2.01986330217	1.37965161816	5.817751475	1.21537371734	2.41641657098	-0.170188341707	0.392857587401	0.623361914755	-0.398787193577	-0.108866377192	0.252937211865	-0.212206939686	-0.0972702597249	0.300824888583	0.348189794793	0.0099999062785	0.0245819187674	0.383037865872	0.0692028390202	0.289174925241	42.5860736245	90.3558269891	-21.9919924099
14	8.25795173719	6.07547324418	-3.01766507691	7.25295581023	-3.77349049418	2.68757745058	0.190170955513	-0.347162810858	1.04138422049	1.21913561097	-0.117950110401	-0.0676794788678	-0.588024412921	0.0424038075122	-0.00319357393048	0.502703273327	0.005146105147	-0.0763600265179	0.438352250517	0.0895298633564	0.663543662671	57.501282015	99.6022675994	-8.12666661511

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain B and resid 177:290)
2	X-RAY DIFFRACTION	2	(chain B and resid 291:335)
3	X-RAY DIFFRACTION	3	(chain B and resid 336:376)
4	X-RAY DIFFRACTION	4	(chain A and resid 3:89)
5	X-RAY DIFFRACTION	5	(chain A and resid 90:148)
6	X-RAY DIFFRACTION	6	(chain A and resid 149:165)
7	X-RAY DIFFRACTION	7	(chain A and resid 166:207)
8	X-RAY DIFFRACTION	8	(chain A and resid 208:259)
9	X-RAY DIFFRACTION	9	(chain A and resid 260:292)
10	X-RAY DIFFRACTION	10	(chain A and resid 293:374)
11	X-RAY DIFFRACTION	11	(chain B and resid 4:19)
12	X-RAY DIFFRACTION	12	(chain B and resid 20:82)
13	X-RAY DIFFRACTION	13	(chain B and resid 83:149)
14	X-RAY DIFFRACTION	14	(chain B and resid 150:176)

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