PDB-4x2d: Clostridium difficile Fic protein_0569 mutant S31A, E35A in compl...

ID or keywords:

Entry

Database: PDB / ID: 4x2d

Title

Clostridium difficile Fic protein_0569 mutant S31A, E35A in complex with ATP

Components

Fic family protein putative filamentation induced by cAMP protein

Keywords

STRUCTURAL PROTEIN / Fic protein / a-helical / SE/AA mutant

Function / homology

Function and homology information

ATP binding / metal ion binding
Similarity search - Function

Biological species

Peptoclostridium difficile (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.5 Å

Authors

Jorgensen, R. / Dedic, E.

Funding support

Denmark, 1items

Citation

Journal: To Be Published
Title: Structure of Clostridium difficile Fic_0569 S31A, E35A mutant at 1.8 Angstroms resolution
Authors: Jorgensen, R. / Dedic, E. / Alsarraf, H. / Welner, D. / van Leeuwen, H.C. / Oestergaard, O.

History

Deposition	Nov 26, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Dec 23, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jan 10, 2024	Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	4x2d_validation.pdf.gz	803.9 KB	Display	wwPDB validaton report
Full document	4x2d_full_validation.pdf.gz	811.5 KB	Display
Data in XML	4x2d_validation.xml.gz	29.3 KB	Display
Data in CIF	4x2d_validation.cif.gz	39.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x2/4x2d ftp://data.pdbj.org/pub/pdb/validation_reports/x2/4x2d	HTTPS FTP

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Related structure data

Related structure data	4x2cC 3cucS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5j8j-1 4kpn-4 5fm0-d 4x2e-4 6wv4-d 4kpo-d 4x2e-1 3mxm-2 4x2e-2 4gbs-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4x2cC

3cucS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Fic family protein putative filamentation induced by cAMP protein

B: Fic family protein putative filamentation induced by cAMP protein

C: Fic family protein putative filamentation induced by cAMP protein

D: Fic family protein putative filamentation induced by cAMP protein

hetero molecules

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

1

A: Fic family protein putative filamentation induced by cAMP protein

hetero molecules

C: Fic family protein putative filamentation induced by cAMP protein

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

2

C: Fic family protein putative filamentation induced by cAMP protein

A: Fic family protein putative filamentation induced by cAMP protein

hetero molecules

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

3

B: Fic family protein putative filamentation induced by cAMP protein

D: Fic family protein putative filamentation induced by cAMP protein

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

4

D: Fic family protein putative filamentation induced by cAMP protein

B: Fic family protein putative filamentation induced by cAMP protein

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

Unit cell

Length a, b, c (Å)	158.080, 60.100, 124.830
Angle α, β, γ (deg.)	90.000, 118.600, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B
3	1	chain C
4	1	chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-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	SER	SER	LYS	LYS	chain A	A	A	4 - 233	4 - 233
2	SER	SER	LYS	LYS	chain B	B	B	4 - 233	4 - 233
3	LEU	LEU	LEU	LEU	chain C	C	C	6 - 231	6 - 231
4	SER	SER	TRP	TRP	chain D	D	D	4 - 232	4 - 232

#1: Protein	Fic family protein putative filamentation induced by cAMP protein / CdFic_0569 Mass: 27296.156 Da / Num. of mol.: 4 / Mutation: S31A, E35A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Peptoclostridium difficile (bacteria) / Strain: R20291 / Gene: CDR20291_0569 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: C9YJ22
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.38 Å³/Da / Density % sol: 48.41 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M MgCl2-6xH2O, 25 % (w/v) PEG 3350, 0.1 M HEPES pH 7.5

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID29 / Wavelength: 0.9 Å

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 15, 2014

Radiation

Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9 Å / Relative weight: 1

Reflection

Resolution: 2.5→48.99 Å / Num. obs: 35941 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / B_iso Wilson estimate: 67.34 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.076 / R_rim(I) all: 0.082 / Χ²: 0.978 / Net I/σ(I): 16.66 / Num. measured all: 248377

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.5-2.6		7.2	0.579	1.442	1.25	28223	3940	3941	1.555	100
2.6-2.7			0.788	0.993	1.87	23896	3375	3371	1.072	99.9
2.7-2.8			0.852	0.698	2.62	20281	2944	2936	0.755	99.7
2.8-3			0.926	0.466	3.92	32713	4792	4781	0.505	99.8
3-3.3			0.982	0.235	7.83	36405	5141	5131	0.254	99.8
3.3-3.6			0.994	0.111	15.32	23724	3594	3587	0.12	99.8
3.6-4			0.997	0.069	24.83	23360	3287	3278	0.074	99.7
4-5			0.999	0.041	37.27	29253	4337	4318	0.045	99.6
5-6			0.999	0.038	42.36	13383	1916	1911	0.041	99.7
6-8			0.999	0.032	46.15	9820	1533	1524	0.035	99.4
8-10			1	0.025	61.36	3773	569	566	0.027	99.5
	10		0.999	0.024	62.89	3546	614	597	0.026	97.2

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	4.59 Å	48.98 Å
Translation	4.59 Å	48.98 Å

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Processing

Software

Name	Version	Classification
XDS		data reduction
PHASER	2.5.5	phasing
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3CUC

3cuc

Resolution: 2.5→19.853 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2325	1076	3 %	Random selection
R_work	0.2048	34763	-	-
obs	0.2056	35839	99.86 %	-

Solvent computation

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

Displacement parameters

B_iso max: 173.91 Å² / B_iso mean: 87.1493 Å² / B_iso min: 43.32 Å²

Refinement step

Cycle: final / Resolution: 2.5→19.853 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6743	0	32	14	6789
B_iso mean	-	-	77.34	60.78	-
Num. residues	-	-	-	-	831

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	6928
X-RAY DIFFRACTION	f_angle_d	0.947	9395
X-RAY DIFFRACTION	f_chiral_restr	0.039	1079
X-RAY DIFFRACTION	f_plane_restr	0.004	1169
X-RAY DIFFRACTION	f_dihedral_angle_d	11.404	2476

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	3790	X-RAY DIFFRACTION	11.926	TORSIONAL
1	2	B	3790	X-RAY DIFFRACTION	11.926	TORSIONAL
1	3	C	3790	X-RAY DIFFRACTION	11.926	TORSIONAL
1	4	D	3790	X-RAY DIFFRACTION	11.926	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
2.5-2.6135	0.3347	134	0.321	4325	4459
2.6135-2.751	0.331	132	0.2977	4254	4386
2.751-2.9229	0.3202	135	0.2802	4346	4481
2.9229-3.1477	0.243	133	0.2582	4316	4449
3.1477-3.463	0.2347	134	0.2273	4332	4466
3.463-3.9606	0.2362	135	0.1975	4359	4494
3.9606-4.9769	0.1888	136	0.1766	4385	4521
4.9769-19.854	0.2267	137	0.1769	4446	4583

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	1.2837	1.2165	0.7849	6.6298	-1.9186	4.7771	1.2784	1.2042	-1.0243	-2.1989	-0.2713	0.2731	-0.4975	-0.7989	-0.7312	1.4713	0.0887	-0.0986	1.0429	-0.1477	0.717	-27.5754	-24.8098	18.6851
2	3.0294	-0.5638	-0.1841	2.5259	1.3826	3.5718	-0.1152	0.1314	0.0508	-0.0805	-0.1393	0.2095	0.0745	-0.1745	0.2382	0.4713	0.0609	0.0102	0.5454	0.0675	0.4661	-28.1383	-16.3668	34.6788
3	7.7131	4.1568	3.994	2.4363	1.8353	2.3233	-0.2249	-0.4415	1.6133	0.1591	-0.3872	0.4312	-0.7367	0.2149	0.7046	0.7682	0.0184	0.0368	0.9056	0.0066	0.7716	-20.4711	-3.3971	42.647
4	8.7402	0.1878	-0.9937	8.1299	4.4699	3.0421	-0.1763	-0.4091	-0.3432	0.3496	-0.1471	-0.4628	-0.2361	0.5576	0.4783	0.5266	0.024	-0.0585	0.7207	0.1064	0.7047	-5.6726	-13.6245	41.3298
5	5.6186	0.7381	0.8773	7.0861	1.2101	1.5607	-0.2015	-0.2026	-0.5525	0.1083	0.1455	-0.2282	0.3096	0.4536	-0.0273	0.4977	0.1124	0.1	0.6513	0.088	0.567	-14.142	-22.4067	35.59
6	7.4578	1.7347	5.32	5.4867	0.39	7.7743	0.5898	-0.0571	-1.2854	0.4814	-0.1168	-0.3371	1.3878	0.1303	-0.2538	0.7496	0.2229	0.1365	0.6183	0.0076	0.8108	-16.1159	-31.5111	35.9627
7	9.4074	-1.912	3.4704	7.0558	-3.8746	8.0048	0.5197	-1.3438	-1.023	1.4971	-0.0692	-0.068	0.5947	-1.0074	-0.4902	0.8881	-0.1025	-0.0653	0.6717	0.0375	0.9771	22.3778	-45.4818	32.1284
8	4.9425	0.2393	-3.0497	0.4989	1.0174	8.9881	-0.2246	0.6777	-0.7905	-0.0927	-0.1726	-0.0867	0.4358	0.0503	0.4212	0.4418	0.01	0.0003	0.6892	-0.0682	0.6109	28.4663	-42.6489	14.4986
9	5.3375	0.4765	-3.5193	6.0882	1.5717	5.5315	0.1747	-0.1377	0.4006	0.0605	-0.1391	-0.1166	-0.4377	0.4348	0.0995	0.4611	0.0661	-0.0835	0.5963	-0.0089	0.5383	27.2291	-28.0573	20.7085
10	7.7485	-1.5589	0.4191	5.4984	-0.7037	6.2499	0.0689	0.8771	0.3104	0.1274	-0.3195	0.6078	-0.744	-0.6782	0.1331	0.4944	0.1457	-0.008	0.6664	-0.0774	0.6404	12.3855	-25.3509	20.067
11	4.6565	-2.3491	3.1242	8.017	0.9077	6.3605	0.2749	0.8145	-0.2432	-0.688	-0.3027	0.8556	0.2564	-0.8424	0.0266	0.4357	0.0935	-0.002	0.9887	-0.1586	0.8183	8.4809	-35.3408	11.8847
12	7.6945	-6.6095	5.7462	8.9443	-6.1461	5.1206	0.6855	-0.5927	-1.4169	0.5263	0.4656	1.644	0.6868	-1.2934	-1.638	0.8135	-0.1396	0.1342	0.9765	0.0137	1.3577	12.5565	-49.1278	25.0549
13	6.4058	2.1377	0.5741	7.3713	-2.178	1.0277	0.6856	-1.8741	1.8286	3.7262	-1.3857	-1.3211	-1.8547	1.2799	0.4519	1.5748	0.0061	-0.4686	1.1582	-0.2743	0.4604	36.5079	-19.139	60.1857
14	7.9984	-2.6881	-1.5914	7.1415	-0.9221	0.9124	-0.4429	-0.4286	-0.1557	0.9443	0.3888	-0.0555	-0.295	-0.2316	0.0407	0.6171	0.0448	0.04	0.6945	-0.0913	0.5076	31.8275	-34.2449	49.3458
15	5.5785	-2.2339	0.3066	7.5798	-0.9747	3.8151	-0.1877	-0.1684	1.1077	0.5586	-0.2084	-1.2025	-0.7433	0.309	0.4594	0.6418	-0.0134	-0.1434	0.677	-0.0133	0.8209	37.2496	-21.2728	42.3082
16	5.6853	-0.3105	1.254	0.5415	-1.2822	3.3655	-1.1216	0.2025	-0.9257	0.3223	0.7416	0.1578	-1.4176	0.4976	-0.1891	0.8145	-0.0286	-0.1668	0.8283	0.1167	0.8554	38.9756	-27.6479	30.5933
17	9.2218	-1.527	-1.1856	4.2279	2.2875	3.1635	-0.3496	-0.0219	1.0338	0.4041	0.1163	0.0676	-0.4551	-0.107	0.1214	0.9947	0.143	-0.1513	0.6198	0.0002	1.1327	24.6504	-10.7466	37.5599
18	3.5861	-0.0924	-2.7544	3.4535	-2.4034	6.3569	-0.1709	0.1307	-0.0104	1.1719	-0.0529	0.2301	-0.8064	-0.4199	0.4011	1.0299	0.1313	0.0508	0.5706	-0.1421	0.9337	24.348	-20.1608	46.9006
19	6.068	0.922	-3.1741	2.0166	-1.2911	6.8775	-0.7341	0.6523	0.676	0.2328	0.8263	1.2344	-0.0551	-1.4121	-0.2791	0.985	0.0866	0.1037	1.1058	-0.1518	1.0152	13.3442	-18.7224	37.2627
20	1.9814	-2.8412	-1.3585	5.1424	2.2644	1.0138	-0.3947	0.3921	-0.2183	0.8967	-0.1235	0.9862	-0.3387	-1.4838	-0.5977	0.6882	0.3691	0.9174	0.9761	-0.5709	2.2389	12.3033	-17.7945	45.5951
21	3.3839	0.5547	-1.7713	6.441	-0.1052	6.624	-1.0692	-0.7973	0.0066	2.0914	-0.3073	1.7866	-0.4197	-1.5322	0.39	1.5895	0.3899	0.43	1.0803	-0.0414	1.1129	22.1657	-22.2609	59.8557
22	9.8351	-2.4134	-1.6725	3.5811	-4.5441	9.3385	0.7967	2.2551	0.3416	0.9266	-0.9796	0.3391	-0.681	-0.6115	0.0148	0.8433	0.0522	0.0749	1.1103	0.2041	0.9088	-22.1926	7.3293	-4.9469
23	4.6064	2.8101	-1.8395	2.7294	-1.0405	2.7822	-0.2985	0.1382	0.0546	0.0687	-0.1371	-0.2051	-0.113	0.0224	0.4003	0.543	0.0857	-0.0494	0.6653	0.0713	0.7252	-27.0451	-1.4591	10.3402
24	7.0292	0.4873	-0.6461	3.5451	0.0569	7.4334	-0.1508	-0.534	-0.3694	0.2776	-0.6691	-1.3488	-0.4204	1.0005	0.578	0.523	-0.0706	-0.1518	0.9349	0.3273	1.2006	-10.7684	0.992	14.3133
25	3.6261	-1.2614	1.9656	6.0772	-3.5166	7.1626	-0.604	0.0621	0.0677	-0.4177	-0.949	-2.0741	0.9292	1.0501	1.2777	0.6866	0.0704	0.4412	0.951	0.3241	1.7103	-8.0079	-6.7796	5.957

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 18 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 95 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 96 through 113 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 114 through 143 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 144 through 197 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 198 through 234 )	A
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 4 through 18 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 19 through 58 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 59 through 129 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 130 through 183 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 184 through 220 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 221 through 233 )	B
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 6 through 18 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 19 through 58 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 59 through 95 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 96 through 131 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 132 through 168 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 169 through 197 )	C
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 198 through 211 )	C
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 212 through 220 )	C
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 221 through 231 )	C
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 4 through 18 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 19 through 131 )	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 132 through 197 )	D
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 198 through 232 )	D

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