PDB-3sn9: Fic protein from NEISSERIA MENINGITIDIS mutant S182A/E186A in com...

ID or keywords:

Entry

Database: PDB / ID: 3sn9

Title

Fic protein from NEISSERIA MENINGITIDIS mutant S182A/E186A in complex with AMPPNP

Components

Cell filamentation protein Fic-related protein

Keywords

TRANSFERASE /

AMPylation /

adenylylation

Function / homology

Function and homology information

AMPylase activity / protein adenylyltransferase / protein adenylylation /

regulation of cell division / protein homodimerization activity /

Biological species

Neisseria meningitidis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.03 Å

Authors

Goepfert, A. / Stanger, F. / Schirmer, T.

Citation

Journal: Nature / Year: 2012
Title: Adenylylation control by intra- or intermolecular active-site obstruction in Fic proteins.
Authors: Engel, P. / Goepfert, A. / Stanger, F.V. / Harms, A. / Schmidt, A. / Schirmer, T. / Dehio, C.

History

Deposition	Jun 29, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 25, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 8, 2012	Group: Database references
Revision 1.2	Feb 15, 2012	Group: Database references
Revision 1.3	Mar 27, 2013	Group: Other
Revision 1.4	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.5	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3sn9.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb3sn9.ent.gz	878 KB	Display	PDB format
PDBx/mmJSON format	3sn9.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/sn/3sn9 ftp://data.pdbj.org/pub/pdb/validation_reports/sn/3sn9	HTTPS FTP

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Related structure data

Related structure data	3s6aC 3se5C 3shgC 2g03S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4z86-d 4zxp-d 5b6j-d 1zuo-d 2ovz-d 5ike-d 2ow1-d 2xz4-d 5d63-d 6wco-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) 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

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#108 - Dec 2008 Hsp90 similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#108 - Dec 2008
Hsp90
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#182 - Feb 2015
Insulin receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: Cell filamentation protein Fic-related protein

B: Cell filamentation protein Fic-related protein

C: Cell filamentation protein Fic-related protein

D: Cell filamentation protein Fic-related protein

E: Cell filamentation protein Fic-related protein

F: Cell filamentation protein Fic-related protein

G: Cell filamentation protein Fic-related protein

H: Cell filamentation protein Fic-related protein

I: Cell filamentation protein Fic-related protein

J: Cell filamentation protein Fic-related protein

K: Cell filamentation protein Fic-related protein

L: Cell filamentation protein Fic-related protein

M: Cell filamentation protein Fic-related protein

N: Cell filamentation protein Fic-related protein

O: Cell filamentation protein Fic-related protein

P: Cell filamentation protein Fic-related protein

hetero molecules

361 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cell filamentation protein Fic-related protein

M: Cell filamentation protein Fic-related protein

hetero molecules

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

2

B: Cell filamentation protein Fic-related protein

D: Cell filamentation protein Fic-related protein

hetero molecules

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

3

C: Cell filamentation protein Fic-related protein

E: Cell filamentation protein Fic-related protein

hetero molecules

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

4

F: Cell filamentation protein Fic-related protein

H: Cell filamentation protein Fic-related protein

hetero molecules

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

5

G: Cell filamentation protein Fic-related protein

L: Cell filamentation protein Fic-related protein

hetero molecules

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

6

I: Cell filamentation protein Fic-related protein

O: Cell filamentation protein Fic-related protein

hetero molecules

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

7

J: Cell filamentation protein Fic-related protein

hetero molecules

N: Cell filamentation protein Fic-related protein

hetero molecules

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

8

K: Cell filamentation protein Fic-related protein

P: Cell filamentation protein Fic-related protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	110.313, 136.919, 114.663
Angle α, β, γ (deg.)	90.000, 100.260, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 13 - 170 / Label seq-ID: 10 - 167

#1: Protein	Cell filamentation protein Fic-related protein Mass: 22049.115 Da / Num. of mol.: 16 / Mutation: S182A, E186A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: serogroup B / Gene: NMB0255 / Plasmid: pRSFDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7DDR9
#2: Chemical	ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Mass: 506.196 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Comment: AMP-PNP, energy-carrying molecule analogue*YM

#1: Protein

Cell filamentation protein Fic-related protein

Mass: 22049.115 Da / Num. of mol.: 16 / Mutation: S182A, E186A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Neisseria meningitidis (bacteria) / Strain: serogroup B / Gene: NMB0255 / Plasmid: pRSFDuet1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7DDR9

#2: Chemical

ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

Mass: 506.196 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.07 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 21% PEG3350, 0.2 M di-ammonium tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06DA / Wavelength: 1 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 3, 2011

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Number: 222147

Reflection

Resolution: 3.02→87.07 Å / Num. obs: 58488 / % possible obs: 88.96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / R_merge(I) obs: 0.112 / Net I/σ(I): 6.9449

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	% possible all
3.02-3.19	2.06	0.35	2.17	8487	4120	43.15
3.19-3.38	2.97	0.31	2.42	21932	7391	81.81
3.38-3.61	3.74	0.27	2.71	31211	8353	98.51
3.61-3.9	4.17	0.19	3.83	33035	7918	100
3.9-4.27	4.17	0.13	5.45	30443	7303	100
4.27-4.78	4.17	0.1	6.85	27595	6618	100
4.78-5.52	4.17	0.11	6.39	24344	5842	100
5.52-6.76	4.16	0.1	6.53	20547	4940	100
6.76-9.56	4.13	0.05	13.09	15923	3851	100
9.56-87.07	4.01	0.04	10.48	8630	2152	99.89

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Processing

Software

Name	Version	Classification
SCALA	CCP4_3.3.16 2010/01/06	data scaling
MOSFLM		data reduction
PHASER		phasing
REFMAC	5.5.0109	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2g03

2g03

Resolution: 3.03→15 Å / Cor.coef. F_o:F_c: 0.911 / Cor.coef. F_o:F_c free: 0.882 / Occupancy max: 1 / Occupancy min: 1 / SU B: 47.919 / SU ML: 0.386 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.491 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.248	2943	5.1 %	RANDOM
R_work	0.222	-	-	-
obs	0.222	57892	89.92 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 60.96 Å² / B_iso mean: 65.684 Å² / B_iso min: 21.13 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.75 Å²	-0 Å²	1.96 Å²
2-	-	-1.2 Å²	-0 Å²
3-	-	-	-0.85 Å²

Refinement step

Cycle: LAST / Resolution: 3.03→15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20624	0	496	0	21120

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	21504
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	14736
X-RAY DIFFRACTION	r_angle_refined_deg	1.114	1.988	29072
X-RAY DIFFRACTION	r_angle_other_deg	0.789	3	35712
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.783	5	2512
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.428	24.286	1120
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.491	15	3920
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.971	15	176
X-RAY DIFFRACTION	r_chiral_restr	0.056	0.2	3152
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	23536
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	4496
X-RAY DIFFRACTION	r_mcbond_it	0.425	1.5	12512
X-RAY DIFFRACTION	r_mcbond_other	0.061	1.5	5152
X-RAY DIFFRACTION	r_mcangle_it	0.95	2	20096
X-RAY DIFFRACTION	r_scbond_it	1.638	3	8992
X-RAY DIFFRACTION	r_scangle_it	2.965	4.5	8976

Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1911 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Type	Rms dev position (Å)	Weight position
A	TIGHT POSITIONAL	0.02	0.05
B	TIGHT POSITIONAL	0.02	0.05
C	TIGHT POSITIONAL	0.02	0.05
D	TIGHT POSITIONAL	0.03	0.05
E	TIGHT POSITIONAL	0.03	0.05
F	TIGHT POSITIONAL	0.02	0.05
G	TIGHT POSITIONAL	0.02	0.05
H	TIGHT POSITIONAL	0.02	0.05
I	TIGHT POSITIONAL	0.02	0.05
J	TIGHT POSITIONAL	0.02	0.05
K	TIGHT POSITIONAL	0.02	0.05
L	TIGHT POSITIONAL	0.02	0.05
M	TIGHT POSITIONAL	0.02	0.05
N	TIGHT POSITIONAL	0.02	0.05
O	TIGHT POSITIONAL	0.02	0.05
P	TIGHT POSITIONAL	0.02	0.05
A	TIGHT THERMAL	0.04	0.5
B	TIGHT THERMAL	0.04	0.5
C	TIGHT THERMAL	0.04	0.5
D	TIGHT THERMAL	0.04	0.5
E	TIGHT THERMAL	0.04	0.5
F	TIGHT THERMAL	0.04	0.5
G	TIGHT THERMAL	0.04	0.5
H	TIGHT THERMAL	0.04	0.5
I	TIGHT THERMAL	0.04	0.5
J	TIGHT THERMAL	0.04	0.5
K	TIGHT THERMAL	0.04	0.5
L	TIGHT THERMAL	0.03	0.5
M	TIGHT THERMAL	0.03	0.5
N	TIGHT THERMAL	0.03	0.5
O	TIGHT THERMAL	0.03	0.5
P	TIGHT THERMAL	0.03	0.5

LS refinement shell

Resolution: 3.03→3.109 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.334	66	-
R_work	0.305	1368	-
all	-	1434	-
obs	-	-	31.2 %

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	3.6463	1.0737	-0.992	2.8451	1.0287	5.495	-0.1647	-0.0002	-0.2107	0.3696	0.0979	0.1614	0.3871	-0.0534	0.0668	0.1146	0.0584	-0.0123	0.0642	-0.0607	0.1237	26.1762	-17.7373	11.5991
2	4.3633	-1.195	0.1453	4.7184	0.8623	3.2362	0.0401	-0.1495	-0.2776	0.288	0.0257	-0.2923	0.3419	0.1192	-0.0657	0.1726	0.0751	0.0117	0.0462	0.0311	0.0599	12.775	-6.8087	40.905
3	2.6424	-0.0352	-0.3669	5.8924	-0.8212	2.7492	0.2753	-0.1242	0.2361	0.4849	-0.1398	0.5378	-0.5911	-0.2524	-0.1355	0.2231	0.0305	0.1114	0.042	-0.0189	0.1017	51.1166	19.7343	41.5345
4	4.4977	0.0134	-0.2014	3.6826	-2.3136	4.3689	0.2471	-0.1885	0.513	0.5245	-0.0535	0.1785	-0.6682	-0.3468	-0.1936	0.1453	0.0507	0.052	0.0921	-0.025	0.0724	-6.1124	21.0263	42.5164
5	4.9614	-0.9156	0.4795	4.2647	0.0118	2.5312	0.3332	-0.0134	-0.4266	-0.0168	-0.226	-0.083	0.1373	0.4415	-0.1071	0.0311	0.0109	-0.0333	0.099	-0.0007	0.0446	73.3097	-5.5837	40.0773
6	3.4787	-0.9127	0.1428	3.6218	-0.7995	3.5793	0.0808	0.2408	0.0845	-0.1132	0.1927	0.3051	0.0661	-0.5058	-0.2735	0.0544	0.0465	0.0248	0.1613	0.102	0.078	-7.3628	26.5676	13.7534
7	3.9962	0.2789	0.5508	4.9058	1.9148	2.6515	0.3102	-0.001	0.2874	-0.1296	-0.2017	-0.2453	-0.1697	0.0513	-0.1084	0.1654	-0.0226	-0.0736	0.0876	0.0457	0.1377	16.9876	20.9344	68.6882
8	2.5957	-2.1328	0.2423	6.6324	0.138	2.6277	0.0388	0.2802	0.6174	-0.1717	0.1241	-1.0746	-0.2932	0.2066	-0.1629	0.044	-0.0222	0.015	0.0655	0.0092	0.3505	25.3521	19.5062	9.0623
9	6.2693	-1.0366	-2.1921	3.1276	0.7108	5.6521	-0.2384	-0.1682	-0.067	0.4921	-0.0497	0.3018	-0.2429	0.1763	0.2881	0.1438	0.0172	0.0918	0.0535	0.0878	0.2159	60.3387	40.4734	17.9016
10	4.2414	-0.6705	-0.4291	5.0527	1.3624	3.0439	0.0509	0.0486	-0.4737	-0.482	-0.0551	-0.3107	0.1922	-0.2295	0.0042	0.3989	0.105	0.1659	0.1034	0.0387	0.1372	37.5546	59.2287	44.8139
11	3.0282	0.4173	-1.2385	4.255	-0.4959	3.941	-0.1024	0.2577	0.2552	-0.2559	0.296	-0.2426	-0.1908	0.1455	-0.1936	0.1287	-0.0051	0.0096	0.3483	0.14	0.135	11.9462	33.8339	-19.7571
12	5.5887	1.3757	1.2621	4.6038	-0.7612	3.4997	0.506	-0.3568	-0.8823	0.2989	-0.2963	-0.0238	0.9339	-0.5117	-0.2097	0.5652	-0.2874	-0.0749	0.2932	0.0648	0.1518	-3.5353	-5.662	71.5585
13	7.7124	-2.3734	-0.227	4.4918	-0.5826	4.6178	0.1564	-0.4715	1.1969	-0.1613	-0.0112	-1.2039	-0.4379	1.227	-0.1452	0.1465	-0.1277	0.0021	0.4951	-0.1934	0.4978	57.5281	-5.9255	7.2874
14	5.8982	-0.3948	-1.3633	4.9282	1.8274	2.7344	0.2101	-0.4968	1.0596	0.1898	0.0899	-0.2713	-0.933	0.6415	-0.3001	0.7266	-0.3696	-0.0333	0.3564	-0.1522	0.2703	69.8528	19.3196	70.3409
15	2.9055	-1.8107	0.0579	4.4044	-0.3839	5.2839	-0.2562	0.9307	-0.817	-0.7184	-0.2591	0.3229	0.8569	0.3227	0.5152	0.4042	-0.1882	0.219	0.4925	-0.288	0.6631	61.0076	24.1017	-11.5838
16	3.4999	-0.1876	0.1327	5.2111	-2.1513	3.6704	-0.0955	0.2925	-0.4362	-0.6898	0.5726	0.7858	1.0296	-1.1206	-0.4771	0.4582	-0.314	-0.1769	0.537	0.0258	0.2706	-3.8419	4.7739	-12.9232

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	13 - 170
2	X-RAY DIFFRACTION	2	B	13 - 170
3	X-RAY DIFFRACTION	3	C	13 - 170
4	X-RAY DIFFRACTION	4	D	13 - 170
5	X-RAY DIFFRACTION	5	E	13 - 170
6	X-RAY DIFFRACTION	6	F	13 - 170
7	X-RAY DIFFRACTION	7	G	13 - 170
8	X-RAY DIFFRACTION	8	H	13 - 170
9	X-RAY DIFFRACTION	9	I	13 - 170
10	X-RAY DIFFRACTION	10	J	13 - 170
11	X-RAY DIFFRACTION	11	K	13 - 170
12	X-RAY DIFFRACTION	12	L	13 - 170
13	X-RAY DIFFRACTION	13	M	13 - 170
14	X-RAY DIFFRACTION	14	N	13 - 170
15	X-RAY DIFFRACTION	15	O	13 - 170
16	X-RAY DIFFRACTION	16	P	13 - 170

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