PDB-9lfx: Streptococcus mutans FtsZ

ID or keywords:

Entry

Database: PDB / ID: 9lfx

Title

Streptococcus mutans FtsZ

Components

Cell division protein FtsZ

Keywords

CELL CYCLE / Cell division

Function / homology

Function and homology information

division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein polymerization / GTPase activity / GTP binding / cytoplasm
Similarity search - Function

Biological species

Streptococcus mutans serotype c (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.49 Å

Authors

Yuxing, C.

Funding support

1items

Citation

Journal: To Be Published
Title: Streptococcus mutans FtsZ
Authors: Yuxing, C.

History

Deposition	Jan 9, 2025	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Jan 14, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9lfx.cif.gz	450.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9lfx.ent.gz	374.4 KB	Display	PDB format
PDBx/mmJSON format	9lfx.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/lf/9lfx ftp://data.pdbj.org/pub/pdb/validation_reports/lf/9lfx	HTTPS FTP

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Related structure data

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
Related items in Molecule of the Month	#175 - Jul 2014 Microtubules similarity (8) #176 - Aug 2014 Dynein similarity (8) #241 - Jan 2020 Twenty Years of Molecules similarity (8)

Deposited unit

B: Cell division protein FtsZ

C: Cell division protein FtsZ

D: Cell division protein FtsZ

A: Cell division protein FtsZ

hetero molecules

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

1

B: Cell division protein FtsZ

hetero molecules

defined by author
Evidence: gel filtration
32.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Cell division protein FtsZ

hetero molecules

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

3

D: Cell division protein FtsZ

hetero molecules

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

4

A: Cell division protein FtsZ

hetero molecules

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

Unit cell

Length a, b, c (Å)	173.119, 173.119, 172.282
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Cell division protein FtsZ Mass: 31805.840 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans serotype c (strain ATCC 700610 / UA159) (bacteria) Gene: ftsZ, SMU_552 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8DVD9
#2: Chemical	ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 5.16 Å³/Da / Density % sol: 76.15 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: PEG10000, Potassium sodium tartrate, MES

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9798 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 19, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9798 Å / Relative weight: 1
Reflection	Resolution: 3.49→34.56 Å / Num. obs: 30537 / % possible obs: 90.08 % / Redundancy: 9.6 % / CC_1/2: 0.99 / Net I/σ(I): 10.67
Reflection shell	Resolution: 3.49→3.62 Å / Num. unique obs: 30537 / CC_1/2: 0.99

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Processing

Software

Name	Version	Classification
PHENIX	(1.19.1_4122: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.49→34.56 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.94 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2708	2012	6.59 %
R_work	0.2218	-	-
obs	0.225	30537	90.24 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.49→34.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8760	0	131	287	9178

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	8959
X-RAY DIFFRACTION	f_angle_d	1.341	12166
X-RAY DIFFRACTION	f_dihedral_angle_d	19.048	1323
X-RAY DIFFRACTION	f_chiral_restr	0.075	1491
X-RAY DIFFRACTION	f_plane_restr	0.009	1577

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 (%)
3.49-3.58	0.3619	83	0.3223	1066	X-RAY DIFFRACTION	49
3.58-3.67	0.3922	99	0.3253	1417	X-RAY DIFFRACTION	64
3.67-3.78	0.3351	126	0.297	1658	X-RAY DIFFRACTION	75
3.78-3.9	0.3659	130	0.2657	1907	X-RAY DIFFRACTION	86
3.9-4.04	0.2972	141	0.254	2085	X-RAY DIFFRACTION	93
4.04-4.21	0.2955	151	0.2317	2192	X-RAY DIFFRACTION	98
4.21-4.4	0.2571	153	0.2062	2222	X-RAY DIFFRACTION	100
4.4-4.63	0.2137	161	0.1864	2232	X-RAY DIFFRACTION	100
4.63-4.92	0.2361	157	0.1814	2250	X-RAY DIFFRACTION	100
4.92-5.29	0.2841	155	0.2113	2256	X-RAY DIFFRACTION	100
5.3-5.83	0.3471	163	0.279	2250	X-RAY DIFFRACTION	100
5.83-6.66	0.2717	161	0.2172	2292	X-RAY DIFFRACTION	100
6.66-8.37	0.2229	161	0.1964	2289	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	0.0801	0.0704	-0.1005	0.0634	-0.0919	0.139	0.0458	-0.0003	-0.0467	0.072	0.0534	0.0642	0.0266	-0.0705	0.093	0.2784	-0.1305	-0.1693	0.1481	0.0294	0.153	4.5118	68.8624	51.9666
2	0.031	0.0327	-0.0248	0.034	-0.026	0.0229	-0.0298	-0.0473	-0.0557	-0.0416	0.0512	0.0502	0.1207	-0.053	0.0139	0.3187	-0.1304	-0.1009	0.1594	0.0923	0.211	7.5607	71.0559	58.5244
3	0.0787	0.0232	-0.0998	0.0539	0.0114	0.1647	0.169	-0.0623	-0.0219	-0.0704	-0.0546	-0.1231	0.068	0.2317	0.0181	0.3324	0.0431	-0.1136	0.3076	0.098	0.5016	20.8337	77.5581	57.0106
4	0.0517	0.0373	0.0632	0.0464	0.0789	0.1421	0.071	0.0564	-0.0154	0.0674	0.012	-0.0001	0.1065	0.0856	0.1159	0.2722	0.0098	-0.0532	0.069	0.0722	0.1499	13.4823	70.3034	47.9245
5	0.1814	-0.0465	0.1045	0.3705	0.0165	0.1734	0.1037	0.029	0.0025	-0.199	0.1248	0.065	0.0822	0.1503	0.0957	0.3249	0.0362	-0.0083	0.121	0.0199	0.088	14.3387	73.3828	44.4827
6	0.0592	-0.0334	-0.0101	0.0723	-0.0595	0.1233	0.066	-0.0314	-0.0363	-0.1457	0.0288	-0.0054	0.1635	0.008	0.0567	0.3447	-0.1295	-0.0415	0.0939	0.0785	0.1678	4.9428	76.3101	41.3081
7	0.0433	-0.0097	-0.0727	0.0647	-0.0083	0.3019	-0.1522	-0.0626	-0.09	0.1218	-0.0786	0.0729	0.3123	0.063	-0.0212	0.5567	-0.0408	-0.1617	0.1854	0.0114	0.2927	5.4591	59.2937	36.395
8	0.0004	0.0005	-0.0003	0.0202	-0.0012	0.0188	-0.0274	0.067	-0.0673	-0.0085	-0.0521	0.0685	0.0527	-0.0958	0.0045	0.5281	-0.0812	-0.1831	0.2415	-0.1106	0.4003	-7.0807	67.6776	29.1322
9	0.0438	0.0264	-0.0166	0.0769	-0.0367	0.0793	0.0362	0.0676	-0.0866	-0.1902	0.081	-0.0374	0.0347	0.0084	0.2124	0.5924	-0.2638	-0.0093	0.1626	-0.1677	0.1791	-1.205	57.9354	29.121
10	0.0725	-0.1224	0.0392	0.2729	-0.0255	0.0541	-0.0096	-0.0393	-0.0196	-0.0468	0.041	0.016	-0.0696	-0.0652	0.219	0.4548	0.0637	0.1362	0.0614	-0.0463	0.2223	-5.7523	61.7482	37.8924
11	0.0119	0.0205	0.0049	0.0458	0.0055	0.0012	0.0552	-0.0219	0.0093	0.0401	0.0025	0.0006	0.0074	0.0046	0.0968	0.9796	0.0092	0.1655	0.1913	-0.0381	0.2297	-0.3979	119.7558	49.5277
12	0.0064	0.0117	0.002	0.0409	0.0387	0.0604	-0.0468	-0.0573	0.0314	-0.0139	-0.0368	0.061	-0.0139	-0.0991	-0.045	0.8881	-0.1234	0.2447	0.2419	-0.2281	0.4197	-0.5734	125.6981	54.2756
13	0.1526	-0.0076	-0.0249	0.0907	-0.0002	0.0059	0.0221	-0.0917	0.089	0.0742	0.061	-0.022	0.181	0.1354	-0.0423	1.5044	-0.2982	0.0272	0.5575	-0.2148	0.5631	12.5231	132.5007	55.9537
14	-0.0007	0.0032	0.0019	0.0013	0.004	0.0062	0.0321	-0.0158	-0.0271	0.1925	0.0206	-0.1186	-0.0282	0.0709	0.1903	1.1307	-0.2392	-0.3337	0.3441	-0.0742	0.2833	12.4118	119.6578	52.6708
15	0.0787	-0.0245	0.0513	0.1279	-0.1272	0.167	-0.0411	-0.0329	0.1957	0.4794	-0.1399	-0.0148	-0.134	0.073	-0.2872	0.7624	-0.2062	-0.0931	-0.058	0.1473	0.2145	7.0988	120.2791	38.6408
16	0.1065	-0.097	0.2164	0.0871	-0.1889	0.4287	-0.0708	0.0032	0.023	0.2896	-0.05	-0.0639	-0.1906	0.1057	-0.2911	0.5388	-0.0345	-0.1173	0.1105	-0.0008	0.082	6.5572	103.584	44.7725
17	0.1832	0.1429	0.0919	0.1224	0.0807	0.0743	-0.0208	0.0418	-0.0214	-0.0092	0.07	-0.002	-0	0.0486	0.0734	0.2752	0.0997	0.0721	0.0902	-0.0126	0.0054	0.41	104.4802	29.3136
18	0.0111	0.0161	-0.005	0.0375	-0.0106	0.0044	-0.0054	-0.0148	-0.0211	0.1266	0.0041	0.0832	-0.058	-0.0033	-0.0355	0.276	-0.0856	0.162	0.1076	0.0063	0.112	2.7834	100.411	38.8637
19	0.0594	-0.0581	0.0062	0.0676	-0.0264	0.1141	-0.0479	-0.0339	0.0023	0.1236	0.011	0.0197	-0.1336	0.0153	-0.4041	0.393	0.045	0.027	0.0643	0.0324	0.0236	1.4739	99.0475	37.4103
20	0.4781	0.0395	-0.0818	0.0082	0.0024	0.0383	-0.0908	0.1451	-0.0126	-0.02	0.0315	0.0883	-0.1261	-0.1033	0.0173	0.5287	0.004	-0.0185	0.1485	-0.007	0.2909	3.6448	158.5661	16.8255
21	0.1933	0.029	0.0879	0.1954	-0.0232	0.0463	-0.2048	0.0554	0.0946	0.0219	-0.0421	0.0618	-0.1476	0.1156	-0.2844	0.449	-0.0551	-0.0366	0.1922	0.1997	0.3592	1.8047	166.132	16.8181
22	0.0687	0.0431	-0.0525	0.0296	-0.0332	0.042	-0.0254	0.0164	0.1195	0.0901	0.01	-0.006	-0.0684	0.0727	-0.014	0.7037	-0.2193	-0.0677	0.2766	0.1359	0.4352	13.3342	174.983	20.2504
23	0.1962	0.1052	0.0337	0.2428	0.0963	0.0563	-0.0756	-0.0079	0.0295	0.1835	0.0242	-0.1604	-0.2277	0.0457	0.1453	0.4162	-0.0402	-0.0185	0.0638	0.0651	0.1712	14.6888	160.848	20.6495
24	0.0176	0.0125	0.003	0.0095	-0.0014	0.005	-0.0424	0.0003	-0.0388	0.1187	0.055	-0.0169	-0.0445	0.119	-0.0003	0.4041	-0.148	-0.1701	0.486	0.1879	0.4638	24.5965	162.4523	16.1368
25	0.6995	-0.2154	-0.3911	0.3127	0.0223	0.5151	-0.0439	0.1816	-0.1934	0.2415	0.0744	0.2654	0.1739	-0.224	0.0607	0.2636	-0.0776	-0.0767	0.1123	0.0069	0.3322	11.0866	150.8732	10.4722
26	0.0278	-0.0174	0.002	0.0502	-0.0038	0.0016	-0.0433	-0.0453	-0.0298	0.0179	0.0243	0.0638	-0.0626	0.0041	-0.1273	0.4915	-0.0472	-0.0183	0.1013	0.1307	0.1919	9.8782	144.1349	25.7413
27	0.0009	-0.0012	-0.0049	0.0064	0.009	0.0127	-0.0799	0.0568	-0.1134	-0.0634	-0.0197	-0.0013	0.2262	-0.0256	-0.0002	0.3518	0.0397	0.0467	0.3209	0.018	0.3902	12.2282	135.3012	11.7029
28	0.0367	-0.0011	0.0128	0.0287	-0.0287	0.0325	0.0703	-0.0094	-0.0769	-0.0657	-0.0279	-0.0067	0.0191	0.0098	0.0549	0.3217	-0.0364	-0.0855	0.1063	0.1228	0.3752	8.623	136.1418	21.1505
29	-0.0009	-0.0018	0.0024	0.0022	-0.0032	0.0014	-0.011	0.0024	-0.058	0.1235	-0.1043	0.0438	-0.028	-0.0547	0.0174	0.5552	-0.0815	-0.2349	0.1531	-0.1128	0.4157	2.6986	22.6094	22.3609
30	0.2767	0.0723	-0.1545	0.0487	0.0186	0.2236	0.1099	-0.1485	0.0224	0.202	-0.0609	-0.0753	0.0129	0.1061	-0.0753	0.5171	-0.0501	-0.3223	0.1917	-0.0171	0.5375	8.7245	25.3387	29.6082
31	0.0564	0.0093	0.0514	0.0022	0.0083	0.0513	0.0765	0.0133	-0.0758	-0.0378	-0.0536	0.0013	-0.0705	0.0994	0.0909	0.5997	0.0031	-0.384	0.4217	-0.2041	0.6759	20.6447	33.6106	26.2918
32	0.019	0.0081	0.0076	0.0357	0.0444	0.0952	0.0743	0.0414	-0.1222	-0.0383	0.0323	-0.0695	0.1534	0.0786	0.0687	0.4858	-0.0815	-0.2416	0.1848	-0.1855	0.52	12.0994	30.9433	17.1225
33	0.031	0.0338	-0.0245	0.0469	-0.0588	0.1033	0.0861	-0.0374	0.0407	0.0851	0.0084	-0.0205	-0.1051	0.0584	0.0867	0.4979	-0.0597	-0.134	0.2203	-0.2506	0.5227	3.5148	39.0057	19.2908
34	0.017	0.0048	0.0436	0.0134	0.0223	0.1861	0.2215	-0.1924	0.0013	0.0208	0.0888	-0.1096	-0.0014	0.0429	0.38	0.5451	-0.2779	-0.1581	0.1355	-0.1256	0.3831	-1.7185	34.498	16.7226
35	0.0039	0.0023	-0.0204	0.0001	-0.0093	0.1085	0.0722	-0.0065	0.0468	0.0896	-0.0828	0.0551	-0.0801	-0.2214	0.004	0.5174	-0.0362	-0.208	0.2559	-0.058	0.5227	-17.7119	34.8977	12.4056
36	0.0888	0.0975	0.0824	0.1585	0.0735	0.0912	-0.0523	0.1118	0.1412	-0.0133	-0.0728	-0.0723	0.1313	0.0073	-0.2213	0.4571	-0.1037	-0.0902	0.1991	0.1612	0.3599	-11.7457	27.1801	7.8689
37	0.0642	-0.069	-0.0563	0.0777	0.0547	0.0578	0.0244	0.0553	0.1328	-0.0183	-0.0364	-0.0769	0.0123	-0.0201	-0.0906	0.5249	-0.2092	-0.1661	0.228	0.1699	0.2843	-14.7894	27.7117	2.7031
38	-0.0006	-0.001	-0.0045	0.0135	0.0188	0.0195	0.0456	-0.1113	0.0857	0.0735	0.0097	-0.0993	0.1058	-0.0498	0.0001	0.4871	-0.1892	-0.093	0.2772	0.0477	0.2771	-13.127	25.7597	15.0445

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 13 through 34 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 35 through 61 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 62 through 94 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 95 through 113 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 114 through 141 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 142 through 203 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 204 through 233 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 234 through 254 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 255 through 299 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 300 through 316 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 13 through 34 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 35 through 61 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 62 through 94 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 95 through 125 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 126 through 203 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 204 through 233 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 234 through 254 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 255 through 272 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 273 through 316 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 13 through 34 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 35 through 61 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 62 through 94 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 95 through 141 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 142 through 158 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 159 through 203 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 204 through 233 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 234 through 254 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 255 through 316 )
29	X-RAY DIFFRACTION	29	chain 'A' and (resid 6 through 34 )
30	X-RAY DIFFRACTION	30	chain 'A' and (resid 35 through 61 )
31	X-RAY DIFFRACTION	31	chain 'A' and (resid 62 through 94 )
32	X-RAY DIFFRACTION	32	chain 'A' and (resid 95 through 125 )
33	X-RAY DIFFRACTION	33	chain 'A' and (resid 126 through 141 )
34	X-RAY DIFFRACTION	34	chain 'A' and (resid 142 through 233 )
35	X-RAY DIFFRACTION	35	chain 'A' and (resid 234 through 254 )
36	X-RAY DIFFRACTION	36	chain 'A' and (resid 255 through 272 )
37	X-RAY DIFFRACTION	37	chain 'A' and (resid 273 through 299 )
38	X-RAY DIFFRACTION	38	chain 'A' and (resid 300 through 316 )

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