PDB-14um: Crystal Structure of FtsZ with F2146-0687

ID or keywords:

Entry

Database: PDB / ID: 14um

Title

Crystal Structure of FtsZ with F2146-0687

Components

Cell division protein FtsZ

Keywords

CELL CYCLE / tuberculosis / FtsZ / 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

Mycobacterium tuberculosis CDC1551 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.948 Å

Authors

Meeks, K.R. / Kreitler, D.F. / Lazo, E.O.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P30GM133893	United States
Department of Energy (DOE, United States)	KP1605010	United States

Citation

Journal: To be published
Title: Crystal Structure of FtsZ with F2146-0687
Authors: Meeks, K.R. / Kreitler, D.F. / Lazo, E.O.

History

Deposition	Jul 15, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 5, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	14um.cif.gz	143.2 KB	Display	PDBx/mmCIF format
PDB format	pdb14um.ent.gz	110 KB	Display	PDB format
PDBx/mmJSON format	14um.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/4u/14um ftp://data.pdbj.org/pub/pdb/validation_reports/4u/14um	HTTPS FTP

-
Group deposition

ID	G_1002379 (150 entries) 14uh 14ui 14uj 14uk 14ul 14um 14un 14uo 14up 14uq
Title	PanDDA analysis group deposition of Mycobacterium tuberculosis FtsZ fragment screen
Type	undefined
Description	M. tuberculosis FtsZ fragment screen against Enamine DSI-poised and Life Chemicals fragment diversity set #3 libraries. Ligands in DMSO were acoustically transferred to crystal drops. Refined ensemble models for hit ligands placed into PanDDA event maps. Changed and ground states within ensembles are designated with altloc labels for each atom. Atoms with no altlocs are assumed to be in the same position in each state. Event maps are primary binding evidence and are appended as additional blocks in structure factor CIF files. All sets of structure factors used for PanDDA analysis are included in this deposition. Structure factors for unmodeled and solvent test datasets not refined to convergence have been concatenated into a multi-block structure factor file with a corresponding representative structure. Chemical information for each added ligand is included for modeled and unmodeled ligand datasets in the _diffrn.crystal_treatment key value pair.

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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

A: Cell division protein FtsZ

B: Cell division protein FtsZ

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	88.968, 88.968, 180.139
Angle α, β, γ (deg.)	90, 90, 120
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	Cell division protein FtsZ Mass: 38790.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis CDC1551 (bacteria) Gene: ftsZ, MT2209 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WN94
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-OK7 / N-(thiophen-2-yl)acetamide Mass: 141.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₇NOS / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.65 Å³/Da / Density % sol: 53.63 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1 M ammonium sulfate, 15.6% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.0.

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.919764 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 6, 2025 / Details: KB
Radiation	Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.919764 Å / Relative weight: 1
Reflection	Resolution: 1.948→44.484 Å / Num. obs: 58766 / % possible obs: 100 % / Redundancy: 13.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.157 / R_pim(I) all: 0.045 / R_rim(I) all: 0.164 / Net I/σ(I): 11.8 / Num. measured all: 784531
Reflection shell	Resolution: 1.948→1.982 Å / % possible obs: 100 % / Redundancy: 13.4 % / R_merge(I) obs: 2.789 / Num. measured all: 39708 / Num. unique obs: 2957 / CC_1/2: 0.324 / R_pim(I) all: 0.79 / R_rim(I) all: 2.899

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
autoPROC	1.0.5	data reduction
Aimless		data scaling
XDS		data reduction
DIMPLE		phasing
PHASER		phasing
Coot		model building
gemmi	0.7.3	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.948→44.524 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.951 / WR_factor R_free: 0.202 / WR_factor R_work: 0.169 / SU B: 4.433 / SU ML: 0.118 / Average fsc free: 0.96 / Average fsc work: 0.9695 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.129
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2137	2958	5.038 %
R_work	0.1811	55754	-
all	0.183	-	-
obs	-	58712	99.886 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 38.702 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.014 Å²	-0.007 Å²	-0 Å²
2-	-	-0.014 Å²	0 Å²
3-	-	-	0.044 Å²

Refinement step

Cycle: LAST / Resolution: 1.948→44.524 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4230	0	23	308	4561

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	4866
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.016	4810
X-RAY DIFFRACTION	r_angle_refined_deg	1.763	1.782	6592
X-RAY DIFFRACTION	r_angle_other_deg	0.668	1.739	11031
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.715	5	676
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.553	6.22	41
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.628	10	818
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.828	10	193
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	795
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	5928
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1016
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	1082
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.576	0.2	6700
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	2455
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.131	0.2	2455
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.207	0.2	329
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.161	0.2	8
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.191	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.186	0.2	66
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.281	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	3.346	3.828	2686
X-RAY DIFFRACTION	r_mcbond_other	3.344	3.828	2686
X-RAY DIFFRACTION	r_mcangle_it	4.723	6.863	3368
X-RAY DIFFRACTION	r_mcangle_other	4.722	6.864	3369
X-RAY DIFFRACTION	r_scbond_it	4.96	4.439	2180
X-RAY DIFFRACTION	r_scbond_other	4.959	4.439	2181
X-RAY DIFFRACTION	r_scangle_it	7.496	7.899	3224
X-RAY DIFFRACTION	r_scangle_other	7.494	7.898	3225
X-RAY DIFFRACTION	r_lrange_it	9.086	38.108	5463
X-RAY DIFFRACTION	r_lrange_other	9.038	37.897	5383

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.948-1.999	0.325	217	0.314	4103	0.315	4335	0.922	0.926	99.654	0.317
1.999-2.053	0.316	209	0.285	3988	0.286	4207	0.934	0.941	99.7623	0.285
2.053-2.113	0.283	191	0.272	3950	0.273	4142	0.943	0.948	99.9759	0.268
2.113-2.178	0.283	169	0.244	3824	0.246	3993	0.947	0.959	100	0.235
2.178-2.249	0.284	179	0.233	3622	0.236	3822	0.95	0.963	99.4505	0.219
2.249-2.328	0.247	177	0.213	3557	0.214	3746	0.956	0.971	99.6797	0.195
2.328-2.415	0.243	221	0.187	3405	0.19	3626	0.962	0.979	100	0.169
2.415-2.514	0.237	210	0.191	3264	0.194	3474	0.966	0.978	100	0.168
2.514-2.625	0.219	176	0.18	3167	0.182	3343	0.971	0.981	100	0.157
2.625-2.753	0.211	167	0.17	3027	0.172	3194	0.969	0.983	100	0.148
2.753-2.901	0.203	157	0.168	2852	0.17	3009	0.976	0.984	100	0.148
2.901-3.076	0.195	143	0.174	2753	0.175	2896	0.976	0.982	100	0.158
3.076-3.287	0.221	132	0.171	2573	0.173	2705	0.965	0.983	100	0.161
3.287-3.549	0.205	119	0.18	2361	0.181	2480	0.978	0.983	100	0.173
3.549-3.885	0.205	119	0.164	2217	0.166	2336	0.977	0.986	100	0.16
3.885-4.34	0.155	85	0.149	2006	0.149	2091	0.984	0.987	100	0.153
4.34-5.003	0.174	91	0.142	1771	0.144	1862	0.983	0.989	100	0.15
5.003-6.108	0.185	94	0.169	1476	0.17	1570	0.982	0.986	100	0.176
6.108-8.558	0.181	71	0.151	1157	0.153	1228	0.983	0.988	100	0.165
8.558-44.524	0.258	31	0.178	681	0.181	712	0.931	0.975	100	0.197

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Group deposition

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Group deposition

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Group deposition

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi