PDB-2f41: Crystal structure of FapR- a global regulator of fatty acid biosy...

ID or keywords:

Entry

Database: PDB / ID: 2f41

Title

Crystal structure of FapR- a global regulator of fatty acid biosynthesis in B. subtilis

Components

Transcription factor fapR

Keywords

GENE REGULATION / 'hot-dog' fold

Function / homology

Function and homology information

negative regulation of fatty acid biosynthetic process / fatty acid biosynthetic process / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Buschiazzo, A. / Guerin, M.E. / Alzari, P.M.

Citation

Journal: Embo J. / Year: 2006
Title: Structural basis of lipid biosynthesis regulation in Gram-positive bacteria.
Authors: Schujman, G.E. / Guerin, M. / Buschiazzo, A. / Schaeffer, F. / Llarrull, L.I. / Reh, G. / Vila, A.J. / Alzari, P.M. / de Mendoza, D.

History

Deposition	Nov 22, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 31, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Feb 14, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim 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.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2f41.cif.gz	87.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2f41.ent.gz	65 KB	Display	PDB format
PDBx/mmJSON format	2f41.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2f41_validation.pdf.gz	448.4 KB	Display	wwPDB validaton report
Full document	2f41_full_validation.pdf.gz	457 KB	Display
Data in XML	2f41_validation.xml.gz	16 KB	Display
Data in CIF	2f41_validation.cif.gz	22.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f4/2f41 ftp://data.pdbj.org/pub/pdb/validation_reports/f4/2f41	HTTPS FTP

-
Related structure data

Related structure data	2f3xC C: citing same article (ref.)
Similar structure data	4ibq-2 5qud-d 5gii-d 1lqw-2 5quh-d 3jrs-2 5qug-d 4agn-2 3owb-d 5o1g-1 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (1)

Deposited unit

A: Transcription factor fapR

B: Transcription factor fapR

C: Transcription factor fapR

D: Transcription factor fapR

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

1

A: Transcription factor fapR

B: Transcription factor fapR

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

2

C: Transcription factor fapR

D: Transcription factor fapR

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

Unit cell

Length a, b, c (Å)	39.239, 84.320, 155.385
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLU	GLU	VAL	VAL	2	A	A	73 - 98	6 - 31
2	1	GLU	GLU	VAL	VAL	2	B	B	73 - 98	6 - 31
3	1	GLU	GLU	VAL	VAL	2	C	C	73 - 98	6 - 31
4	1	GLU	GLU	VAL	VAL	2	D	D	73 - 98	6 - 31
1	2	ALA	ALA	VAL	VAL	2	A	A	105 - 155	38 - 88
2	2	ALA	ALA	VAL	VAL	2	B	B	105 - 155	38 - 88
3	2	ALA	ALA	VAL	VAL	2	C	C	105 - 155	38 - 88
4	2	ALA	ALA	VAL	VAL	2	D	D	105 - 155	38 - 88
1	3	ARG	ARG	TYR	TYR	2	A	A	161 - 183	94 - 116
2	3	ARG	ARG	TYR	TYR	2	B	B	161 - 183	94 - 116
3	3	ARG	ARG	TYR	TYR	2	C	C	161 - 183	94 - 116
4	3	ARG	ARG	TYR	TYR	2	D	D	161 - 183	94 - 116
1	4	VAL	VAL	ILE	ILE	6	A	A	98 - 104	31 - 37
2	4	VAL	VAL	ILE	ILE	6	B	B	98 - 104	31 - 37
3	4	VAL	VAL	ILE	ILE	6	D	D	98 - 104	31 - 37

NCS ensembles :

ID
1
2
3
4

Details

The asymmetric unit contains two dimers. The biological unit is a dimer.

#1: Protein	Transcription factor fapR / Fatty acid and phospholipid biosynthesis regulator Mass: 13515.244 Da / Num. of mol.: 4 / Fragment: C-teminal domain (residues 68-188) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: fapR / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O34835
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Transcription factor fapR / Fatty acid and phospholipid biosynthesis regulator

Mass: 13515.244 Da / Num. of mol.: 4 / Fragment: C-teminal domain (residues 68-188)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus subtilis (bacteria) / Gene: fapR / Plasmid: pQE30 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O34835

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.26 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.2M ammonium sulfate, 2% PEG 400, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07175 Å
Detector	Type: MARRESEARCH / Detector: CCD / Date: Jul 9, 2004 / Details: toroidal mirror
Radiation	Monochromator: Si 111 CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.07175 Å / Relative weight: 1
Reflection	Resolution: 2.5→57.17 Å / Num. all: 14880 / Num. obs: 14880 / % possible obs: 80.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / R_merge(I) obs: 0.083 / R_sym value: 0.083 / Net I/σ(I): 13.7
Reflection shell	Resolution: 2.5→2.64 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.287 / Mean I/σ(I) obs: 4.8 / R_sym value: 0.287 / % possible all: 50

-
Processing

Software

Name	Version	Classification
SCALA		data scaling
REFMAC		refinement
PDB_EXTRACT	1.701	data extraction
MOSFLM		data reduction
CCP4	(SCALA)	data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.892 / SU B: 19.696 / SU ML: 0.204 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.707 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27377	790	5.3 %	RANDOM
R_work	0.21889	-	-	-
obs	0.22162	14035	79.76 %	-
all	-	14825	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 61.423 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.7 Å²	0 Å²	0 Å²
2-	-	11.16 Å²	0 Å²
3-	-	-	-6.45 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2964	0	0	8	2972

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.022	2991
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2933
X-RAY DIFFRACTION	r_angle_refined_deg	1.826	1.913	4077
X-RAY DIFFRACTION	r_angle_other_deg	0.955	3	6656
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.928	5	419
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.705	23.4	100
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.121	15	401
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	28.418	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.113	0.2	531
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3465
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	618
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	495
X-RAY DIFFRACTION	r_nbd_other	0.19	0.2	2715
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	1452
X-RAY DIFFRACTION	r_nbtor_other	0.091	0.2	1991
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	75
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.145	0.2	10
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.219	0.2	25
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.016	0.2	1
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.109	1.5	2630
X-RAY DIFFRACTION	r_mcbond_other	0.193	1.5	892
X-RAY DIFFRACTION	r_mcangle_it	1.301	2	3294
X-RAY DIFFRACTION	r_scbond_it	1.98	3	969
X-RAY DIFFRACTION	r_scangle_it	3.113	4.5	783
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	101	tight positional	0.06	0.05
1	2	B	101	tight positional	0.04	0.05
1	3	C	101	tight positional	0.06	0.05
1	4	D	101	tight positional	0.06	0.05
2	1	A	250	tight positional	0.06	0.05
2	2	B	250	tight positional	0.06	0.05
2	3	C	250	tight positional	0.06	0.05
2	4	D	250	tight positional	0.06	0.05
3	1	A	124	tight positional	0.06	0.05
3	2	B	124	tight positional	0.05	0.05
3	3	C	124	tight positional	0.06	0.05
3	4	D	124	tight positional	0.06	0.05
1	1	A	165	medium positional	0.43	0.5
1	2	B	165	medium positional	0.51	0.5
1	3	C	165	medium positional	0.36	0.5
1	4	D	165	medium positional	0.32	0.5
2	1	A	318	medium positional	0.26	0.5
2	2	B	318	medium positional	0.25	0.5
2	3	C	318	medium positional	0.32	0.5
2	4	D	318	medium positional	0.26	0.5
3	1	A	182	medium positional	0.3	0.5
3	2	B	182	medium positional	0.3	0.5
3	3	C	182	medium positional	0.4	0.5
3	4	D	182	medium positional	0.3	0.5
4	1	A	77	loose positional	1.64	5
4	2	B	77	loose positional	1.08	5
4	3	D	77	loose positional	0.85	5
1	1	A	101	tight thermal	0.1	0.5
1	2	B	101	tight thermal	0.15	0.5
1	3	C	101	tight thermal	0.12	0.5
1	4	D	101	tight thermal	0.12	0.5
2	1	A	250	tight thermal	0.13	0.5
2	2	B	250	tight thermal	0.13	0.5
2	3	C	250	tight thermal	0.13	0.5
2	4	D	250	tight thermal	0.12	0.5
3	1	A	124	tight thermal	0.12	0.5
3	2	B	124	tight thermal	0.14	0.5
3	3	C	124	tight thermal	0.12	0.5
3	4	D	124	tight thermal	0.15	0.5
1	1	A	165	medium thermal	0.39	2
1	2	B	165	medium thermal	0.4	2
1	3	C	165	medium thermal	0.32	2
1	4	D	165	medium thermal	0.37	2
2	1	A	318	medium thermal	0.55	2
2	2	B	318	medium thermal	0.6	2
2	3	C	318	medium thermal	0.67	2
2	4	D	318	medium thermal	0.71	2
3	1	A	182	medium thermal	0.55	2
3	2	B	182	medium thermal	0.49	2
3	3	C	182	medium thermal	0.49	2
3	4	D	182	medium thermal	0.53	2
4	1	A	77	loose thermal	2.56	10
4	2	B	77	loose thermal	1.24	10
4	3	D	77	loose thermal	1.63	10

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	Num. reflection all	% reflection obs (%)
2.5-2.565	0.281	38	0.228	528	1317	42.976
2.565-2.634	0.319	45	0.25	689	1339	54.817
2.634-2.71	0.36	50	0.243	756	1231	65.475
2.71-2.793	0.315	46	0.248	926	1254	77.512
2.793-2.884	0.352	66	0.254	954	1192	85.57
2.884-2.984	0.251	64	0.251	960	1170	87.521
2.984-3.095	0.322	50	0.257	921	1120	86.696
3.095-3.22	0.298	58	0.243	896	1098	86.885
3.22-3.362	0.273	45	0.253	848	1032	86.531
3.362-3.524	0.275	39	0.241	829	1006	86.282
3.524-3.711	0.276	43	0.221	771	955	85.236
3.711-3.933	0.242	38	0.199	750	923	85.374
3.933-4.199	0.311	36	0.174	673	841	84.304
4.199-4.528	0.161	29	0.162	658	804	85.448
4.528-4.949	0.229	30	0.152	604	762	83.202
4.949-5.515	0.241	38	0.213	535	678	84.513
5.515-6.332	0.377	25	0.265	545	605	94.215
6.332-7.67	0.259	22	0.226	520	542	100
7.67-10.509	0.177	16	0.204	403	431	97.216
10.509-30	0.374	12	0.316	269	286	98.252

-
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

-
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

-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

-
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