PDB-3wg9: Crystal structure of RSP, a Rex-family repressor

ID or keywords:

Entry

Database: PDB / ID: 3wg9

Title

Crystal structure of RSP, a Rex-family repressor

Components

Redox-sensing transcriptional repressor rex

Keywords

TRANSCRIPTION / winged helix / Rossmann fold / repressor

Function / homology

Function and homology information

response to redox state / DNA-binding transcription factor activity / nucleotide binding / negative regulation of DNA-templated transcription / DNA binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Thermoanaerobacter ethanolicus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.97 Å

Authors

Zheng, Y. / Ko, T.-P. / Guo, R.-T.

Citation

Journal: J.Struct.Biol. / Year: 2014
Title: Distinct structural features of Rex-family repressors to sense redox levels in anaerobes and aerobes.
Authors: Zheng, Y. / Ko, T.-P. / Sun, H. / Huang, C.-H. / Pei, J. / Qiu, R. / Wang, A.H.-J. / Wiegel, J. / Shao, W. / Guo, R.-T.

History

Deposition	Aug 3, 2013	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 13, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 25, 2019	Group: Database references / Category: citation Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Nov 8, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3wg9.cif.gz	360.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3wg9.ent.gz	295.5 KB	Display	PDB format
PDBx/mmJSON format	3wg9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3wg9_validation.pdf.gz	468.5 KB	Display	wwPDB validaton report
Full document	3wg9_full_validation.pdf.gz	492.3 KB	Display
Data in XML	3wg9_validation.xml.gz	42.8 KB	Display
Data in CIF	3wg9_validation.cif.gz	62.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wg/3wg9 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/3wg9	HTTPS FTP

-
Related structure data

Related structure data	3wghC 3wgiC 1xcbS 3wgg C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3wgh-d 3wgg-d 1xcb-2 2egi-1 6sty-1 4riq-1 5t06-d 5efy-2 4riq-2 6lis-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	#154 - Oct 2012 Citric Acid Cycle similarity (3)

Deposited unit

A: Redox-sensing transcriptional repressor rex

B: Redox-sensing transcriptional repressor rex

C: Redox-sensing transcriptional repressor rex

D: Redox-sensing transcriptional repressor rex

hetero molecules

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

1

A: Redox-sensing transcriptional repressor rex

B: Redox-sensing transcriptional repressor rex

hetero molecules

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

2

C: Redox-sensing transcriptional repressor rex

D: Redox-sensing transcriptional repressor rex

hetero molecules

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

Unit cell

Length a, b, c (Å)	73.412, 90.098, 171.637
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	C
1	4	B
2	4	D

NCS domain segments:

Refine code: 5

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	THR	THR	GLY	GLY	A	A	5 - 57	5 - 57
2	1	1	THR	THR	GLY	GLY	B	B	5 - 57	5 - 57
3	1	1	THR	THR	GLY	GLY	C	C	5 - 57	5 - 57
4	1	1	THR	THR	GLY	GLY	D	D	5 - 57	5 - 57
1	2	1	TYR	TYR	ALA	ALA	A	A	66 - 92	66 - 92
2	2	1	TYR	TYR	ALA	ALA	B	B	66 - 92	66 - 92
3	2	1	TYR	TYR	ALA	ALA	C	C	66 - 92	66 - 92
4	2	1	TYR	TYR	ALA	ALA	D	D	66 - 92	66 - 92
1	3	1	LYS	LYS	PHE	PHE	A	A	113 - 177	113 - 177
2	3	1	LYS	LYS	PHE	PHE	B	B	113 - 177	113 - 177
3	3	1	LYS	LYS	PHE	PHE	C	C	113 - 177	113 - 177
4	3	1	LYS	LYS	PHE	PHE	D	D	113 - 177	113 - 177
1	1	2	ILE	ILE	LEU	LEU	A	A	118 - 215	118 - 215
2	1	2	ILE	ILE	LEU	LEU	B	B	118 - 215	118 - 215
3	1	2	ILE	ILE	LEU	LEU	C	C	118 - 215	118 - 215
4	1	2	ILE	ILE	LEU	LEU	D	D	118 - 215	118 - 215
1	1	3	ILE	ILE	GLY	GLY	A	A	90 - 114	90 - 114
2	1	3	ILE	ILE	GLY	GLY	C	C	90 - 114	90 - 114
1	2	3	ASN	ASN	ILE	ILE	A	A	176 - 189	176 - 189
2	2	3	ASN	ASN	ILE	ILE	C	C	176 - 189	176 - 189
1	1	4	ILE	ILE	GLY	GLY	B	B	90 - 114	90 - 114
2	1	4	ILE	ILE	GLY	GLY	D	D	90 - 114	90 - 114
1	2	4	ASN	ASN	ILE	ILE	B	B	176 - 189	176 - 189
2	2	4	ASN	ASN	ILE	ILE	D	D	176 - 189	176 - 189

NCS ensembles :

ID
1
2
3
4

#1: Protein	Redox-sensing transcriptional repressor rex / RSP repressor Mass: 25474.279 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacter ethanolicus (bacteria) Strain: JW200 / Gene: rex, rsp / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D5KM69
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 793 / 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: 2.79 Å³/Da / Density % sol: 55.84 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% w/v PEG 3350, 0.4M ammonium sulfate, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2010
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.97→25 Å / Num. all: 81058 / Num. obs: 80854 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 12.1 % / B_iso Wilson estimate: 31.3 Å² / R_merge(I) obs: 0.049 / Net I/σ(I): 44.5
Reflection shell	Resolution: 1.97→2.04 Å / Redundancy: 11.7 % / R_merge(I) obs: 0.361 / Mean I/σ(I) obs: 7.1 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
Blu-Ice	Control Software	data collection
CNS		refinement
HKL-2000		data reduction
HKL-2000		data scaling
CNS		phasing
REFMAC	5.5.0109	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB 1XCB

1xcb

Resolution: 1.97→25 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.94 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.905 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2523	3945	5.1 %	RANDOM
R_work	0.19804	-	-	-
obs	0.20085	77796	100 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 49.626 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.59 Å²	0 Å²	0 Å²
2-	-	3.47 Å²	0 Å²
3-	-	-	-1.88 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.32 Å	0.26 Å
Luzzati d res low	-	5 Å
Luzzati sigma a	0.22 Å	0.2 Å

Refinement step

Cycle: LAST / Resolution: 1.97→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6736	0	25	793	7554

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	6857
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.773	1.978	9245
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.668	5	830
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	43.656	24.32	331
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.992	15	1290
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.342	15	52
X-RAY DIFFRACTION	r_chiral_restr	0.132	0.2	1053
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	5067
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	1.524	1.5	4142
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.573	2	6703
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.439	3	2715
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.584	4.5	2542
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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	580	medium positional	0.5	0.5
1	2	B	580	medium positional	0.33	0.5
1	3	C	580	medium positional	0.27	0.5
1	4	D	580	medium positional	0.29	0.5
2	1	A	392	medium positional	0.35	0.5
2	2	B	392	medium positional	0.43	0.5
2	3	C	392	medium positional	0.34	0.5
2	4	D	392	medium positional	0.31	0.5
3	1	A	156	medium positional	0.1	0.5
4	1	B	156	medium positional	0.13	0.5
1	1	A	597	loose positional	0.94	5
1	2	B	597	loose positional	0.74	5
1	3	C	597	loose positional	0.73	5
1	4	D	597	loose positional	0.75	5
2	1	A	405	loose positional	0.87	5
2	2	B	405	loose positional	0.85	5
2	3	C	405	loose positional	0.79	5
2	4	D	405	loose positional	0.8	5
3	1	A	136	loose positional	0.44	5
4	1	B	136	loose positional	0.47	5
1	1	A	580	medium thermal	3.88	2
1	2	B	580	medium thermal	3.65	2
1	3	C	580	medium thermal	3.57	2
1	4	D	580	medium thermal	3.36	2
2	1	A	392	medium thermal	2.69	2
2	2	B	392	medium thermal	3.05	2
2	3	C	392	medium thermal	3.31	2
2	4	D	392	medium thermal	2.67	2
3	1	A	156	medium thermal	1.35	2
4	1	B	156	medium thermal	1.14	2
1	1	A	597	loose thermal	3.2	10
1	2	B	597	loose thermal	3.15	10
1	3	C	597	loose thermal	3.25	10
1	4	D	597	loose thermal	2.99	10
2	1	A	405	loose thermal	2.36	10
2	2	B	405	loose thermal	2.53	10
2	3	C	405	loose thermal	2.64	10
2	4	D	405	loose thermal	2.34	10
3	1	A	136	loose thermal	1.35	10
4	1	B	136	loose thermal	1.31	10

LS refinement shell

Resolution: 1.972→2.078 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.282	483	-
R_work	0.218	9919	-
obs	-	-	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	0.8428	0.0475	0.1488	0.2725	0.2931	0.3818	0.0955	-0.0014	0.0295	0.0549	-0.0877	0.0523	0.1021	-0.0676	-0.0078	0.0974	-0.0204	-0.0124	0.0723	-0.0112	0.0859	19.9545	39.2282	78.5311
2	1.4739	-0.141	0.0861	0.0424	-0.1055	0.3978	0.1132	0.0346	0.0297	0.0115	-0.0123	0.0102	-0.0497	0.0155	-0.1009	0.0745	-0.0147	0.0179	0.064	-0.0138	0.0709	29.3542	47.0665	88.8551
3	0.7843	-0.1806	-0.4301	0.1058	0.2215	0.5321	0.0314	0.0876	0.0019	-0.0058	-0.0202	0.0234	-0.0151	-0.1068	-0.0112	0.0778	-0.0264	0.0083	0.1383	0.0384	0.0588	19.9622	-5.025	46.5627
4	1.0913	-0.0335	-0.2036	0.1863	-0.2078	0.4346	0.1314	0.0864	0.0261	0.0274	0.0074	0.0403	-0.0895	0.0676	-0.1388	0.057	-0.0133	0.0285	0.1306	-0.034	0.0624	29.7386	1.8598	56.5635

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 217
2	X-RAY DIFFRACTION	2	B	4 - 215
3	X-RAY DIFFRACTION	3	C	4 - 216
4	X-RAY DIFFRACTION	4	D	4 - 215

Xplor file

Refine-ID	Serial no	Param file
X-RAY DIFFRACTION	1	protein_rep.param
X-RAY DIFFRACTION	2	water_rep.param
X-RAY DIFFRACTION	3	ion.param

-
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