PDB-3laj: The Structure of the Intermediate Complex of the Arginine Repress...

ID or keywords:

Entry

Database: PDB / ID: 3laj

Title

The Structure of the Intermediate Complex of the Arginine Repressor from Mycobacterium tuberculosis Bound to its DNA Operator and L-arginine.

Components

5'-D(*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*A)-3'
5'-D(*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*A)-3'
Arginine repressor

Keywords

TRANSCRIPTION REGULATOR / Mycobacterium tuberculosis / arginine repressor / DNA binding / ArgR-DNA complex / Structural Genomics / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB / Amino-acid biosynthesis / Arginine biosynthesis / Cytoplasm / DNA-binding / Repressor / Transcription

Function / homology

Function and homology information

regulation of arginine biosynthetic process / : / L-arginine biosynthetic process / arginine binding / protein complex oligomerization / cis-regulatory region sequence-specific DNA binding / transcription regulator complex / DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.306 Å

Authors

Cherney, L.T. / Cherney, M.M. / Garen, C.R. / James, M.N.G. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)

Citation

Journal: J.Mol.Biol. / Year: 2010
Title: crystal structure of the intermediate complex of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator reveals detailed mechanism of arginine repression.
Authors: Cherney, L.T. / Cherney, M.M. / Garen, C.R. / James, M.N.

History

Deposition	Jan 6, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 5, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 6, 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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	3laj.cif.gz	240.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3laj.ent.gz	187.3 KB	Display	PDB format
PDBx/mmJSON format	3laj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3laj_validation.pdf.gz	527.8 KB	Display	wwPDB validaton report
Full document	3laj_full_validation.pdf.gz	558.4 KB	Display
Data in XML	3laj_validation.xml.gz	43.9 KB	Display
Data in CIF	3laj_validation.cif.gz	61.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/la/3laj ftp://data.pdbj.org/pub/pdb/validation_reports/la/3laj	HTTPS FTP

-
Related structure data

Related structure data	3lapC 3ereS 2zfz 3bue 3cag 3fhz S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3lap-d 5c3m-1 3oe9-d 5hy4-1 5axl-1 6o1a-2 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	#67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #133 - Jan 2011 Nitric Oxide Synthase similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)
#133 - Jan 2011
Nitric Oxide Synthase
similarity (1)

Deposited unit

A: Arginine repressor

B: Arginine repressor

C: Arginine repressor

D: Arginine repressor

E: Arginine repressor

F: Arginine repressor

G: 5'-D(*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*A)-3'

H: 5'-D(*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*A)-3'

I: 5'-D(*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*A)-3'

J: 5'-D(*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*A)-3'

K: 5'-D(*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*A)-3'

L: 5'-D(*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*A)-3'

hetero molecules

135 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	185.686, 106.788, 119.080
Angle α, β, γ (deg.)	90.00, 121.75, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
1	2
2	2
3	2
1	3
2	3
3	3
1	4
2	4
3	4
1	5
2	5
3	5

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain F and (resseq 17:170 )
2	1	1	chain E and (resseq 17:170 )
3	1	1	chain D and (resseq 17:170 )
1	1	2	chain B and (resseq 90:170 )
2	1	2	chain A and (resseq 90:170 )
3	1	2	chain C and (resseq 90:170 )
1	1	3	chain A and (resseq 15:82 )
2	1	3	chain B and (resseq 15:82 )
3	1	3	chain C and (resseq 15:82 )
1	1	4	chain G and (resseq 1:16 )
2	1	4	chain I and (resseq 1:16 )
3	1	4	chain K and (resseq 1:16 )
1	1	5	chain H and (resseq 1:16 )
2	1	5	chain J and (resseq 1:16 )
3	1	5	chain L and (resseq 1:16 )

NCS ensembles :

ID
1
2
3
4
5

#1: Protein	Arginine repressor Mass: 17366.635 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: ahrC, argR, MT1695, MTCY06H11.22, Rv1657 / Plasmid: PGST-1657 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P0A4Y8, UniProt: P9WPY9*PLUS
#2: DNA chain	5'-D(TPTPGPCPAPTPAPAPCPGPAPTPGPCPAPA)-3' Mass: 4906.217 Da / Num. of mol.: 3 / Fragment: ARG box DNA segment, strand G / Source method: obtained synthetically
#3: DNA chain	5'-D(TPTPGPCPAPTPCPGPTPTPAPTPGPCPAPA)-3' Mass: 4888.189 Da / Num. of mol.: 3 / Fragment: ARG box DNA segment, strand H / Source method: obtained synthetically
#4: Chemical	ChemComp-ARG / ARGININE Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₅N₄O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 435 / 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: 3.73 Å³/Da / Density % sol: 67.01 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion / pH: 5.5 Details: 1M ammonium sulfate, 100 mM bis-tris buffer, 1% PEG 3350, pH 5.5, VAPOR DIFFUSION, temperature 295K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.11587 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. all: 86698 / Num. obs: 84444 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / B_iso Wilson estimate: 58.3 Å² / R_merge(I) obs: 0.041 / R_sym value: 0.041 / Net I/σ(I): 16.6
Reflection shell	Resolution: 2.3→2.38 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.85 / Mean I/σ(I) obs: 1.9 / Num. unique all: 8608 / R_sym value: 0.424 / % possible all: 98.6

-
Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHENIX	(phenix.automr)	model building
PHENIX	(phenix.refine: 1.4_58)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3ere

3ere

Resolution: 2.306→39.237 Å / SU ML: 0.27 / σ(F): 1.34 / σ(I): 0 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2072	4219	5 %
R_work	0.1838	-	-
obs	0.185	84429	96.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 66.496 Å² / k_sol: 0.359 e/Å³

Refinement step

Cycle: LAST / Resolution: 2.306→39.237 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6571	1950	72	435	9028

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	8869
X-RAY DIFFRACTION	f_angle_d	1.74	12428
X-RAY DIFFRACTION	f_dihedral_angle_d	22.092	3386
X-RAY DIFFRACTION	f_chiral_restr	0.09	1490
X-RAY DIFFRACTION	f_plane_restr	0.006	1313

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	F	1112	X-RAY DIFFRACTION	POSITIONAL
1	2	E	1112	X-RAY DIFFRACTION	POSITIONAL	0.106
1	3	D	1112	X-RAY DIFFRACTION	POSITIONAL	0.051
2	1	B	583	X-RAY DIFFRACTION	POSITIONAL
2	2	A	583	X-RAY DIFFRACTION	POSITIONAL	0.135
2	3	C	583	X-RAY DIFFRACTION	POSITIONAL	0.144
3	1	A	492	X-RAY DIFFRACTION	POSITIONAL
3	2	B	492	X-RAY DIFFRACTION	POSITIONAL	0.035
3	3	C	492	X-RAY DIFFRACTION	POSITIONAL	0.033
4	1	G	326	X-RAY DIFFRACTION	POSITIONAL
4	2	I	326	X-RAY DIFFRACTION	POSITIONAL	0.035
4	3	K	326	X-RAY DIFFRACTION	POSITIONAL	0.032
5	1	H	324	X-RAY DIFFRACTION	POSITIONAL
5	2	J	324	X-RAY DIFFRACTION	POSITIONAL	0.035
5	3	L	324	X-RAY DIFFRACTION	POSITIONAL	0.033

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 (%)
2.3062-2.3324	0.3212	109	0.287	2383	X-RAY DIFFRACTION	85
2.3324-2.3598	0.3048	144	0.2724	2654	X-RAY DIFFRACTION	99
2.3598-2.3886	0.2808	157	0.2638	2704	X-RAY DIFFRACTION	98
2.3886-2.4188	0.3152	152	0.2666	2708	X-RAY DIFFRACTION	99
2.4188-2.4507	0.2761	131	0.2505	2709	X-RAY DIFFRACTION	99
2.4507-2.4842	0.2708	146	0.2457	2726	X-RAY DIFFRACTION	99
2.4842-2.5197	0.258	140	0.2276	2711	X-RAY DIFFRACTION	99
2.5197-2.5573	0.27	137	0.2326	2698	X-RAY DIFFRACTION	99
2.5573-2.5973	0.3019	138	0.2174	2705	X-RAY DIFFRACTION	99
2.5973-2.6399	0.2639	160	0.2133	2687	X-RAY DIFFRACTION	98
2.6399-2.6854	0.2553	130	0.208	2738	X-RAY DIFFRACTION	98
2.6854-2.7342	0.2373	142	0.2103	2692	X-RAY DIFFRACTION	98
2.7342-2.7868	0.2719	141	0.2043	2698	X-RAY DIFFRACTION	99
2.7868-2.8436	0.2511	114	0.2042	2720	X-RAY DIFFRACTION	98
2.8436-2.9054	0.2656	149	0.2075	2746	X-RAY DIFFRACTION	98
2.9054-2.973	0.2451	131	0.2031	2693	X-RAY DIFFRACTION	98
2.973-3.0473	0.2189	155	0.1988	2697	X-RAY DIFFRACTION	98
3.0473-3.1297	0.2688	144	0.2051	2682	X-RAY DIFFRACTION	98
3.1297-3.2217	0.2054	142	0.1871	2689	X-RAY DIFFRACTION	97
3.2217-3.3257	0.2038	141	0.1766	2709	X-RAY DIFFRACTION	98
3.3257-3.4445	0.2225	142	0.1776	2691	X-RAY DIFFRACTION	98
3.4445-3.5823	0.1961	140	0.1766	2710	X-RAY DIFFRACTION	98
3.5823-3.7452	0.2035	136	0.1723	2644	X-RAY DIFFRACTION	97
3.7452-3.9425	0.1799	148	0.1589	2730	X-RAY DIFFRACTION	97
3.9425-4.1892	0.1659	137	0.1546	2646	X-RAY DIFFRACTION	97
4.1892-4.5123	0.1627	152	0.1425	2650	X-RAY DIFFRACTION	96
4.5123-4.9655	0.1732	125	0.1407	2645	X-RAY DIFFRACTION	95
4.9655-5.6822	0.1383	154	0.1481	2645	X-RAY DIFFRACTION	95
5.6822-7.1519	0.1813	145	0.1646	2699	X-RAY DIFFRACTION	97
7.1519-39.2428	0.1595	137	0.1582	2401	X-RAY DIFFRACTION	85

-
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