PDB-2w24: M. tuberculosis Rv3291c complexed to Lysine

Basic information

• Entry: Database: PDB / ID: 2w24
• Title: M. tuberculosis Rv3291c complexed to Lysine
• Components: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN
• Keywords: TRANSCRIPTION / RV3291C / DNA-BINDING / LYSINE COMPLEX / TRANSCRIPTION REGULATOR / TRANSCRIPTION REGULATION

Function / homology

Function:

amino acid binding / response to amino acid / protein homooligomerization / sequence-specific DNA binding / DNA binding / cytosol

Domain/homology:

AsnC-type HTH domain profile. / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / AsnC-type HTH domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / Winged helix-turn-helix DNA-binding / Dimeric alpha-beta barrel / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta

Component:

LYSINE / Leucine-responsive regulatory protein

• Biological species: MYCOBACTERIUM TUBERCULOSIS (bacteria)
• Method: X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
• Authors: Shrivastava, T. / Ramachandran, R.
• Citation: Journal: J.Mol.Biol. / Year: 2009; Title: Ligand-Induced Structural Transitions, Mutational Analysis, and 'Open' Quaternary Structure of the M. Tuberculosis Feast/Famine Regulatory Protein (Rv3291C).; Authors: Shrivastava, T. / Dey, A. / Ramachandran, R.

History

Deposition	Oct 24, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 17, 2009	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

• Remark 700: SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

Assembly

Deposited unit

A: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN

B: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN

hetero molecules

Summary:

• 33.2 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	33,208	3
Polymers	33,061	2
Non-polymers	147	1
Water	811	45

1

A: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN

B: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN

hetero molecules

A: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN

B: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN

hetero molecules

A: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN

B: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN

hetero molecules

A: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN

B: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN

hetero molecules

Summary:

• defined by software
• 133 kDa, 8 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	132,834	12
Polymers	132,245	8
Non-polymers	589	4
Water	144	8

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-x,-y,z	1
crystal symmetry operation	7_555	y,x,-z	1
crystal symmetry operation	8_555	-y,-x,-z	1

Calculated values:

Buried area	32800 Å2
ΔGint	-147.97 kcal/mol
Surface area	48950 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	100.980, 100.980, 99.311
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	94
Space group name H-M	P42212

Components

#1: Protein

A B PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN / FEAST OR FAMINE REGULATORY PROTEIN / LEUCINE-RESPONSIVE REGULATORY PROTEIN / RV3291C

Details:

Mass: 16530.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Variant: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96896

#2: Chemical

A-1151 ChemComp-LYS / LYSINE

Details:

Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₅N₂O₂

#3: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 3.8 ų/Da / Density % sol: 68.5 % / Description: NONE
• Crystal grow: pH: 6 / Details: pH 6.0

Data collection

• Diffraction: Mean temperature: 287 K
• Diffraction source: Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
• Detector: Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRROR
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1.5418 Å / Relative weight: 1
• Reflection: Resolution: 2.5→71.43 Å / Num. obs: 18364 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / R_merge(I) obs: 0.09 / Net I/σ(I): 5.29
• Reflection shell: Resolution: 2.5→2.64 Å / Redundancy: 5.6 % / R_merge(I) obs: 0.63 / Mean I/σ(I) obs: 2.7 / % possible all: 100

Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
MOSFLM		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IVM

2ivm

Resolution: 2.5→71.43 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.93 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.228	938	5.1 %	RANDOM
Rwork	0.191	-	-	-
obs	0.193	17382	99.8 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 45.65 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.52 Å2	0 Å2	0 Å2
2-	-	0.52 Å2	0 Å2
3-	-	-	-1.05 Å2

Refinement step

Cycle: LAST / Resolution: 2.5→71.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2239	0	9	45	2293

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.026	0.022	2276
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.54	1.976	3097
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.526	5	292
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.501	22.427	103
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	23.598	15	374
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.275	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.225	0.2	378
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.02	1718
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.248	0.2	842
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.322	0.2	1542
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.175	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	0.271	0.2	32
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.185	0.2	6
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	1.315	1.5	1472
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.499	2	2370
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	4.179	3	804
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	7.222	4.5	727
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

LS refinement shell

Resolution: 2.5→2.56 Å / Total num. of bins used: 20 /

	Rfactor	Num. reflection
Rfree	0.395	82
Rwork	0.296	1245