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- PDB-7wh4: Crystal structure of the PadR-family transcriptional regulator Rv... -

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Basic information

Entry
Database: PDB / ID: 7wh4
TitleCrystal structure of the PadR-family transcriptional regulator Rv3488 of Mycobacterium tuberculosis H37Rv in complex with Manganese ion
ComponentsTranscriptional regulator Rv3488
KeywordsDNA BINDING PROTEIN / Transcriptional regulator
Function / homology: / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / DNA binding / metal ion binding / : / Transcriptional regulator Rv3488
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsArora, A. / Zohib, M. / Biswal, B.K. / Pal, R.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India) India
CitationJournal: To Be Published
Title: Crystal structure of PadR-family transcriptional regulator Rv3488 of Mycobacterium tuberculosis H37Rv in complex with Manganese ion
Authors: Arora, A. / Zohib, M. / Biswal, B.K. / Pal, R.K.
History
DepositionDec 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 2.0Mar 23, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_src_gen / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / software / struct_conf / struct_conn / struct_ncs_dom_lim / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _entity.pdbx_number_of_molecules / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_prop.value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R_Free / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr_ncs.pdbx_number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.classification / _software.name / _software.version / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_ncs_dom_lim.pdbx_component_id / _struct_ncs_dom_lim.pdbx_refine_code / _struct_sheet.number_strands
Description: Model completeness
Details: one water molecule is filled in the positive density around ligand
Provider: author / Type: Coordinate replacement
Revision 2.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator Rv3488
B: Transcriptional regulator Rv3488
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3924
Polymers25,2822
Non-polymers1102
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size exclusion chromatography purification was done using Superdex 75 10/300 GL column (GE Healthcare)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-35 kcal/mol
Surface area10360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.491, 47.899, 129.878
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: -4 - 96 / Label seq-ID: 2 - 102

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Transcriptional regulator Rv3488


Mass: 12641.155 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv3488 / Plasmid: pET-NH6 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: I6X7F9
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1M Sodium Acetate pH 4.6, 2M Sodium Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.8→26.89 Å / Num. obs: 5103 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.996 / Net I/σ(I): 9.7
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 717 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZHC

5zhc


Resolution: 2.8→26.89 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.908 / SU B: 38.229 / SU ML: 0.353 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.471 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.272 587 11.6 %RANDOM
Rwork0.2207 ---
obs0.2271 4484 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.27 Å2 / Biso mean: 49.609 Å2 / Biso min: 24.47 Å2
Baniso -1Baniso -2Baniso -3
1--3.52 Å20 Å2-0 Å2
2--9.92 Å2-0 Å2
3----6.41 Å2
Refinement stepCycle: final / Resolution: 2.8→26.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 2 15 1569
Biso mean--69.2 41.34 -
Num. residues----202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0121591
X-RAY DIFFRACTIONr_angle_refined_deg1.0191.6422159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5985202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.1919.23191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.36215239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7961519
X-RAY DIFFRACTIONr_chiral_restr0.0890.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021214
Refine LS restraints NCS

Ens-ID: 1 / Number: 2796 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.801→2.874 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 37 -
Rwork0.319 325 -
all-362 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.1221-0.0629-0.11150.37250.22651.75440.0294-0.0220.0267-0.0112-0.0212-0.0207-0.00990.0077-0.00820.0782-0.0233-0.01370.03970.01690.0873-6.9187118.0157111.1192
20.2487-0.10690.21210.1926-0.16472.48080.0335-0.04760.0858-0.00970.04720.04330.0988-0.0304-0.08070.0925-0.0113-0.00260.0144-0.00380.0968-7.562118.7909138.7546
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 96
2X-RAY DIFFRACTION2B-4 - 96

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