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- PDB-5zhc: Crystal structure of the PadR-family transcriptional regulator Rv... -

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Basic information

Entry
Database: PDB / ID: 5zhc
TitleCrystal structure of the PadR-family transcriptional regulator Rv3488 of Mycobacterium tuberculosis H37Rv
ComponentsTranscriptional regulatorTranscriptional regulation
KeywordsDNA BINDING PROTEIN
Function / homologyTranscription 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 / ACETATE ION / Transcriptional regulator Rv3488
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsMeera, K. / Pal, R.K. / Arora, A. / Biswal, B.K.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific and Industrial Research (CSIR) Network ProjectsBSC0113 India
CitationJournal: Biochem. J. / Year: 2018
Title: Structural and functional characterization of the transcriptional regulator Rv3488 ofMycobacterium tuberculosisH37Rv.
Authors: Kumari, M. / Pal, R.K. / Mishra, A.K. / Tripathi, S. / Biswal, B.K. / Srivastava, K.K. / Arora, A.
History
DepositionMar 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,4125
Polymers25,2822
Non-polymers1303
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-46 kcal/mol
Surface area10390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.633, 49.099, 127.325
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: -5 - 96 / Label seq-ID: 1 - 102

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

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Components

#1: Protein Transcriptional regulator / Transcriptional regulation


Mass: 12641.155 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv3488 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: I6X7F9
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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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: 2.01 Å3/Da / Density % sol: 35.05 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M sodium acetate, 2.0 M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.97→63.66 Å / Num. obs: 14217 / % possible obs: 99.8 % / Redundancy: 10.9 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.023 / Rrim(I) all: 0.079 / Χ2: 1.18 / Net I/σ(I): 34.06
Reflection shellResolution: 1.97→2.01 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.06 / CC1/2: 0.89 / Rpim(I) all: 0.25 / Rrim(I) all: 0.7 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EJO

4ejo


Resolution: 1.97→63.66 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.925 / SU B: 9.691 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.171 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23773 703 5 %RANDOM
Rwork0.18509 ---
obs0.18766 13466 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.427 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--1.38 Å20 Å2
3----1.19 Å2
Refinement stepCycle: 1 / Resolution: 1.97→63.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 6 75 1695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191677
X-RAY DIFFRACTIONr_bond_other_d0.0020.021581
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.9582280
X-RAY DIFFRACTIONr_angle_other_deg1.00133619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2015212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.5721.42984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7915278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1221525
X-RAY DIFFRACTIONr_chiral_restr0.1050.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211901
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02375
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9221.743825
X-RAY DIFFRACTIONr_mcbond_other0.9171.736823
X-RAY DIFFRACTIONr_mcangle_it1.4782.5951029
X-RAY DIFFRACTIONr_mcangle_other1.4782.5981030
X-RAY DIFFRACTIONr_scbond_it1.2371.99852
X-RAY DIFFRACTIONr_scbond_other1.2361.994853
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0762.9141247
X-RAY DIFFRACTIONr_long_range_B_refined4.67320.9331848
X-RAY DIFFRACTIONr_long_range_B_other4.67320.9621849
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6020 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.971→2.022 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 45 -
Rwork0.272 920 -
obs--94.33 %
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)
113.27450.87714.51391.5099-2.19065.80330.0171-0.0946-0.0419-0.2360.03750.02660.4208-0.1284-0.05460.1535-0.0439-0.01590.1455-0.05490.1872-17.2844119.3748127.9668
26.57011.08324.92658.28341.315511.0271-0.04920.0466-0.1857-0.2839-0.0648-0.23170.5264-0.10250.1140.1301-0.00960.01890.1542-0.00430.1019-11.1088120.0514134.4182
33.72980.71090.80030.8870.439610.1181-0.12750.05340.3405-0.00660.0578-0.0802-0.09710.16170.06970.10280.0359-0.02570.1217-0.01950.1397-6.3801123.9742148.5355
49.1215-0.32247.02492.4843-5.092614.9176-0.2684-0.36120.3980.0560.1190.0718-0.2612-0.56640.14940.1166-0.004-0.00420.2177-0.08840.2002-15.1699121.9559150.5185
52.70710.5304-5.55441.5724-5.696726.20930.20620.17050.2004-0.042-0.1142-0.0858-0.1993-0.1822-0.0920.05210.0719-0.03990.30170.01120.2525-17.9992122.4844142.6878
64.80941.872-0.32151.9427-1.23141.46550.0213-0.05180.0329-0.0376-0.05030.03590.2948-0.04910.0290.190.02030.01320.1247-0.02150.1212-5.5828113.1636146.6724
73.95220.4445-9.28446.6928-2.611922.3582-0.1666-0.38160.08330.23710.29510.23530.51670.8652-0.12850.2981-0.00150.04310.29030.0170.105-1.7361115.4483159.8346
80.85730.3675-2.25020.57730.630612.2197-0.00830.05130.11680.0931-0.05830.16290.5828-0.34370.06660.17460.0216-0.02910.1471-0.01760.1664-7.0004116.3793161.8707
92.9773-2.39423.65023.672-5.781313.1064-0.1591-0.19060.2811-0.1294-0.0888-0.23360.03660.16030.24790.07780.002-0.02490.1434-0.01780.16933.1971124.9271144.1671
103.8048-0.79283.38574.5874-3.603911.0239-0.0746-0.09390.16150.048-0.06690.006-0.18580.18820.14150.0942-0.0042-0.01840.0944-0.00720.193-3.7296131.4212129.9006
119.6851-3.03715.08691.0552-0.530313.8011-0.3218-0.12490.19380.19520.0805-0.04940.80240.18640.24130.25790.0559-0.01850.0781-0.02960.1489-0.4416118.6245135.1668
121.6142-0.07870.9190.26850.81424.9975-0.0948-0.01920.0837-0.00690.0974-0.03640.0263-0.0264-0.00260.1212-0.0339-0.00110.102-0.00140.1605-8.543123.8131117.6379
137.79282.91637.53561.50180.844216.8741-0.06570.19150.152-0.06410.09610.08610.05330.2063-0.03040.0945-0.02990.02590.1579-0.01620.2182-0.7199123.586114.6285
1410.5532-7.62635.21397.1274-0.336813.13760.4401-0.01240.2111-0.3750.1174-0.0325-0.30540.7332-0.55750.1404-0.06220.0960.1832-0.06190.31661.8503124.8383121.0626
1510.30040.92173.0151.2152.82046.6290.01710.16260.01010.00760.1885-0.08870.03490.4282-0.20560.2207-0.01550.01360.2139-0.00410.2313-3.1743113.8171116.9415
162.8649-0.9798-0.92924.84381.08231.094-0.11590.02520.01770.19720.1946-0.04230.27060.0357-0.07870.1402-0.0235-0.00790.1134-0.01240.142-15.477115.7582115.5951
172.26961.0293-2.6980.5872-2.314613.12870.0147-0.1877-0.0606-0.0397-0.0919-0.03250.37160.17570.07720.14820.03920.04140.17510.05580.1464-8.736117.908298.2427
183.5127-4.2112-5.49026.4916.35078.63620.06440.22560.1482-0.20750.096-0.2938-0.0503-0.3849-0.16040.11090.00560.00920.20280.01560.1574-12.0903119.2117107.2728
195.76392.05012.22194.2855.99358.47210.00210.0080.3886-0.0521-0.07890.0751-0.0667-0.14120.07680.09980.0077-0.01250.1179-0.01180.2065-18.6745127.6716122.5358
2012.18450.57476.08564.94092.24939.1803-0.1757-1.17860.98090.26120.09610.0230.0516-0.71640.07960.09280.0677-0.010.2269-0.13010.2563-11.1279132.028135.9775
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 2
2X-RAY DIFFRACTION2A3 - 8
3X-RAY DIFFRACTION3A9 - 23
4X-RAY DIFFRACTION4A24 - 32
5X-RAY DIFFRACTION5A33 - 38
6X-RAY DIFFRACTION6A39 - 56
7X-RAY DIFFRACTION7A57 - 61
8X-RAY DIFFRACTION8A62 - 72
9X-RAY DIFFRACTION9A73 - 84
10X-RAY DIFFRACTION10A85 - 96
11X-RAY DIFFRACTION11B-5 - 4
12X-RAY DIFFRACTION12B5 - 25
13X-RAY DIFFRACTION13B26 - 32
14X-RAY DIFFRACTION14B33 - 37
15X-RAY DIFFRACTION15B38 - 46
16X-RAY DIFFRACTION16B47 - 58
17X-RAY DIFFRACTION17B59 - 66
18X-RAY DIFFRACTION18B67 - 74
19X-RAY DIFFRACTION19B75 - 86
20X-RAY DIFFRACTION20B87 - 96

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