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- PDB-4nqw: Structure of Mycobacterium tuberculosis extracytoplasmic function... -

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Basic information

Entry
Database: PDB / ID: 4nqw
TitleStructure of Mycobacterium tuberculosis extracytoplasmic function sigma factor SigK in complex with the cytosolic domain of its cognate anti-sigma factor RskA
Components
  • Anti-sigma-K factor RskA
  • ECF RNA polymerase sigma factor SigK
KeywordsDNA BINDING PROTEIN/PROTEIN BINDING / sigma factor / transcription initiation / DNA binding / Promoter DNA binding and transcription initiation / anti-sigma factor / DNA BINDING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


sigma factor antagonist activity / cell wall / sigma factor activity / membrane => GO:0016020 / peptidoglycan-based cell wall / DNA-templated transcription initiation / regulation of translation / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / plasma membrane
Similarity search - Function
Anti-sigma K factor RskA / : / Anti-sigma-K factor rskA, C-terminal / Anti-sigma-K factor RskA, N-terminal domain / : / Anti-sigma factor, zinc-finger domain / Anti-sigma factor, zinc-finger domain superfamily / RNA polymerase sigma-70 like / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A ...Anti-sigma K factor RskA / : / Anti-sigma-K factor rskA, C-terminal / Anti-sigma-K factor RskA, N-terminal domain / : / Anti-sigma factor, zinc-finger domain / Anti-sigma factor, zinc-finger domain superfamily / RNA polymerase sigma-70 like / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Anti-sigma-K factor RskA / ECF RNA polymerase sigma factor SigK / ECF RNA polymerase sigma factor SigK / Anti-sigma-K factor RskA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.4 Å
AuthorsShukla, J.K. / Gopal, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural basis for the redox sensitivity of the Mycobacterium tuberculosis SigK-RskA sigma-anti-sigma complex
Authors: Shukla, J. / Gupta, R. / Thakur, K.G. / Gokhale, R. / Gopal, B.
History
DepositionNov 25, 2013Deposition site: RCSB / Processing site: PDBJ
SupersessionJan 22, 2014ID: 3VDO
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ECF RNA polymerase sigma factor SigK
B: Anti-sigma-K factor RskA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,65112
Polymers31,5272
Non-polymers1,12410
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-85 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.390, 57.390, 150.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ECF RNA polymerase sigma factor SigK / ECF sigma factor SigK / Alternative RNA polymerase sigma factor SigK / RNA polymerase sigma-K ...ECF sigma factor SigK / Alternative RNA polymerase sigma factor SigK / RNA polymerase sigma-K factor / Sigma-K factor


Mass: 22971.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0445c, sigK / Plasmid: pETDUET-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: O53730, UniProt: P9WGH7*PLUS
#2: Protein Anti-sigma-K factor RskA / Regulator of SigK / Sigma-K anti-sigma factor RskA


Mass: 8555.508 Da / Num. of mol.: 1 / Fragment: UNP residues 1-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: rskA, Rv0444c / Plasmid: pETDUET-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: O53729, UniProt: P9WGX4*PLUS
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 37.57 %
Crystal growTemperature: 295 K / Method: microbatch underoil / pH: 7.5
Details: 0.1M HEPES, 1M sodium acetate trihydrate, 0.05M cadmium sulphate hydrate, 12%(v/v) 2,5 hexanediol, pH 7.5, Microbatch underoil, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 28, 2010
RadiationMonochromator: VariMaxHF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→28.695 Å / Num. all: 9753 / Num. obs: 9747 / Redundancy: 14.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 20.1
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 8.1 / Num. unique all: 1480 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→28.69 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.909 / SU B: 20.303 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25986 916 9.9 %RANDOM
Rwork0.20463 ---
obs0.21018 8305 87.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.018 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.4→28.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 10 89 1839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191765
X-RAY DIFFRACTIONr_bond_other_d0.0010.021700
X-RAY DIFFRACTIONr_angle_refined_deg0.8421.9562387
X-RAY DIFFRACTIONr_angle_other_deg0.7273.0013864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0525218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.25321.72487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.17215298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9571526
X-RAY DIFFRACTIONr_chiral_restr0.0460.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021992
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02424
X-RAY DIFFRACTIONr_rigid_bond_restr1.60233465
X-RAY DIFFRACTIONr_sphericity_free33.799536
X-RAY DIFFRACTIONr_sphericity_bonded12.08853504
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 71 -
Rwork0.218 637 -
obs--94.65 %
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)
10.43450.1811-0.33940.9101-1.07791.31660.04660.0443-0.00070.0680.01450.0494-0.0891-0.0292-0.06110.05070.0019-0.00820.0295-0.01390.014315.65056.456846.9331
20.17190.2205-0.18721.4819-1.10920.85250.0086-0.0370.0062-0.02660.05150.1057-0.0074-0.0344-0.06010.0431-0.0021-0.01580.0822-0.00660.02788.91892.480246.7229
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 185
2X-RAY DIFFRACTION2B7 - 79

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