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- PDB-3hug: Crystal structure of Mycobacterium tuberculosis anti-sigma factor... -

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Basic information

Entry
Database: PDB / ID: 3hug
TitleCrystal structure of Mycobacterium tuberculosis anti-sigma factor RslA in complex with -35 promoter binding domain of sigL
Components
  • PROBABLE CONSERVED MEMBRANE PROTEIN
  • RNA polymerase sigma factor
KeywordsTranscription/MEMBRANE PROTEIN / ECF sigma factor / Zinc binding anti-sigma factor / oxidative stress / transcription regulation / DNA binding / metal binding / HXXXCXXC motif / DNA-binding / Sigma factor / Transcription / Transcription-MEMBRANE PROTEIN COMPLEX
Function / homology
Function and homology information


sigma factor antagonist activity / sigma factor activity / : / DNA-templated transcription initiation / membrane => GO:0016020 / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / zinc ion binding / metal ion binding / plasma membrane
Similarity search - Function
Anti-sigma factor, zinc-finger domain / Putative zinc-finger / Putative zinc-finger / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain ...Anti-sigma factor, zinc-finger domain / Putative zinc-finger / Putative zinc-finger / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / 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
ECF RNA polymerase sigma factor SigL / Anti-sigma-L factor RslA / Anti-sigma-L factor RslA / ECF RNA polymerase sigma factor SigL
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsThakur, K.G. / Gopal, B.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural and biochemical bases for the redox sensitivity of Mycobacterium tuberculosis RslA
Authors: Thakur, K.G. / Praveena, T. / Gopal, B.
History
DepositionJun 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 28, 2011Group: Database references / Refinement description
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_seq_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: RNA polymerase sigma factor
B: PROBABLE CONSERVED MEMBRANE PROTEIN
C: RNA polymerase sigma factor
D: PROBABLE CONSERVED MEMBRANE PROTEIN
E: RNA polymerase sigma factor
F: PROBABLE CONSERVED MEMBRANE PROTEIN
G: RNA polymerase sigma factor
H: PROBABLE CONSERVED MEMBRANE PROTEIN
I: RNA polymerase sigma factor
J: PROBABLE CONSERVED MEMBRANE PROTEIN
K: RNA polymerase sigma factor
L: PROBABLE CONSERVED MEMBRANE PROTEIN
M: RNA polymerase sigma factor
N: PROBABLE CONSERVED MEMBRANE PROTEIN
O: RNA polymerase sigma factor
P: PROBABLE CONSERVED MEMBRANE PROTEIN
Q: RNA polymerase sigma factor
R: PROBABLE CONSERVED MEMBRANE PROTEIN
S: RNA polymerase sigma factor
T: PROBABLE CONSERVED MEMBRANE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,45640
Polymers215,84220
Non-polymers1,61520
Water4,846269
1
A: RNA polymerase sigma factor
B: PROBABLE CONSERVED MEMBRANE PROTEIN
C: RNA polymerase sigma factor
D: PROBABLE CONSERVED MEMBRANE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4918
Polymers43,1684
Non-polymers3234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-83 kcal/mol
Surface area12670 Å2
MethodPISA
2
E: RNA polymerase sigma factor
F: PROBABLE CONSERVED MEMBRANE PROTEIN
G: RNA polymerase sigma factor
H: PROBABLE CONSERVED MEMBRANE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3957
Polymers43,1684
Non-polymers2273
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-64 kcal/mol
Surface area11950 Å2
MethodPISA
3
I: RNA polymerase sigma factor
J: PROBABLE CONSERVED MEMBRANE PROTEIN
K: RNA polymerase sigma factor
L: PROBABLE CONSERVED MEMBRANE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5879
Polymers43,1684
Non-polymers4195
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-79 kcal/mol
Surface area12620 Å2
MethodPISA
4
M: RNA polymerase sigma factor
N: PROBABLE CONSERVED MEMBRANE PROTEIN
O: RNA polymerase sigma factor
P: PROBABLE CONSERVED MEMBRANE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4918
Polymers43,1684
Non-polymers3234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-78 kcal/mol
Surface area12040 Å2
MethodPISA
5
Q: RNA polymerase sigma factor
R: PROBABLE CONSERVED MEMBRANE PROTEIN
S: RNA polymerase sigma factor
T: PROBABLE CONSERVED MEMBRANE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4918
Polymers43,1684
Non-polymers3234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-94 kcal/mol
Surface area12520 Å2
MethodPISA
6


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.070, 166.770, 178.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
RNA polymerase sigma factor


Mass: 10249.418 Da / Num. of mol.: 10
Fragment: -35 promoter binding region of SigL, UNP residues 99-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: sigL / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q7D9D4, UniProt: P9WGH5*PLUS
#2: Protein
PROBABLE CONSERVED MEMBRANE PROTEIN / Putative uncharacterized protein


Mass: 11334.758 Da / Num. of mol.: 10
Fragment: SigL interacting Zinc binding cystosolic domain of RslA, UNP residues 1-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: RslA (Rv0736) / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q7D9D3, UniProt: P9WJ67*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.0-1.2M Ammonium Sulphate, 0.1M Bis Tris Propane, 0.5-5% peg 8000 , pH 7.0-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9762 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.35→44.72 Å / Num. obs: 103640 / % possible obs: 99.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 12.4
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3 / Num. unique all: 60924

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Processing

Software
NameVersionClassification
PHENIXmodel building
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→41.88 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 14.094 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 1.078 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26014 5174 5 %RANDOM
Rwork0.21089 ---
obs0.21332 98462 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.425 Å2
Baniso -1Baniso -2Baniso -3
1-2.9 Å2-0 Å20 Å2
2---2.03 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.35→41.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10423 0 60 269 10752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02110543
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.95514323
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.90951349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33822.084475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.036151646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.88115123
X-RAY DIFFRACTIONr_chiral_restr0.0980.21662
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027961
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8241.56747
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.508210626
X-RAY DIFFRACTIONr_scbond_it2.00533796
X-RAY DIFFRACTIONr_scangle_it3.2694.53694
X-RAY DIFFRACTIONr_rigid_bond_restr1.286310543
X-RAY DIFFRACTIONr_sphericity_free5.1423288
X-RAY DIFFRACTIONr_sphericity_bonded2.151310392
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 394 -
Rwork0.273 7192 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: -10.729 Å / Origin y: 152.037 Å / Origin z: 28.625 Å
111213212223313233
T0.0057 Å2-0.0004 Å20.0013 Å2-0.0022 Å2-0.0016 Å2--0.0033 Å2
L0.0182 °2-0.0116 °2-0.0051 °2-0.2006 °20.1037 °2--0.2935 °2
S0.0054 Å °-0.0014 Å °-0.0024 Å °0.0065 Å °0.0196 Å °-0.0101 Å °-0.0252 Å °0.0178 Å °-0.0251 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A98 - 177
2X-RAY DIFFRACTION1B25 - 86
3X-RAY DIFFRACTION1C101 - 177
4X-RAY DIFFRACTION1D24 - 85
5X-RAY DIFFRACTION1E105 - 177
6X-RAY DIFFRACTION1F24 - 79
7X-RAY DIFFRACTION1G104 - 177
8X-RAY DIFFRACTION1H24 - 84
9X-RAY DIFFRACTION1I104 - 177
10X-RAY DIFFRACTION1J24 - 87
11X-RAY DIFFRACTION1K107 - 177
12X-RAY DIFFRACTION1L24 - 86
13X-RAY DIFFRACTION1M104 - 177
14X-RAY DIFFRACTION1N24 - 84
15X-RAY DIFFRACTION1O105 - 177
16X-RAY DIFFRACTION1P24 - 83
17X-RAY DIFFRACTION1Q101 - 177
18X-RAY DIFFRACTION1R24 - 86
19X-RAY DIFFRACTION1S105 - 177
20X-RAY DIFFRACTION1T24 - 85

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