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- PDB-6gho: Crystal structure of Spx in complex with YjbH -

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Basic information

Entry
Database: PDB / ID: 6gho
TitleCrystal structure of Spx in complex with YjbH
Components
  • Regulatory protein Spx
  • UPF0413 protein GK0824
KeywordsPROTEIN BINDING / Regulatory protein spx Adaptor protein YjbH
Function / homology
Function and homology information


negative regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
ClpXP adapter protein SpxH / Thioredoxin / Global transcriptional regulator Spx / Transcriptional regulator Spx/MgsR / Arsenate reductase-like / ArsC family / ArsC family profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...ClpXP adapter protein SpxH / Thioredoxin / Global transcriptional regulator Spx / Transcriptional regulator Spx/MgsR / Arsenate reductase-like / ArsC family / ArsC family profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Global transcriptional regulator Spx / ClpXP adapter protein SpxH
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
Geobacillus kaustophilus HTA426 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 Å
AuthorsAwad, W. / Logan, D.T. / von Wachenfeldt, C.
CitationJournal: Structure / Year: 2019
Title: Structural Basis for YjbH Adaptor-Mediated Recognition of Transcription Factor Spx.
Authors: Awad, W. / Al-Eryani, Y. / Ekstrom, S. / Logan, D.T. / von Wachenfeldt, C.
History
DepositionMay 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein Spx
B: UPF0413 protein GK0824
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3913
Polymers49,3562
Non-polymers351
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-13 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.100, 85.340, 109.530
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 Regulatory protein Spx


Mass: 15638.970 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: spxA, yjbD, BSU11500 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: O31602
#2: Protein UPF0413 protein GK0824


Mass: 33716.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus HTA426 (bacteria)
Gene: GK0824 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q5L1S1
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 3350, MgCl2 and Bis-Tris pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→42.7 Å / Num. obs: 46753 / % possible obs: 99.9 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.047 / Net I/σ(I): 20.43
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.91 / Num. unique obs: 4619 / CC1/2: 0.719 / Rrim(I) all: 0.943 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Cootmodel building
XDSdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.79→42.67 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.05
RfactorNum. reflection% reflection
Rfree0.2214 2000 4.28 %
Rwork0.1866 --
obs0.1881 46747 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.79→42.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 1 248 3445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053307
X-RAY DIFFRACTIONf_angle_d0.7764490
X-RAY DIFFRACTIONf_dihedral_angle_d19.82044
X-RAY DIFFRACTIONf_chiral_restr0.047499
X-RAY DIFFRACTIONf_plane_restr0.004580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.83480.26351390.26423123X-RAY DIFFRACTION100
1.8348-1.88440.25581420.25313157X-RAY DIFFRACTION100
1.8844-1.93990.28781400.23143158X-RAY DIFFRACTION100
1.9399-2.00250.24951420.21873165X-RAY DIFFRACTION100
2.0025-2.0740.27121420.20463167X-RAY DIFFRACTION100
2.074-2.15710.21971400.19773142X-RAY DIFFRACTION100
2.1571-2.25520.25241420.1923181X-RAY DIFFRACTION100
2.2552-2.37410.22541430.19393193X-RAY DIFFRACTION100
2.3741-2.52290.23771410.18843165X-RAY DIFFRACTION100
2.5229-2.71760.22761430.19863189X-RAY DIFFRACTION100
2.7176-2.99110.26791430.1953206X-RAY DIFFRACTION100
2.9911-3.42370.22731450.19273235X-RAY DIFFRACTION100
3.4237-4.31290.18031450.16383257X-RAY DIFFRACTION100
4.3129-42.68210.20671530.17413409X-RAY DIFFRACTION100
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)
10.12630.605-0.4783.1348-3.83684.7275-0.2112-0.57580.28391.0733-0.0401-0.5942-0.52690.28610.21780.42960.0101-0.01350.3745-0.14590.297131.240944.790989.0182
21.8455-0.75450.17073.5096-0.79021.5244-0.0884-0.34480.30590.04180.1620.4368-0.3696-0.2039-0.06740.23580.02180.03110.2859-0.0650.275720.86343.614577.0538
31.82270.39180.48142.77670.05242.0643-0.0723-0.1586-0.0547-0.05110.0221-0.37280.08870.24820.04740.17830.02450.03540.24580.04890.236237.849723.219279.4069
41.72660.93831.51751.70720.80712.1698-0.1437-0.04140.4929-0.4846-0.03870.2449-0.60080.11870.09470.5067-0.0494-0.01390.3222-0.0410.349118.197541.932656.7209
50.0409-0.1023-0.4914-0.0597-0.01252.71650.5660.47770.094-0.95280.3812-1.4242-0.08130.5106-0.40820.7668-0.04010.23320.89080.1651.056936.319653.440657.8262
62.08990.66190.62893.60340.40691.51170.01010.12160.26-0.1854-0.0721-0.2178-0.3466-0.1052-0.06610.5097-0.0503-0.03580.2477-0.00620.310223.769747.561760.5358
70.9496-0.45760.31071.6881-0.38482.34490.0806-0.0544-0.5049-0.2032-0.0315-0.34230.2559-0.15250.13170.2877-0.0633-0.07190.23920.04160.346917.727522.858262.6369
82.6697-0.8027-0.21793.29620.56021.33890.038-0.16580.1742-0.23540.0482-0.1493-0.03580.0155-0.09280.1651-0.01360.04240.19340.020.212929.400825.574574.7094
9-0.1383-0.044-0.0276-0.08560.0124-0.00580.2454-1.11570.08790.53640.10250.5958-0.2052-0.8862-0.07350.87520.21830.23421.1127-0.19260.906916.053132.614394.2757
101.6265-0.37281.2043.6577-0.83722.7811-0.0754-0.46650.05320.50690.04680.1386-0.25-0.25420.05040.27090.0030.04340.3462-0.06740.217828.407434.525289.4228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 142 through 157 )
2X-RAY DIFFRACTION2chain 'B' and (resid 158 through 187 )
3X-RAY DIFFRACTION3chain 'B' and (resid 188 through 294 )
4X-RAY DIFFRACTION4chain 'A' and (resid 0 through 61 )
5X-RAY DIFFRACTION5chain 'A' and (resid 62 through 75 )
6X-RAY DIFFRACTION6chain 'A' and (resid 76 through 100 )
7X-RAY DIFFRACTION7chain 'A' and (resid 101 through 125 )
8X-RAY DIFFRACTION8chain 'B' and (resid 21 through 63 )
9X-RAY DIFFRACTION9chain 'B' and (resid 64 through 77 )
10X-RAY DIFFRACTION10chain 'B' and (resid 78 through 141 )

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