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- PDB-1z3e: Crystal Structure of Spx in Complex with the C-terminal Domain of... -

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Basic information

Entry
Database: PDB / ID: 1z3e
TitleCrystal Structure of Spx in Complex with the C-terminal Domain of the RNA Polymerase Alpha Subunit
Components
  • DNA-directed RNA polymerase alpha chain
  • Regulatory protein spx
KeywordsTRANSCRIPTION / bacterial transcription regulation / disulfide stress
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / negative regulation of DNA-templated transcription / DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
Global transcriptional regulator Spx / Transcriptional regulator Spx/MgsR / Arsenate reductase-like / ArsC family / ArsC family profile. / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / 5' to 3' exonuclease, C-terminal subdomain / DNA-directed RNA polymerase, insert domain ...Global transcriptional regulator Spx / Transcriptional regulator Spx/MgsR / Arsenate reductase-like / ArsC family / ArsC family profile. / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / 5' to 3' exonuclease, C-terminal subdomain / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / Glutaredoxin / Glutaredoxin / DNA polymerase; domain 1 / Thioredoxin-like superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Global transcriptional regulator Spx / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsNewberry, K.J. / Nakano, S. / Zuber, P. / Brennan, R.G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Crystal structure of the Bacillus subtilis anti-alpha, global transcriptional regulator, Spx, in complex with the {alpha} C-terminal domain of RNA polymerase
Authors: Newberry, K.J. / Nakano, S. / Zuber, P. / Brennan, R.G.
History
DepositionMar 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein spx
B: DNA-directed RNA polymerase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4566
Polymers24,0722
Non-polymers3844
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.440, 96.440, 57.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Regulatory protein spx


Mass: 15690.040 Da / Num. of mol.: 1 / Fragment: transcription regulator
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: spxA / Plasmid: pSN17 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O31602
#2: Protein DNA-directed RNA polymerase alpha chain / RNAP alpha subunit / Transcriptase alpha chain / RNA polymerase alpha subunit


Mass: 8381.699 Da / Num. of mol.: 1 / Fragment: c-terminal domain of RNA polymerase alpha subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: rpoA / Plasmid: pSN106 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P20429, DNA-directed RNA polymerase
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.5 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 273 K / Method: vapor diffusion / pH: 5.6
Details: lithium sulfate, ammonium sulfate, sodium citrate, pH 5.6, VAPOR DIFFUSION, temperature 273K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.111.00003
SYNCHROTRONALS 8.2.120.9794, 0.9796, 0.9952
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 20, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal SiSINGLE WAVELENGTHMx-ray1
2double crystal SiMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.000031
20.97941
30.97961
40.99521
ReflectionResolution: 1.5→33.71 Å / Num. all: 31461 / Num. obs: 31461 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 12.5
Reflection shellResolution: 1.5→1.58 Å / % possible obs: 98.5 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.5 / Num. measured obs: 4550 / Rsym value: 0.311 / % possible all: 98.5

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
CNSrefinement
PDB_EXTRACT1.6data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3108 9.8 %random
Rwork0.196 ---
all0.196 31689 --
obs0.196 31435 99.2 %-
Solvent computationBsol: 52.035 Å2
Displacement parametersBiso mean: 17.484 Å2
Baniso -1Baniso -2Baniso -3
1--1.132 Å2-1.107 Å20 Å2
2---1.132 Å20 Å2
3---2.265 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1509 0 20 143 1672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetWeight
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.2720
X-RAY DIFFRACTIONc_mcbond_it2.12901.5
X-RAY DIFFRACTIONc_scbond_it4.29402
X-RAY DIFFRACTIONc_mcangle_it2.7502
X-RAY DIFFRACTIONc_scangle_it5.7902.5
LS refinement shellResolution: 1.5→1.55 Å
RfactorNum. reflection% reflection
Rfree0.2719 295 -
Rwork0.2547 --
obs-2820 99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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