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- PDB-4g8x: G1 ORF67 / Staphyloccus aureus sigmaA domain 4 complex -

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Basic information

Entry
Database: PDB / ID: 4g8x
TitleG1 ORF67 / Staphyloccus aureus sigmaA domain 4 complex
Components
  • ORF067
  • RNA polymerase sigma factor rpoD
KeywordsDNA BINDING PROTEIN / RNAP binding protein
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / DNA binding / cytoplasm
Similarity search - Function
Helix Hairpins - #1800 / : / : / Phage G1 gp67, N-terminal domain / Phage G1 gp67, C-terminal domain / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal ...Helix Hairpins - #1800 / : / : / Phage G1 gp67, N-terminal domain / Phage G1 gp67, C-terminal domain / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / Helix Hairpins / 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 / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA polymerase sigma factor SigA / ORF067
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
Staphylococcus phage G1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.001 Å
AuthorsDarst, S.A. / Osmundson, J.S. / Montero-Diaz, C.M. / Hochschild, A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Promoter-specific transcription inhibition in Staphylococcus aureus by a phage protein.
Authors: Osmundson, J. / Montero-Diez, C. / Westblade, L.F. / Hochschild, A. / Darst, S.A.
History
DepositionJul 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA polymerase sigma factor rpoD
B: ORF067
C: RNA polymerase sigma factor rpoD
D: ORF067


Theoretical massNumber of molelcules
Total (without water)61,6474
Polymers61,6474
Non-polymers00
Water00
1
A: RNA polymerase sigma factor rpoD
B: ORF067


Theoretical massNumber of molelcules
Total (without water)30,8232
Polymers30,8232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA polymerase sigma factor rpoD
D: ORF067


Theoretical massNumber of molelcules
Total (without water)30,8232
Polymers30,8232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)219.137, 56.951, 57.030
Angle α, β, γ (deg.)90.00, 104.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RNA polymerase sigma factor rpoD


Mass: 7409.352 Da / Num. of mol.: 2 / Fragment: UNP Residues 296-357
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: NCTC 8325 / Gene: plaC, rpoD, SAOUHSC_01662, sigA, Sigma A domain 4 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0J0
#2: Protein ORF067


Mass: 23413.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage G1 (virus) / Gene: ORF67 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4Z9Y5

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.16M Calcium acetate, 0.08 M Sodium Cacodylate pH 6.5, 15% PEG 8000, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1701
2701
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C11.0389
SYNCHROTRONNSLS X3A20.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 14, 2008
MAR CCD 165 mm2CCDJan 8, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.03891
20.9791
ReflectionResolution: 3→40 Å / Num. obs: 13818 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3→3.11 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.001→37.71 Å / SU ML: 0.5 / σ(F): 1.35 / Phase error: 36.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3277 1380 9.99 %
Rwork0.2806 --
obs0.2853 13812 99.8 %
all-13818 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.001→37.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 0 0 3325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033369
X-RAY DIFFRACTIONf_angle_d0.694554
X-RAY DIFFRACTIONf_dihedral_angle_d12.2691121
X-RAY DIFFRACTIONf_chiral_restr0.051513
X-RAY DIFFRACTIONf_plane_restr0.002614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.001-3.10820.41521330.34861203X-RAY DIFFRACTION99
3.1082-3.23260.32881420.32691229X-RAY DIFFRACTION100
3.2326-3.37960.41971380.31661231X-RAY DIFFRACTION100
3.3796-3.55770.41261450.30681250X-RAY DIFFRACTION100
3.5577-3.78040.33431250.29581231X-RAY DIFFRACTION100
3.7804-4.0720.29261350.25771250X-RAY DIFFRACTION100
4.072-4.48120.28291440.25961241X-RAY DIFFRACTION100
4.4812-5.12820.36371350.26761250X-RAY DIFFRACTION100
5.1282-6.45580.32711390.31421250X-RAY DIFFRACTION100
6.4558-37.71340.30081440.25931297X-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)
13.59053.80552.53746.40753.65163.43990.54530.5086-0.8677-0.5754-0.3747-0.29790.6924-0.16650.0121.18330.1242-0.18380.732-0.22821.194535.541320.3815-6.2264
23.7704-2.4223-0.85011.77520.24964.09380.2484-0.3204-0.10710.096-0.0839-0.56240.250.0959-0.19020.8202-0.1078-0.12280.31130.10330.831853.046114.50116.3607
31.2868-0.8623-1.45222.426-1.145.7774-0.6556-0.96290.8411.18910.6605-0.33010.9204-1.9214-0.20722.0671.0976-0.02512.7494-0.9387-0.019414.822739.13226.7481
46.63411.7337-0.44085.6185-0.33634.0662-1.1869-0.54892.04082.01311.35150.9783-0.7619-1.93090.61011.26671.1219-0.3152.5836-0.3871.26063.519949.304313.0204
53.8973-0.73862.45732.3986-1.79494.376-1.3902-1.82791.34950.70820.96430.5966-1.0259-1.64670.00451.02880.3722-0.00091.6989-0.33250.867321.889137.130514.2429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain 'A'
2X-RAY DIFFRACTION2chain 'B' and ((resseq 1:92))
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D' and ((resseq 1:92))
5X-RAY DIFFRACTION5chain 'D' and ((resseq 93:198))

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