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- PDB-4g6d: G1 ORF67 / Staphyloccus aureus sigmaA domain 4 complex -

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Basic information

Entry
Database: PDB / ID: 4g6d
TitleG1 ORF67 / Staphyloccus aureus sigmaA domain 4 complex
Components
  • ORF067
  • RNA polymerase sigma factor rpoD
KeywordsDNA BINDING PROTEIN / Staphylococcus aureus RNA polymerase
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 / 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 Hairpins / 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: 1.9971 Å
AuthorsDarst, S.A. / Osmundson, J.S.
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 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)31,9572
Polymers31,9572
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-2 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.381, 64.724, 108.721
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 rpoD


Mass: 8731.062 Da / Num. of mol.: 1 / Fragment: UNP Residues 296-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: NCTC 8325 / Gene: rpoD, plaC, sigA, SAOUHSC_01662 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0J0
#2: Protein ORF067


Mass: 23226.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage G1 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q4Z9Y5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES pH 6.5, 10% (w/v) PEG5000MME, 12% (v/v) Isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1701
2701
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.97949
SYNCHROTRONAPS 24-ID-C20.97918
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDOct 19, 2009
ADSC QUANTUM 3152CCD
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979491
20.979181
ReflectionResolution: 1.997→30 Å / Num. all: 19002 / Num. obs: 18679 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.997→2.12 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.879 / Mean I/σ(I) obs: 2.75 / % possible all: 98.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9971→26.35 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 30.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2426 935 5.01 %
Rwork0.2046 --
obs0.2065 18678 97.95 %
all-19002 -
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9971→26.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 0 54 2130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112130
X-RAY DIFFRACTIONf_angle_d1.4312881
X-RAY DIFFRACTIONf_dihedral_angle_d14.906812
X-RAY DIFFRACTIONf_chiral_restr0.106329
X-RAY DIFFRACTIONf_plane_restr0.007373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9971-2.10230.38461300.33222481X-RAY DIFFRACTION98
2.1023-2.2340.30761330.27462524X-RAY DIFFRACTION99
2.234-2.40630.25861350.23852551X-RAY DIFFRACTION99
2.4063-2.64830.29961330.22412531X-RAY DIFFRACTION100
2.6483-3.0310.24261360.21122572X-RAY DIFFRACTION100
3.031-3.81690.24311370.19282609X-RAY DIFFRACTION100
3.8169-26.35240.20511310.18042475X-RAY DIFFRACTION90
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)
12.8767-0.0810.53925.44230.61093.29630.10040.0011-0.4375-0.09590.2118-0.90050.70160.1125-0.29070.42040.0136-0.07240.3242-0.00990.54438.1898-11.141614.7924
22.9488-1.4534-0.5177.3491.38445.879-0.1021-0.40620.54741.23230.030.4663-0.2377-0.39290.02240.4814-0.03470.03180.4426-0.13650.471927.30516.749527.1013
30.9814-0.6070.02032.1533-2.24654.442-0.03960.4738-0.0594-0.7918-0.07070.35170.0909-0.36950.02030.4998-0.0314-0.09290.5013-0.04150.416927.1447-1.40466.9925
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and resseq 92:198
2X-RAY DIFFRACTION2chain 'B' and resseq 1:91
3X-RAY DIFFRACTION3chain 'A' and resseq 538:599

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