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- PDB-1wv3: Crystal structure of N-terminal domain of hypothetical protein SA... -

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Basic information

Entry
Database: PDB / ID: 1wv3
TitleCrystal structure of N-terminal domain of hypothetical protein SAV0287 from Staphylococcus aureus
Componentssimilar to DNA segregation ATPase and related proteins
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ATPase
Function / homology
Function and homology information


: / membrane => GO:0016020 / DNA binding / ATP binding / plasma membrane
Similarity search - Function
Firmicutes EssC, N-terminal / Firmicutes EssC, C-terminal / DNA transporter / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / Sandwich ...Firmicutes EssC, N-terminal / Firmicutes EssC, C-terminal / DNA transporter / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Type VII secretion system protein EssC
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsTanaka, Y. / Yasutake, Y. / Tanaka, I.
CitationJournal: Proteins / Year: 2007
Title: Crystal structure analysis reveals a novel forkhead-associated domain of ESAT-6 secretion system C protein in Staphylococcus aureus.
Authors: Tanaka, Y. / Kuroda, M. / Yasutake, Y. / Yao, M. / Tsumoto, K. / Watanabe, N. / Ohta, T. / Tanaka, I.
History
DepositionDec 10, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: similar to DNA segregation ATPase and related proteins
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9962
Polymers27,9601
Non-polymers351
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.368, 66.010, 88.287
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 similar to DNA segregation ATPase and related proteins / hypothetical protein SAV0287


Mass: 27960.383 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Species: Staphylococcus aureus / Strain: Mu50 / ATCC 700699 / Gene: SAV0287 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q8NYF3
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Bis-Tris, PEG3350, Magnesium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97938 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2004
RadiationProtocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. all: 27431 / Num. obs: 27431 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 26.147 Å2 / Rsym value: 0.083 / Net I/σ(I): 11.4
Reflection shellResolution: 1.75→1.81 Å / Num. unique all: 2697 / Rsym value: 0.313 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.75→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 1377 -RANDOM
Rwork0.1948 ---
all-27431 --
obs-27431 100 %-
Displacement parametersBiso mean: 22.1368 Å2
Baniso -1Baniso -2Baniso -3
1--3.82 Å20 Å20 Å2
2--1.566 Å20 Å2
3---2.254 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1501 0 1 196 1698
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006517
X-RAY DIFFRACTIONc_angle_deg1.43567
X-RAY DIFFRACTIONc_dihedral_angle_d27.03935
X-RAY DIFFRACTIONc_improper_angle_d0.78974
LS refinement shellResolution: 1.75→1.81 Å
RfactorNum. reflection% reflection
Rfree0.2484 133 -
Rwork0.2174 --
obs-2695 100 %

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