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- PDB-1s4k: Putative cytoplasmic protein from Salmonella typhimurium -

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Basic information

Entry
Database: PDB / ID: 1s4k
TitlePutative cytoplasmic protein from Salmonella typhimurium
Componentsputative cytoplasmic protein ydil
Keywordsstructural genomics / unknown function / MCSG / Salmonella typhimurium / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


Putative cytoplasmic protein / Putative cytoplasmic protein / Protein of unknown function DUF1870 / Domain of unknown function (DUF1870) / YdiL domain superfamily / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Putative cytoplasmic protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsCuff, M.E. / Li, H. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Putative cytoplasmic protein from Salmonella typhimurium
Authors: Cuff, M.E. / Li, H. / Collart, F. / Joachimiak, A.
History
DepositionJan 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative cytoplasmic protein ydil
B: putative cytoplasmic protein ydil


Theoretical massNumber of molelcules
Total (without water)28,7972
Polymers28,7972
Non-polymers00
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-5 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.596, 90.258, 78.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-121-

HOH

21B-290-

HOH

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Components

#1: Protein putative cytoplasmic protein ydil


Mass: 14398.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: ydiL / Plasmid: pMAGIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8ZPR1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: NaH2PO4, K2HPO4, acetate, sucrose, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97885 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 21, 2003 / Details: SBC2
RadiationMonochromator: sagitally focussed Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97885 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 22681 / Num. obs: 22681 / % possible obs: 86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.8 Å2 / Limit h max: 40 / Limit h min: 0 / Limit k max: 47 / Limit k min: 0 / Limit l max: 41 / Limit l min: 0 / Observed criterion F max: 1820160.98 / Observed criterion F min: 7.6
Reflection shellResolution: 1.85→1.92 Å / Mean I/σ(I) obs: 3.34 / Num. unique all: 1536 / Rsym value: 0.37 / % possible all: 59.2

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
d*TREKdata reduction
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→28.89 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1140 5 %RANDOM
Rwork0.191 ---
obs0.191 22681 93.1 %-
all-24366 --
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 57.2816 Å2 / ksol: 0.378132 e/Å3
Displacement parametersBiso max: 87.07 Å2 / Biso mean: 32.19 Å2 / Biso min: 16.06 Å2
Baniso -1Baniso -2Baniso -3
1--11.22 Å20 Å20 Å2
2--18.12 Å20 Å2
3----6.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.21 Å
Luzzati d res high-1.9
Refinement stepCycle: LAST / Resolution: 1.9→28.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1985 0 0 394 2379
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_torsion_deg19.2
X-RAY DIFFRACTIONx_torsion_impr_deg0.7
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.9-1.990.2731115.10.26720830.0263000219473.1
1.99-2.090.2421274.60.21726440.0213025277191.6
2.09-2.220.2411695.70.20327800.0193022294997.6
2.22-2.390.2311444.90.20228040.0193025294897.5
2.39-2.630.2511374.60.19528160.0213019295397.8
2.63-3.020.23514750.1928160.0193046296397.3
3.02-3.80.2011444.90.17128000.0173062294496.1
3.8-28.890.1971615.40.18527980.0163196295992.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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