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- PDB-1s9u: Atomic structure of a putative anaerobic dehydrogenase component -

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Basic information

Entry
Database: PDB / ID: 1s9u
TitleAtomic structure of a putative anaerobic dehydrogenase component
Componentsputative component of anaerobic dehydrogenases
KeywordsStructural Genomics / unknown function / anaerobic dehydrogenases component / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


signal sequence binding / chaperone-mediated protein folding
Similarity search - Function
Tat proofreading chaperone DmsD-type / Tat proofreading chaperone DmsD / TorD-like / TorD-like / DMSO/Nitrate reductase chaperone / TorD-like superfamily / Nitrate reductase delta subunit / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Tat proofreading chaperone DmsD
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.38 Å
AuthorsQiu, Y. / Zhang, R. / Tereshko, V. / Kim, Y. / Collart, F. / Joachimiak, A. / Kossiakoff, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2008
Title: The 1.38 A crystal structure of DmsD protein from Salmonella typhimurium, a proofreading chaperone on the Tat pathway.
Authors: Qiu, Y. / Zhang, R. / Binkowski, T.A. / Tereshko, V. / Joachimiak, A. / Kossiakoff, A.
History
DepositionFeb 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative component of anaerobic dehydrogenases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6988
Polymers23,9751
Non-polymers7237
Water4,756264
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.401, 79.355, 43.470
Angle α, β, γ (deg.)90.00, 115.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-622-

HOH

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Components

#1: Protein putative component of anaerobic dehydrogenases


Mass: 23975.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8ZPK0
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 300, ammonium sulfate, imidazole, glycerol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945, 0.97929
DetectorType: SBC-2 / Detector: CCD / Date: Dec 9, 2003
RadiationMonochromator: Double Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979451
20.979291
ReflectionResolution: 1.4→50 Å / Num. obs: 85983 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.04
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 1.56 / Num. unique all: 7337 / % possible all: 32.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.38→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.848 / SU ML: 0.034 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18527 2481 5.1 %RANDOM
Rwork0.16133 ---
obs0.16253 45922 89.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.365 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20.19 Å2
2---0.35 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.38→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1633 0 45 264 1942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211741
X-RAY DIFFRACTIONr_bond_other_d0.0020.021541
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9372369
X-RAY DIFFRACTIONr_angle_other_deg1.2333586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5915199
X-RAY DIFFRACTIONr_chiral_restr0.1170.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021899
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02369
X-RAY DIFFRACTIONr_nbd_refined0.2580.2389
X-RAY DIFFRACTIONr_nbd_other0.2430.21705
X-RAY DIFFRACTIONr_nbtor_other0.0880.2937
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2165
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0890.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2930.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.220
X-RAY DIFFRACTIONr_mcbond_it0.8561.51012
X-RAY DIFFRACTIONr_mcangle_it1.58421625
X-RAY DIFFRACTIONr_scbond_it2.3753729
X-RAY DIFFRACTIONr_scangle_it3.7774.5743
LS refinement shellResolution: 1.38→1.416 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.31 112
Rwork0.299 1704
Refinement TLS params.Method: refined / Origin x: 21.9164 Å / Origin y: 6.9277 Å / Origin z: 5.2914 Å
111213212223313233
T0.0013 Å20.0019 Å2-0.0007 Å2-0.0071 Å20.0045 Å2--0.0077 Å2
L0.3292 °2-0.0861 °2-0.0301 °2-0.3301 °2-0.0788 °2--0.493 °2
S0.0072 Å °0.028 Å °0.0201 Å °-0.0014 Å °-0.01 Å °-0.0119 Å °-0.0064 Å °-0.0349 Å °0.0027 Å °

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