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- PDB-1u2m: Crystal Structure of Skp -

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Basic information

Entry
Database: PDB / ID: 1u2m
TitleCrystal Structure of Skp
ComponentsHistone-like protein HLP-1
KeywordsCHAPERONE / coiled coil
Function / homology
Function and homology information


protein insertion into membrane from inner side / Gram-negative-bacterium-type cell outer membrane assembly / protein maturation by protein folding / chaperone-mediated protein folding / lipopolysaccharide binding / unfolded protein binding / protein folding / outer membrane-bounded periplasmic space / protein stabilization / identical protein binding / cytosol
Similarity search - Function
Skp domain / Protein Binding, DinI Protein; Chain A / Chaperone protein Skp / Skp domain superfamily / Outer membrane protein (OmpH-like) / Outer membrane protein (OmpH-like) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chaperone protein Skp
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsWalton, T.A. / Sousa, M.C.
CitationJournal: Mol.Cell / Year: 2004
Title: Crystal Structure of Skp, a Prefoldin-like Chaperone that Protects Soluble and Membrane Proteins from Aggregation
Authors: Walton, T.A. / Sousa, M.C.
History
DepositionJul 19, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-like protein HLP-1
B: Histone-like protein HLP-1
C: Histone-like protein HLP-1


Theoretical massNumber of molelcules
Total (without water)48,5563
Polymers48,5563
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-27 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.828, 84.190, 160.181
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 Histone-like protein HLP-1 / Skp / DNA-binding 17 kDa protein


Mass: 16185.424 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HLPA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta (Novagen) / References: UniProt: P0AEU7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 4 Å3/Da / Density % sol: 68.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 350 monomethy ether, ammonium dihydrogen phosphate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9794, 0.9795, 0.9649
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 8, 2004
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97951
30.96491
ReflectionResolution: 2.5→25 Å / Num. all: 64798 / Num. obs: 64535 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 38.4 Å2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
Blu-Icedata collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→58.03 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2025344.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3147 4.9 %RANDOM
Rwork0.232 ---
obs0.232 64535 99.6 %-
all-64798 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.3626 Å2 / ksol: 0.349872 e/Å3
Displacement parametersBiso mean: 58.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--15.82 Å20 Å2
3----15.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→58.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2615 0 0 47 2662
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 312 4.8 %
Rwork0.28 10257 -
obs-6426 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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