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- PDB-1sg2: Crystal structure of the periplasmic chaperone Skp -

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Basic information

Entry
Database: PDB / ID: 1sg2
TitleCrystal structure of the periplasmic chaperone Skp
ComponentsSeventeen Kilodalton Protein
KeywordsCHAPERONE / protein folding / outer membrane protein / molecular dipole / hydrophobic surface
Function / homology
Function and homology information


protein insertion into membrane from inner side / : / Gram-negative-bacterium-type cell outer membrane assembly / : / 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: 2.35 Å
AuthorsKorndorfer, I.P. / Dommel, M.K. / Skerra, A.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structure of the periplasmic chaperone Skp suggests functional similarity with cytosolic chaperones despite differing architecture.
Authors: Korndorfer, I.P. / Dommel, M.K. / Skerra, A.
#1: Journal: To be Published
Title: The periplasmic E. coli chaperone Skp is a trimer in solution: biophysical and preliminary crystallographic characterization
Authors: Schlapschy, M. / Dommel, M.K. / Hadian, K. / Fogarasi, M. / Korndoerfer, I.P. / Skerra, A.
History
DepositionFeb 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE ASWSHPQFEK IS THE SEQUENCE OF THE N-TERMINAL STREP-TAGII, WHICH THE AUTHORS USED TO PURIFY ...SEQUENCE ASWSHPQFEK IS THE SEQUENCE OF THE N-TERMINAL STREP-TAGII, WHICH THE AUTHORS USED TO PURIFY THE PROTEIN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Seventeen Kilodalton Protein
B: Seventeen Kilodalton Protein
C: Seventeen Kilodalton Protein


Theoretical massNumber of molelcules
Total (without water)51,1333
Polymers51,1333
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-20 kcal/mol
Surface area23400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.985, 83.911, 158.378
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the trimer in the crystallographic asymmetric unit.

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Components

#1: Protein Seventeen Kilodalton Protein


Mass: 17044.240 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: HLPA, SKP, OMPH, B0178, C0215, Z0190, ECS0180, SF0168, S0171
Plasmid: pASK75-IBA4-Skp / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P0AEU7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 3.6 Å3/Da / Density % sol: 65.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 34.5% (v/v) ethanol, 7% (w/v) polyethylene glycol 1000, 50 mM Na-phosphate, 50 mM Na-citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.93221 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 6, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93221 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 63722 / Num. obs: 31346 / % possible obs: 94.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.076 / Rsym value: 0.059 / Net I/σ(I): 7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 17.7 / Num. unique all: 4407 / Rsym value: 0.325 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.899 / SU B: 6.878 / SU ML: 0.161 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.244 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27914 1439 4.9 %RANDOM
Rwork0.22331 ---
obs0.22608 28015 94.13 %-
all-29454 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.951 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å20 Å20 Å2
2--4.79 Å20 Å2
3----2.76 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 0 86 3119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223043
X-RAY DIFFRACTIONr_bond_other_d0.0010.022810
X-RAY DIFFRACTIONr_angle_refined_deg2.6471.9494069
X-RAY DIFFRACTIONr_angle_other_deg1.10836567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.215388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1570.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023398
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02555
X-RAY DIFFRACTIONr_nbd_refined0.270.3751
X-RAY DIFFRACTIONr_nbd_other0.2650.33345
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1110.52143
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.3181
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.37
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.340
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.321
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it4.65121944
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.34433106
X-RAY DIFFRACTIONr_scbond_it5.04821099
X-RAY DIFFRACTIONr_scangle_it7.4533963
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.328 108
Rwork0.301 1977
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)
11.03981.3879-2.38411.0892-0.64681.432-0.1168-0.4107-0.2237-0.10350.0362-0.06480.295-0.01050.08060.15140.02960.00720.11650.05150.133446.3855.3468.123
20.9748-1.37750.09341.69351.2914.48270.00030.01490.30090.130.1059-0.21010.00110.3266-0.10620.1055-0.0436-0.01720.1427-0.0840.13338.30829.18410.603
33.27031.0573-3.41832.146-1.56782.19930.0295-0.1853-0.1194-0.01270.06690.22680.0831-0.0788-0.09640.1095-0.0202-0.02810.2030.10610.103821.27810.03812.858
40.18090.2506-0.210.2942-0.95071.0805-0.0131-0.0572-0.10550.1777-0.1985-0.0486-0.22750.2540.21160.30070.0247-0.03180.17950.08140.092252.824.97533.517
50.4492-0.0917-0.08140.19080.65250.7254-0.0367-0.16930.15890.1644-0.0625-0.1470.12990.13020.09920.2436-0.053-0.03940.2095-0.07050.115934.06829.04126.543
6-0.52710.16570.01990.3792-0.79291.62790.0540.02330.00730.07820.0703-0.0784-0.0462-0.0134-0.12430.17160.0493-0.07830.31960.09350.079831.173.48437.989
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA13 - 3013 - 30
2X-RAY DIFFRACTION1AA142 - 153142 - 153
3X-RAY DIFFRACTION2BB12 - 3012 - 30
4X-RAY DIFFRACTION2BB142 - 152142 - 152
5X-RAY DIFFRACTION3CC13 - 3013 - 30
6X-RAY DIFFRACTION3CC142 - 153142 - 153
7X-RAY DIFFRACTION4AA31 - 14131 - 141
8X-RAY DIFFRACTION5BB31 - 14131 - 141
9X-RAY DIFFRACTION6CC31 - 14131 - 141

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