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- PDB-4dt4: Crystal structure of the PPIase-chaperone SlpA with the chaperone... -

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Basic information

Entry
Database: PDB / ID: 4dt4
TitleCrystal structure of the PPIase-chaperone SlpA with the chaperone binding site occupied by the linker of the purification tag
ComponentsFKBP-type 16 kDa peptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / FKBP domain / IF domain / chaperone / peptidyl-prolyl isomerase / PPIase
Function / homology
Function and homology information


chaperone-mediated protein folding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cytosol
Similarity search - Function
Thrombin, subunit H - #330 / : / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Thrombin, subunit H / Roll ...Thrombin, subunit H - #330 / : / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Thrombin, subunit H / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FKBP-type 16 kDa peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsQuistgaard, E.M. / Nordlund, P. / Loew, C.
CitationJournal: Faseb J. / Year: 2012
Title: High-resolution insights into binding of unfolded polypeptides by the PPIase chaperone SlpA.
Authors: Quistgaard, E.M. / Nordlund, P. / Low, C.
History
DepositionFeb 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FKBP-type 16 kDa peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)18,2651
Polymers18,2651
Non-polymers00
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.120, 29.230, 60.690
Angle α, β, γ (deg.)90.00, 93.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FKBP-type 16 kDa peptidyl-prolyl cis-trans isomerase / PPIase / Rotamase


Mass: 18265.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fkpB, slpA, yaaD, b0028, JW0026 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AEM0, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 1.95 Å3/Da / Density % sol: 36.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 28% PEG 3350, 6% MPD (2-methyl-2,4-pentane diol), 100 mM MgCl2 and 100 mM Bis-Tris pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93927 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2011
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93927 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 29909 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 %
Reflection shellResolution: 1.35→1.43 Å / % possible all: 93.8

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→34.31 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.311 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.069 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20107 1200 4 %RANDOM
Rwork0.15956 ---
obs0.16126 29909 95.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.577 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20.04 Å2
2--0.74 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.35→34.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1209 0 0 229 1438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0211290
X-RAY DIFFRACTIONr_angle_refined_deg2.2971.9781767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1945178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27324.91257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96615216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.062156
X-RAY DIFFRACTIONr_chiral_restr0.1460.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021995
X-RAY DIFFRACTIONr_mcbond_it2.8741.5824
X-RAY DIFFRACTIONr_mcangle_it4.1821338
X-RAY DIFFRACTIONr_scbond_it5.8873466
X-RAY DIFFRACTIONr_scangle_it8.2894.5419
X-RAY DIFFRACTIONr_rigid_bond_restr3.22831290
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 62 -
Rwork0.244 2122 -
obs--93.41 %
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)
10.2352-0.0373-0.02640.0819-0.22681.19150.01740.03260.01830.00670.0154-0.00430.0367-0.0592-0.03290.0221-0.0029-0.00270.0180.00530.038110.46133.91913.6968
20.2755-0.2977-0.6750.60250.39712.92460.0539-0.03080.0377-0.02070.0357-0.0101-0.04910.1722-0.08960.03150.01330.01040.0554-0.02320.024527.869310.162326.4146
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 79
2X-RAY DIFFRACTION1A124 - 149
3X-RAY DIFFRACTION2A80 - 123

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