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- PDB-3cgm: Crystal structure of thermophilic SlyD -

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Basic information

Entry
Database: PDB / ID: 3cgm
TitleCrystal structure of thermophilic SlyD
ComponentsPeptidyl-prolyl cis-trans isomeraseProlyl isomerase
KeywordsISOMERASE / Prolyl cis trans isomerase / chaperone function / two domain protein / Rotamase
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein refolding / metal ion binding
Similarity search - Function
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 / Roll / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / THIOCYANATE ION / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.41 Å
AuthorsLoew, C. / Neumann, P. / Stubbs, M.T. / Balbach, J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structure Determination and Functional Characterization of the Metallochaperone SlyD from Thermus thermophilus
Authors: Loew, C. / Neumann, P. / Tidow, H. / Weininger, U. / Haupt, C. / Friedrich-Epler, B. / Scholz, C. / Stubbs, M.T. / Balbach, J.
History
DepositionMar 6, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Dec 25, 2019Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs ..._reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rsym_value / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,99210
Polymers17,4001
Non-polymers5919
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peptidyl-prolyl cis-trans isomerase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)107,95060
Polymers104,4016
Non-polymers3,54854
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/21
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation12_544x,x-y-1,-z-1/21
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation11_654-x+y+1,y,-z-1/21
Buried area22350 Å2
ΔGint-215.9 kcal/mol
Surface area46910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.780, 121.780, 76.260
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase / Prolyl isomerase / SlyD


Mass: 17400.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pet11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5SLE7, peptidylprolyl isomerase
#2: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 4.69 Å3/Da / Density % sol: 73.78 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 60mg/ml protein, 1:1 mixing, 2M Ammonium sulfate, 2% PEG 400, 1% Thiocyanate, 100mM HEPES, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 7, 2007 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.41→30 Å / Num. all: 13374 / Num. obs: 12921 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Biso Wilson estimate: 43.405 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.107 / Net I/σ(I): 21.98
Reflection shellResolution: 2.41→2.55 Å / Redundancy: 11.32 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 4.4 / Num. measured obs: 21342 / Num. unique all: 1885 / Num. unique obs: 1885 / Rsym value: 0.45 / % possible all: 92.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
MAR345dtbdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 1D6O

1d6o


Resolution: 2.41→28.27 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.394 / SU ML: 0.129 / Isotropic thermal model: Isotropic/TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.214 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.226 969 7.5 %RANDOM
Rwork0.187 ---
obs0.19 11955 96.6 %-
all-13374 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.556 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.06 Å20 Å2
2---0.13 Å20 Å2
3---0.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.214 Å
Luzzati d res low-3 Å
Luzzati sigma a0.129 Å0 Å
Refinement stepCycle: LAST / Resolution: 2.41→28.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 31 98 1346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211313
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9591781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9945164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39825.71470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94815198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.68154
X-RAY DIFFRACTIONr_chiral_restr0.0930.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211049
X-RAY DIFFRACTIONr_mcbond_it1.2532818
X-RAY DIFFRACTIONr_mcangle_it2.18731310
X-RAY DIFFRACTIONr_scbond_it1.4092495
X-RAY DIFFRACTIONr_scangle_it2.1893471
LS refinement shellResolution: 2.409→2.471 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 63 -
Rwork0.257 768 -
all-831 -
obs-0 100 %
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)
12.99650.2094.42551.47691.055813.36280.07410.03710.3144-0.26710.00170.1982-0.7147-0.7832-0.0758-0.1432-0.0050.0377-0.00580.0436-0.088321.083-49.683-18.823
22.63470.4783-0.14863.5657-0.01811.4589-0.00450.26970.0033-0.11760.07650.0057-0.0298-0.0707-0.072-0.2437-0.03070.0224-0.10420.0238-0.225944.761-39.15-7.051
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA59 - 12359 - 123
2X-RAY DIFFRACTION2AA1 - 581 - 58
3X-RAY DIFFRACTION2AA124 - 157124 - 157

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