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- PDB-3cgn: Crystal Structure of thermophilic SlyD -

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Basic information

Entry
Database: PDB / ID: 3cgn
TitleCrystal Structure of thermophilic SlyD
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / SlyD / prolyl cis trans isomerase / chaperone / Rotamase
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein refolding / metal ion binding / cytoplasm
Similarity search - Function
Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsNeumann, P. / Loew, C. / 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: Version format compliance
Revision 1.2Nov 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)17,4962
Polymers17,4001
Non-polymers961
Water37821
1


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

A: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9934
Polymers34,8002
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544x,-y-1/2,-z-1/21
Buried area1760 Å2
ΔGint-26.8 kcal/mol
Surface area17450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.180, 85.090, 92.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

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Components

#1: Protein Peptidyl-prolyl cis-trans 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES, pH6.5, 1.6M Na/K-Tartrate, 26mg/ml, 1:1 mixing, VAPOR DIFFUSION, HANGING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 27, 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: 2.7→20 Å / Num. all: 4577 / Num. obs: 4147 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.13 % / Biso Wilson estimate: 69.918 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.054 / Net I/σ(I): 16.83
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.14 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.8 / Num. measured obs: 1846 / Num. unique all: 359 / Num. unique obs: 359 / Rsym value: 0.526 / % possible all: 78.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å19.32 Å
Translation2.7 Å19.32 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
CNS1.2refinement
PDB_EXTRACT3.004data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CGM

3cgm


Resolution: 2.7→19.76 Å / Rfactor Rfree error: 0.013 / FOM work R set: 0.795 / Data cutoff high absF: 4013434 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.257 363 8 %RANDOM
Rwork0.209 ---
obs0.211 4141 90.6 %-
all-4577 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 85.79 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 84.6 Å2
Baniso -1Baniso -2Baniso -3
1--15.42 Å20 Å20 Å2
2--16.3 Å20 Å2
3----0.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.35 Å
Luzzati d res low-4 Å
Luzzati sigma a0.47 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1163 0 5 21 1189
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it4.941.5
X-RAY DIFFRACTIONc_mcangle_it7.992
X-RAY DIFFRACTIONc_scbond_it92
X-RAY DIFFRACTIONc_scangle_it11.622.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 59 8 %
Rwork0.291 676 -
all-735 -
obs-359 78.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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