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- PDB-3prb: Structural analysis of protein folding by the Methanococcus janna... -

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Basic information

Entry
Database: PDB / ID: 3prb
TitleStructural analysis of protein folding by the Methanococcus jannaschii chaperone FKBP26
ComponentsFKBP-type peptidyl-prolyl cis-trans isomerase
KeywordsChaperone / Isomerase / FKBP
Function / homology
Function and homology information


organic substance metabolic process / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity
Similarity search - Function
Alpha-Beta Plaits - #2210 / FKBP26, C-terminal / FKBP26_C-terminal / 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 ...Alpha-Beta Plaits - #2210 / FKBP26, C-terminal / FKBP26_C-terminal / 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 / Alpha-Beta Plaits / Roll / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Long-type peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsMartinez-Hackert, E. / Hendrickson, W.A.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural Analysis of Protein Folding by the Long-Chain Archaeal Chaperone FKBP26.
Authors: Martinez-Hackert, E. / Hendrickson, W.A.
History
DepositionNov 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,9752
Polymers51,9752
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-8 kcal/mol
Surface area24840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.532, 65.199, 148.616
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsdimer

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Components

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


Mass: 25987.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0825 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58235, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 298 K / Method: hanging drop
Details: 15% PMME550, 100NaCl, pH 100 mM BICINE, pH 9.0, hanging drop, temperature 298K
PH range: 100 mM BICINE, pH 9.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONNSLS X4A1
SYNCHROTRONNSLS X4A2
DetectorDetector: CCD / Date: Jul 1, 2000
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthRelative weight: 1
ReflectionNumber: 57031 / Rmerge(I) obs: 0.064 / Χ2: 1.14 / D res high: 2.8 Å / D res low: 20 Å / Num. obs: 11712 / % possible obs: 84.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
2.82.981.710.3940.978
2.93.0283.510.2861.008
3.023.1582.110.2031.011
3.153.3282.910.1451.059
3.323.5283.510.1081.142
3.523.7984.610.0791.255
3.794.1785.310.0621.271
4.174.7786.410.0511.187
4.775.9887.310.0441.21
5.982084.210.0341.326
ReflectionResolution: 2.2→19.84 Å / Num. obs: 25822

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
3 wavelength110.97924.31-8.79
3 wavelength120.9794.49-7.02
3 wavelength130.96863.28-2.98
Phasing dmFOM : 0.58 / FOM acentric: 0.58 / FOM centric: 0.58 / Reflection: 10632 / Reflection acentric: 9278 / Reflection centric: 1354
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.3-19.9660.930.930.92465331134
5.2-8.30.870.880.8215201252268
4.1-5.20.810.830.7118751619256
3.6-4.10.670.690.5418091593216
3.1-3.60.450.450.3731042795309
2.9-3.10.130.130.1218591688171

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.02phasing
RESOLVE2.02phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.2→19.84 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2803 / WRfactor Rwork: 0.2276 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7942 / SU B: 6.672 / SU ML: 0.172 / SU R Cruickshank DPI: 0.3122 / SU Rfree: 0.2378 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2736 1314 5.1 %RANDOM
Rwork0.2265 ---
obs0.2289 24476 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 83.47 Å2 / Biso mean: 43.025 Å2 / Biso min: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å20 Å20 Å2
2---0.49 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3507 0 0 179 3686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223565
X-RAY DIFFRACTIONr_angle_refined_deg1.2832.0054801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4985445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.95225.211142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19715706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.0781518
X-RAY DIFFRACTIONr_chiral_restr0.080.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212584
X-RAY DIFFRACTIONr_mcbond_it0.7841.52227
X-RAY DIFFRACTIONr_mcangle_it1.48823633
X-RAY DIFFRACTIONr_scbond_it2.13131338
X-RAY DIFFRACTIONr_scangle_it3.7054.51168
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 79 -
Rwork0.258 1353 -
all-1432 -
obs--100 %

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