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

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Basic information

Entry
Database: PDB / ID: 3prd
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: 3.3 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


Theoretical massNumber of molelcules
Total (without water)25,9871
Polymers25,9871
Non-polymers00
Water0
1
A: FKBP-type peptidyl-prolyl cis-trans isomerase

A: FKBP-type peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)51,9752
Polymers51,9752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area1850 Å2
ΔGint-10 kcal/mol
Surface area25680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.950, 137.950, 114.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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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.: 1
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

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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: 5.24 Å3/Da / Density % sol: 76.54 %
Crystal growTemperature: 298 K / Method: hanging drop
Details: 1.5 M (NH4)2SO4, pH 100 mM Tris, pH 8.0, hanging drop, temperature 298K
PH range: 100 mM Tris, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
DetectorDetector: CCD / Date: Oct 1, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.3→25 Å / Num. obs: 8151

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MAD / Resolution: 3.3→25 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.883 / Occupancy max: 1 / Occupancy min: 1 / SU B: 85.965 / SU ML: 0.589 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.531
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3279 375 4.6 %RANDOM
Rwork0.3147 ---
obs0.3153 8151 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 170.92 Å2 / Biso mean: 139.453 Å2 / Biso min: 98.92 Å2
Baniso -1Baniso -2Baniso -3
1--7.08 Å20 Å20 Å2
2---7.08 Å20 Å2
3---14.16 Å2
Refinement stepCycle: LAST / Resolution: 3.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 0 0 1751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221780
X-RAY DIFFRACTIONr_angle_refined_deg1.0562.0052397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5525222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.7625.21171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.715353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.782159
X-RAY DIFFRACTIONr_chiral_restr0.070.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021290
X-RAY DIFFRACTIONr_nbd_refined0.2180.2801
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21197
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.255
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0590.21
X-RAY DIFFRACTIONr_mcbond_it0.3631.51148
X-RAY DIFFRACTIONr_mcangle_it0.65821813
X-RAY DIFFRACTIONr_scbond_it0.483702
X-RAY DIFFRACTIONr_scangle_it0.8594.5584
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 27 -
Rwork0.441 551 -
all-578 -
obs--93.38 %
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)
15.5995-0.83890.90861.7136-0.44825.5870.2669-0.35-0.82740.41550.1210.45870.5953-0.8929-0.3879-0.315-0.17430.078-0.23340.0699-0.007236.990259.125613.6576
211.3549-4.9692-3.31695.01144.33378.25870.6816-0.30030.1438-0.2421-0.136-0.3423-0.42620.3628-0.5456-0.6107-0.0304-0.07280.12050.00510.144645.317970.9781-13.8856
310.02332.1395-1.53387.85170.23120.55-0.1516-1.028-0.1401-0.47640.15770.38940.0475-0.1747-0.00610.14930.1133-0.0546-0.27890.0459-0.671260.36365.578725.5003
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 85
2X-RAY DIFFRACTION1A130 - 150
3X-RAY DIFFRACTION2A86 - 129
4X-RAY DIFFRACTION3A151 - 223

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