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- PDB-1q6i: Crystal structure of a truncated form of FkpA from Escherichia co... -

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Basic information

Entry
Database: PDB / ID: 1q6i
TitleCrystal structure of a truncated form of FkpA from Escherichia coli, in complex with immunosuppressant FK506
ComponentsFKBP-type peptidyl-prolyl cis-trans isomerase fkpA
KeywordsISOMERASE / chaperone / peptidyl-prolyl isomerase / heat shock protein / FKBP family / immunosuppressant FK506 / ascomycin
Function / homology
Function and homology information


protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / outer membrane-bounded periplasmic space / protein refolding
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase, FKBP-type, N-terminal domain / Peptidyl-prolyl cis-trans isomerase, FKBP-type, N-terminal / Peptidyl-prolyl cis-trans isomerase, FKBP-type, N-terminal domain superfamily / Domain amino terminal to FKBP-type peptidyl-prolyl isomerase / 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 ...Peptidyl-prolyl cis-trans isomerase, FKBP-type, N-terminal domain / Peptidyl-prolyl cis-trans isomerase, FKBP-type, N-terminal / Peptidyl-prolyl cis-trans isomerase, FKBP-type, N-terminal domain superfamily / Domain amino terminal to FKBP-type peptidyl-prolyl isomerase / 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 / Helix Hairpins / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / FKBP-type peptidyl-prolyl cis-trans isomerase FkpA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid-body refinement / Resolution: 2.25 Å
AuthorsSaul, F.A. / Arie, J.-P. / Vulliez-le Normand, B. / Kahn, R. / Betton, J.-M. / Bentley, G.A.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structural and functional studies of FkpA from Escherichia coli, a cis/trans peptidyl-prolyl isomerase with chaperone activity.
Authors: Saul, F.A. / Arie, J.P. / Vulliez-le Normand, B. / Kahn, R. / Betton, J.M. / Bentley, G.A.
History
DepositionAug 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 3, 2024Group: 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Refinement description / Category: pdbx_initial_refinement_model / Item: _pdbx_initial_refinement_model.accession_code
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 fkpA
B: FKBP-type peptidyl-prolyl cis-trans isomerase fkpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1884
Polymers48,5802
Non-polymers1,6082
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-39 kcal/mol
Surface area23270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.140, 85.440, 159.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer (chains A, B)

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Components

#1: Protein FKBP-type peptidyl-prolyl cis-trans isomerase fkpA / PPiase / Rotamase


Mass: 24290.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FKPA OR B3347 / Plasmid: pTfkpDCT / Production host: Escherichia coli (E. coli) / Strain (production host): MC4100 derivative / References: UniProt: P45523, peptidylprolyl isomerase
#2: Chemical ChemComp-FK5 / 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / K506


Mass: 804.018 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H69NO12 / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsFK5 301 IS ASSOCIATED WITH MOLECULE A. FK5 401 IS ASSOCIATED WITH MOLECULE B.

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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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 2000, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %PEG20001reservoir
20.1 Msodium acetate1reservoirpH4.5
33.1 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 22702 / Num. obs: 22702 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 39.47 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.068 / Net I/σ(I): 7.1
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2744 / Rsym value: 0.22 / % possible all: 81.2
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 81.2 % / Num. unique obs: 2744 / Rmerge(I) obs: 0.22

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: rigid-body refinement
Starting model: FkpA (individual N- and C-domains)

Resolution: 2.25→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.443 / SU ML: 0.266 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.332 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25344 700 3.1 %RANDOM
Rwork0.20642 ---
all0.2079 21956 --
obs0.2079 21956 90.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.929 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å20 Å2
2--3.3 Å20 Å2
3----2.21 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 114 230 3568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223406
X-RAY DIFFRACTIONr_bond_other_d0.0010.023129
X-RAY DIFFRACTIONr_angle_refined_deg1.7582.0264581
X-RAY DIFFRACTIONr_angle_other_deg1.1337388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0433418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.02515674
X-RAY DIFFRACTIONr_chiral_restr0.1090.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023693
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02583
X-RAY DIFFRACTIONr_nbd_refined0.2370.3816
X-RAY DIFFRACTIONr_nbd_other0.2160.32966
X-RAY DIFFRACTIONr_nbtor_other0.3330.54
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.5283
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2340.54
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.312
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.329
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.523
X-RAY DIFFRACTIONr_mcbond_it1.11122079
X-RAY DIFFRACTIONr_mcangle_it1.83833319
X-RAY DIFFRACTIONr_scbond_it1.93931327
X-RAY DIFFRACTIONr_scangle_it3.07541262
LS refinement shellResolution: 2.25→2.279 Å / Total num. of bins used: 40
RfactorNum. reflection
Rfree0.451 17
Rwork0.268 651
obs-651
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)
14.40190.74133.7870.32771.00694.3795-0.04240.3735-0.0134-0.0450.032-0.165-0.16620.29670.01050.1578-0.0330.06540.13680.02770.2074-6.638356.397638.5617
218.8629-7.8334-19.87873.55038.452520.72830.21330.047-0.1704-0.0575-0.34530.1845-0.2019-0.23330.13190.1596-0.01860.00550.1709-0.01450.1828-5.310240.094917.793
32.9328-0.4563-0.06971.7065-0.32253.0790.0049-0.24140.07330.2448-0.0617-0.0729-0.12360.0760.05680.0432-0.0265-0.01310.01630.00650.076317.509224.839913.6266
43.50910.34911.90340.71250.50536.5769-0.12120.14730.2028-0.1257-0.1165-0.0408-0.1139-0.28740.23770.12450.02770.06110.08280.02080.1611-9.106456.514643.7269
512.692510.4254-14.82658.1548-11.818916.4538-0.0341-0.0147-0.3890.0554-0.2493-0.298-0.01240.17710.28340.1624-0.01840.0470.10640.00470.1653-4.907243.971166.2018
63.6921.46520.74581.46350.12732.348-0.06130.32870.1765-0.34980.02870.05-0.274-0.01810.03250.1440.02250.01520.0188-0.00120.1015-26.423428.359867.491
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 6915 - 69
2X-RAY DIFFRACTION2AA70 - 11270 - 112
3X-RAY DIFFRACTION3AA113 - 224113 - 224
4X-RAY DIFFRACTION3AC3011
5X-RAY DIFFRACTION4BB15 - 6915 - 69
6X-RAY DIFFRACTION5BB70 - 11270 - 112
7X-RAY DIFFRACTION6BB113 - 224113 - 224
8X-RAY DIFFRACTION6AD4011
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.76

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