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- PDB-1q6h: Crystal structure of a truncated form of FkpA from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1q6h
TitleCrystal structure of a truncated form of FkpA from Escherichia coli
ComponentsFKBP-type peptidyl-prolyl cis-trans isomerase fkpA
KeywordsISOMERASE / chaperone / peptidyl-prolyl isomerase / heat shock protein / FKBP family
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
FKBP-type peptidyl-prolyl cis-trans isomerase FkpA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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
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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)48,5802
Polymers48,5802
Non-polymers00
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-36 kcal/mol
Surface area22870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.030, 85.230, 160.740
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.87 %
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: 23 ℃ / pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 %(w/v)Jeffamine M6001reservoir
20.1 MMES1reservoirpH6.5
30.05 M1reservoirCsCl
44.4 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9788 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 22, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.97→28 Å / Num. all: 31307 / Num. obs: 31307 / % possible obs: 84.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Biso Wilson estimate: 25.39 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.056 / Net I/σ(I): 9.7
Reflection shellResolution: 1.97→2.08 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3298 / Rsym value: 0.206 / % possible all: 74.2
Reflection
*PLUS
Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 74.2 % / Num. unique obs: 3298 / Rmerge(I) obs: 0.206

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FkpA (C-domain 95-226)

Resolution: 1.97→28 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.655 / SU ML: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 965 3.1 %RANDOM
Rwork0.1824 ---
all0.1838 30278 --
obs0.18383 30278 84.44 %-
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: 14.105 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2--1.1 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.97→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 0 468 3692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223278
X-RAY DIFFRACTIONr_bond_other_d0.0010.022990
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.9894398
X-RAY DIFFRACTIONr_angle_other_deg0.67637060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7493418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.34515668
X-RAY DIFFRACTIONr_chiral_restr0.0790.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023630
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02578
X-RAY DIFFRACTIONr_nbd_refined0.2310.3741
X-RAY DIFFRACTIONr_nbd_other0.1910.32826
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.5375
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0390.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.318
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.348
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.532
X-RAY DIFFRACTIONr_mcbond_it1.02522078
X-RAY DIFFRACTIONr_mcangle_it1.67833316
X-RAY DIFFRACTIONr_scbond_it2.04231200
X-RAY DIFFRACTIONr_scangle_it3.32141082
LS refinement shellResolution: 1.97→1.995 Å / Total num. of bins used: 40
RfactorNum. reflection
Rfree0.269 22
Rwork0.193 789
obs-789
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)
12.99430.9642.44751.01981.26642.706-0.0420.1859-0.0052-0.08740.046-0.1169-0.10220.2253-0.0040.12560.00710.04110.09230.03890.1299-6.493956.1938.7821
214.0189-6.1326-15.21972.88326.753216.2720.09470.12320.17860.0428-0.05880.01260.109-0.2545-0.03590.15520.0068-0.01250.1218-0.00610.1551-5.281939.811818.0948
32.5498-0.47710.23350.8898-0.46382.4147-0.0314-0.13420.08170.1477-0.0182-0.0516-0.09440.07180.04960.0816-0.0187-0.00810.0263-0.00290.075817.897224.722512.9249
42.5150.61221.58650.58250.85434.9677-0.10620.08270.0331-0.0926-0.040.0523-0.0703-0.1920.14620.12050.05360.04040.033-0.01820.1572-8.95256.413244.0007
510.35458.7471-12.28077.0525-10.2113.95250.0748-0.0982-0.25060.1653-0.289-0.2351-0.09760.21140.21420.1833-0.00960.01670.1236-0.0130.1761-4.773243.932366.3862
63.04421.08840.05131.23280.26641.9569-0.04080.19990.1754-0.2750.01480.049-0.2506-0.04120.0260.1380.0090.00150.02540.0030.0966-26.676128.03668.65
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 DIFFRACTION4BB15 - 6915 - 69
5X-RAY DIFFRACTION5BB70 - 11270 - 112
6X-RAY DIFFRACTION6BB113 - 224113 - 224
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 28 Å / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.36

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