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- PDB-1q6u: Crystal structure of FkpA from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1q6u
TitleCrystal structure 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 domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / 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 domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / 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: 2.45 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 14, 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 / Derived calculations / Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE No density was interpreted for the main polypeptide chain at TYR160, THR161, ARG162 and ...SEQUENCE No density was interpreted for the main polypeptide chain at TYR160, THR161, ARG162 and GLY163. Occupancy factors are set to zero for these residues.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3972
Polymers26,2641
Non-polymers1331
Water2,090116
1
A: FKBP-type peptidyl-prolyl cis-trans isomerase fkpA
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)52,7934
Polymers52,5272
Non-polymers2662
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area4770 Å2
ΔGint-77 kcal/mol
Surface area23580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)115.180, 132.750, 41.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a dimer. The second part of the biological assembly is generated by the symmetry operation: x, -y, 1-z

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Components

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


Mass: 26263.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FKPA OR B3347 / Plasmid: pTfkp / Production host: Escherichia coli (E. coli) / Strain (production host): MC4100 derivative / References: UniProt: P45523, peptidylprolyl isomerase
#2: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cs
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 3.04 Å3/Da / Density % sol: 59.53 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MES, jeffamine M600, CsCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 4.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %(v/v)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: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 9, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. all: 12110 / Num. obs: 12110 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.089 / Rsym value: 0.081 / Net I/σ(I): 7.5
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.394 / % possible all: 99.2
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 99.2 % / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 99.2 % / Num. unique obs: 1695 / Rmerge(I) obs: 0.394

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1fd9

1fd9


Resolution: 2.45→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.889 / SU B: 11.426 / SU ML: 0.265 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.324 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27663 602 5 %RANDOM
Rwork0.21071 ---
obs0.21391 11498 99.12 %-
all-11498 --
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: 27.207 Å2
Baniso -1Baniso -2Baniso -3
1-4.75 Å20 Å20 Å2
2---2.63 Å20 Å2
3----2.12 Å2
Refinement stepCycle: LAST / Resolution: 2.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1609 0 1 116 1726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221634
X-RAY DIFFRACTIONr_bond_other_d0.0010.021486
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.9932194
X-RAY DIFFRACTIONr_angle_other_deg0.78833510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1213212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.84515339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021821
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02282
X-RAY DIFFRACTIONr_nbd_refined0.2690.3396
X-RAY DIFFRACTIONr_nbd_other0.2250.31455
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2650.5117
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0120.51
X-RAY DIFFRACTIONr_metal_ion_refined0.0670.52
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.328
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.382
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7420.527
X-RAY DIFFRACTIONr_symmetry_hbond_other0.1510.51
X-RAY DIFFRACTIONr_mcbond_it1.25321052
X-RAY DIFFRACTIONr_mcangle_it2.22231673
X-RAY DIFFRACTIONr_scbond_it2.133582
X-RAY DIFFRACTIONr_scangle_it3.6794521
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.481 Å / Total num. of bins used: 40 /
RfactorNum. reflection
Rfree0.359 20
Rwork0.213 394
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)
11.5660.53160.3594-0.1350.99067.01150.0075-0.03640.239-0.11360.06410.0993-0.8067-0.0514-0.07150.20810.02210.02230.0835-0.02250.101921.03252.887120.8206
21.385510.46381.984848.0148.72580.7215-0.24630.0582-0.0022-0.99860.3228-0.059-0.16520.083-0.07660.1804-0.03960.00440.1242-0.02830.277631.361123.29898.1993
36.69730.02643.14271.61240.36124.57790.029-0.3102-0.36710.2379-0.06160.06170.42780.22180.03260.02470.01260.02530.0915-0.00530.029848.973742.236818.8992
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 - 227113 - 227
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.7

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