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- PDB-7dek: Pseudomonas aeruginosa FK506-binding protein PaFkbA -

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Basic information

Entry
Database: PDB / ID: 7dek
TitlePseudomonas aeruginosa FK506-binding protein PaFkbA
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / dimer / chaperone
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding
Similarity search - Function
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 / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsYnag, J. / Huang, Q. / Bao, R.
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: Structural characterization of PaFkbA: A periplasmic chaperone from Pseudomonas aeruginosa .
Authors: Huang, Q. / Yang, J. / Li, C. / Song, Y. / Zhu, Y. / Zhao, N. / Mou, X. / Tang, X. / Luo, G. / Tong, A. / Sun, B. / Tang, H. / Li, H. / Bai, L. / Bao, R.
History
DepositionNov 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase
G: Peptidyl-prolyl cis-trans isomerase
F: Peptidyl-prolyl cis-trans isomerase
D: Peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)89,4934
Polymers89,4934
Non-polymers00
Water1,02757
1
A: Peptidyl-prolyl cis-trans isomerase
G: Peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)44,7472
Polymers44,7472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-43 kcal/mol
Surface area21070 Å2
MethodPISA
2
F: Peptidyl-prolyl cis-trans isomerase
D: Peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)44,7472
Polymers44,7472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-44 kcal/mol
Surface area21990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.073, 94.223, 117.437
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain "A" and resid 27 through 228)
21chain "F"
31chain "G"
41(chain "D" and resid 27 through 228)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
111GLULYSA3 - 204
211GLULYSF1 - 202
311GLULYSG1 - 202
411GLULYSD5 - 206

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Components

#1: Protein
Peptidyl-prolyl cis-trans isomerase


Mass: 22373.309 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA3262 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYX8, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.17 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris pH 8.0, 28% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 19438 / % possible obs: 99.8 % / Redundancy: 8.6 % / Biso Wilson estimate: 68.52 Å2 / CC1/2: 0.992 / Net I/σ(I): 2.154
Reflection shellResolution: 2.9→3 Å / Num. unique obs: 1904 / CC1/2: 0.69

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1q6u

1q6u


Resolution: 2.9→38.54 Å / SU ML: 0.4545 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 31.269
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2807 1935 9.99 %
Rwork0.2459 17428 -
obs0.2493 19363 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.19 Å2
Refinement stepCycle: LAST / Resolution: 2.9→38.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6138 0 0 57 6195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01186230
X-RAY DIFFRACTIONf_angle_d1.598400
X-RAY DIFFRACTIONf_chiral_restr0.1078949
X-RAY DIFFRACTIONf_plane_restr0.00511101
X-RAY DIFFRACTIONf_dihedral_angle_d25.0062372
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
12AX-RAY DIFFRACTIONTorsion NCS1.59701223205
13AX-RAY DIFFRACTIONTorsion NCS5.16656078
14AX-RAY DIFFRACTIONTorsion NCS5.21681293119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.980.38641300.3751175X-RAY DIFFRACTION94.5
2.98-3.060.42551360.35581224X-RAY DIFFRACTION99.71
3.06-3.150.36391350.33971221X-RAY DIFFRACTION99.63
3.15-3.250.35491370.33211235X-RAY DIFFRACTION99.64
3.25-3.360.31951370.30481242X-RAY DIFFRACTION99.64
3.36-3.50.30291370.27851221X-RAY DIFFRACTION99.78
3.5-3.660.3271370.26491241X-RAY DIFFRACTION99.57
3.66-3.850.30481370.24831243X-RAY DIFFRACTION99.86
3.85-4.090.27021390.25311233X-RAY DIFFRACTION99.64
4.09-4.410.25651370.20631238X-RAY DIFFRACTION99.49
4.41-4.850.23291390.18621262X-RAY DIFFRACTION99.22
4.85-5.550.22831410.22131265X-RAY DIFFRACTION99.5
5.55-6.980.26261420.24241276X-RAY DIFFRACTION99.65
6.98-38.540.24661510.20741352X-RAY DIFFRACTION99.67
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)
12.591312573410.124992796694-0.6167583992952.89920466384-0.7194034831141.14091464643-0.5667909788231.48276634511-0.588345675317-1.350728683641.25655030234-1.634021501590.7163078699430.67051293685-0.2642653619611.26966124785-0.175560940996-0.2876711436841.19509337919-0.1876839889610.812390510377-0.33716276609811.55304511460.660176830551
22.28235973609-2.30440634531-0.1201983004456.358452520041.111521268780.1281963404270.547662266850.3810589424340.50573079991-1.24492147036-0.589373378525-0.530762431779-0.147912644930.638988391243-0.2666992624641.07185011523-0.1243890972230.2365282592511.04832855130.04643693940140.83308361804713.44752122526.93943235097.94880779849
37.03989889972-1.33652331571-0.8239149596918.61083176659-0.07987568306234.24367268106-0.31165431073-0.2476897121360.703182489924-1.103839508450.7638700557861.60480472815-0.044729211925-0.618570379951-0.4543759206830.447210228498-0.0953913989873-0.1247286210550.4748028685950.1156206310880.841213633087-7.207350338839.987867151723.3196950675
46.44175120103-1.27653854488-0.2278523328156.780656123551.78193174563.93972908797-0.3961346413960.127135101305-0.820067793247-0.6019187715210.4795109146480.1819427826480.03312786037880.136688277471-0.2585126627610.492111876452-0.0756912975352-0.05987142820560.4200719956580.0662049072420.825531490278-3.2698199016737.562429002321.0442985477
55.860628628071.026607656710.5118984437292.83430113115-0.4646201108731.07713366635-0.271260458340.7017914562320.36665461254-0.6054507335070.5924280559130.06417143741091.055816357730.5003031953360.142890573711.579156968970.267854079043-0.1950420095711.0839248475-0.02971320620590.820419224026-0.37366518406311.93745411780.977804930293
63.26290410158-2.292481727460.1304855165532.12902520376-4.108736810853.72673893763-0.3565842532820.08914706478010.54211378239-1.421753824970.9136908192621.184994844460.0675809354091-0.585133157838-0.5337766136120.612665369352-0.0433682792288-0.001920364342830.701502598424-0.02802779170080.667663089416-14.9417434707-4.7701006546615.3246748881
76.39363869528-1.649081787321.921946088138.069395755010.7058755583783.87535700440.1724778166670.106519080036-0.211686223542-0.7294864579170.371074550487-0.513177320532-0.07226296982020.357896136639-0.423827904860.459047394154-0.07064429736860.2247546702080.401142901024-0.1065529913740.585045120050.680105400897-25.400942311626.6815072835
88.547068938761.27550183792-0.9967121160224.819975393331.223615624743.598107502330.391562642804-0.526118533171.246468961210.1574629684620.2638647921720.661606781282-0.3093492889750.0494539986637-0.6641555012340.651669694391-0.06357150945290.1585253907410.6816820809110.1110762613990.709226212984-0.29428355453661.16987404791.16587061501
91.882432071860.939251074402-0.6611346073617.06148520859-4.12202341972.719131604270.423705306710.0241801190955-0.05184945854690.2092371714340.3219515509132.041230050030.125752852378-0.35773715844-0.7475967590280.557474641977-0.0839042456196-0.01483601080680.5660976818840.04239816410050.885862922031-15.474865715383.4375015753-16.8095862468
107.349767152421.145512001411.605438293818.841549176393.922765202416.11558475345-0.0563920447617-0.599950612747-0.834538016382-0.2146871712980.542912002754-1.523777925190.3576537817920.275152010204-0.5645622087990.5108285978780.09646790394880.02953421942380.416854531070.04429599302770.6436547371440.89380659457397.3493780344-26.0801531241
116.352273953161.794935502162.086450674934.15612156144-0.8313479174314.62836078661-0.507987035562-0.590593104850.295882235690.1867484503040.550399803241-0.276794833265-0.9033282988790.3066564994260.002549314182040.726833416853-0.04898714839880.04187280197990.743584328667-0.004866136399810.473946810828-0.19461696660561.50462218220.189782142211
123.646623403750.9866416820730.827458038926.74174990464.256661502362.36966691372-0.4448949281110.2608619337420.362841688490.6332819894680.984636672505-0.08451022766140.122075390640.744292080096-0.5442449064310.71005363273-0.003214232485350.08597794171710.7234080024620.1175538968520.62834129568612.655444036144.9915198575-7.17021464356
136.57050553648-0.638255727141.142485471094.56797545343-0.8977308351521.37569409403-0.0908538533972-0.01518755070510.6313883300970.4750202838360.247481617325-0.0173377479152-0.511304587315-0.261487598633-0.268280502970.7860459900460.009282278466920.2849115151220.506809209668-0.02126482575810.440784112889-5.9575959054333.6138103952-22.6039089389
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 25 through 76 )AA25 - 761 - 52
22chain 'A' and (resid 77 through 115 )AA77 - 11553 - 91
33chain 'A' and (resid 116 through 186 )AA116 - 18692 - 162
44chain 'A' and (resid 187 through 228 )AA187 - 228163 - 204
55chain 'G' and (resid 27 through 76 )GB27 - 761 - 50
66chain 'G' and (resid 77 through 115 )GB77 - 11551 - 89
77chain 'G' and (resid 116 through 228 )GB116 - 22890 - 202
88chain 'F' and (resid 23 through 76 )FC23 - 761 - 54
99chain 'F' and (resid 77 through 126 )FC77 - 12655 - 104
1010chain 'F' and (resid 127 through 228 )FC127 - 228105 - 206
1111chain 'D' and (resid 27 through 76 )DD27 - 761 - 50
1212chain 'D' and (resid 77 through 115 )DD77 - 11551 - 89
1313chain 'D' and (resid 116 through 228 )DD116 - 22890 - 202

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