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- PDB-6mke: Crystal Structure of Peptidylprolyl Isomerase from Naegleria fowl... -

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Basic information

Entry
Database: PDB / ID: 6mke
TitleCrystal Structure of Peptidylprolyl Isomerase from Naegleria fowleri with bound FK506
ComponentsPeptidylprolyl isomerase
KeywordsISOMERASE / SSGCID / peptidylprolyl isomerase / Naegleria fowleri / FK506 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity
Similarity search - Function
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 / Roll / Alpha Beta
Similarity search - Domain/homology
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / peptidylprolyl isomerase
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Peptidylprolyl Isomerase from Naegleria fowleri with bound FK506
Authors: Dranow, D.M. / Bertolin, B.A. / Fox III, D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionSep 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Peptidylprolyl isomerase
B: Peptidylprolyl isomerase
C: Peptidylprolyl isomerase
D: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0418
Polymers56,8254
Non-polymers3,2164
Water6,918384
1
A: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0102
Polymers14,2061
Non-polymers8041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0102
Polymers14,2061
Non-polymers8041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0102
Polymers14,2061
Non-polymers8041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0102
Polymers14,2061
Non-polymers8041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.050, 60.160, 73.340
Angle α, β, γ (deg.)90.000, 97.120, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Peptidylprolyl isomerase


Mass: 14206.163 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Gene: NF0084240 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A2H4A315, peptidylprolyl isomerase
#2: Chemical
ChemComp-FK5 / 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / K506


Mass: 804.018 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H69NO12 / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: NafoA.18272.a.B1.PS38284 at 22.7 mg/ml was incubated with 5 mM FK-506, then was mixed 1:1 MCSG1(e12): 2.4 M sodium malonate, pH=7.0. Tray: 303683e12, puck: pvb8-5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 2, 2017
RadiationMonochromator: Rigaku Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→48.683 Å / Num. obs: 31313 / % possible obs: 97.1 % / Redundancy: 16.751 % / Biso Wilson estimate: 30.287 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.062 / Χ2: 0.914 / Net I/σ(I): 37 / Num. measured all: 524516 / Scaling rejects: 9290
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.05-2.112.2540.2598.4128257239823060.9820.2796.2
2.1-2.1613.8010.2339.9430777229022300.990.24297.4
2.16-2.2214.0680.3549.4329374225520880.9720.36892.6
2.22-2.2912.3970.17135.4725290216620400.9890.17994.2
2.29-2.3716.060.24413.1129631213718450.9910.25286.3
2.37-2.4517.5010.12620.2134826201919900.9980.1398.6
2.45-2.5418.7460.1321.1836648198419550.9970.13498.5
2.54-2.6518.8630.10425.4835237189518680.9980.10698.6
2.65-2.7618.7920.08929.9233958182918070.9990.09298.8
2.76-2.918.8410.07135.8732595174617300.9990.07399.1
2.9-3.0618.7980.05844.2631524169116770.9990.0699.2
3.06-3.2418.9110.05249.31292171557154510.05399.2
3.24-3.4718.7810.04456.63276641480147310.04599.5
3.47-3.7415.3640.06265.321126138213750.9990.06499.5
3.74-4.118.2960.04467.68229061273125210.04598.4
4.1-4.5818.4780.0384.9216011172116910.03199.7
4.58-5.2918.6260.0385.3191291027102710.031100
5.29-6.4818.5270.03180.141604486686610.032100
6.48-9.1718.040.02979.171221367867710.0399.9
9.17-48.68316.5370.02595.06649939639310.02699.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B4P

6b4p


Resolution: 2.05→48.683 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.1
RfactorNum. reflection% reflection
Rfree0.2567 1965 6.28 %
Rwork0.2134 --
obs0.2162 31308 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.9 Å2 / Biso mean: 29.2184 Å2 / Biso min: 1.39 Å2
Refinement stepCycle: final / Resolution: 2.05→48.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3600 0 228 388 4216
Biso mean--23.63 34.29 -
Num. residues----468
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.10120.28691180.23252095221396
2.1012-2.1580.31451350.2682091222697
2.158-2.22160.50951460.34841976212293
2.2216-2.29330.54551300.48681991212194
2.2933-2.37520.45151260.3371905203188
2.3752-2.47030.26021420.23332093223598
2.4703-2.58270.27511370.20952106224399
2.5827-2.71890.24711410.20472162230399
2.7189-2.88920.26451290.20632120224999
2.8892-3.11230.27081550.21092137229299
3.1123-3.42540.23051530.19222130228399
3.4254-3.92090.24631510.174621522303100
3.9209-4.93910.15121480.13122159230799
4.9391-48.69650.14551540.143322262380100
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)
13.7516-1.0108-0.39746.2195-2.60481.64740.0903-0.4846-0.01991.2595-0.2846-0.27270.15820.1649-0.04170.2816-0.0479-0.03660.20310.11440.16685.9785-8.36816.5601
26.1039-0.76921.5316.7178-0.48432.9262-0.0091-0.51740.33910.5456-0.0051-0.3882-0.41040.03430.03530.2749-0.0202-0.05730.2116-0.0210.11034.7121.31716.6633
33.19811.61192.82353.04320.77832.67960.0422-0.98030.46330.74360.07680.4733-0.1604-0.52440.04570.29890.07890.11450.4349-0.05430.3371-10.6860.705616.1803
41.0539-0.0998-0.17650.42150.03680.03020.03380.00040.16560.1094-0.01320.0157-0.0223-0.0043-0.21230.1108-0.014-0.00540.05590.04910.2698-1.60054.34874.42
51.8541-1.33980.58351.0991-0.24520.41860.04840.13330.4804-0.1075-0.0569-0.1819-0.07510.08120.05340.083-0.0150.04240.09210.0340.30527.00066.2708-0.2463
61.6653-0.635-1.52522.55490.54211.4862-0.15560.3332-0.0831-0.12940.16810.4701-0.0032-0.3095-0.03750.0747-0.0049-0.00510.26160.11390.2243-7.4385-0.20481.5778
71.72191.35631.32331.6993-0.01732.8040.0149-0.14780.03210.0635-0.00980.1945-0.0437-0.28190.0030.0905-0.01440.00270.06370.02150.2491-0.8047-1.550311.2727
85.9257-0.12480.03821.5098-0.63557.70910.09720.4990.0409-0.0848-0.18350.0014-0.05680.25190.10060.1154-0.0116-0.02690.0735-0.01330.17248.1651-8.0746-2.1036
91.104-0.7021-0.40590.45370.33020.91640.0446-0.02850.31220.02380.00830.0501-0.0959-0.2562-0.04170.06850.01580.00960.14190.01270.3465-1.97543.72448.7819
103.3238-1.51852.17935.7844-0.55671.88160.09410.6115-0.6174-0.6887-0.2208-0.09980.96610.1618-0.18970.28070.01820.07560.2021-0.11640.311118.0961-15.19892.0277
112.17260.71071.86986.7586-0.27273.80950.17310.9383-0.1383-0.5656-0.36590.0216-0.4183-0.17810.05820.22530.07260.03250.2941-0.04750.160524.647-8.2887-1.524
123.2636-0.60690.64781.5322-0.70851.4366-0.0040.099-0.1305-0.3388-0.2194-0.310.30810.25490.05630.1230.04470.09570.15240.06750.297431.5949-5.47797.8538
130.33350.5104-0.33691.23970.39263.07310.0618-0.2134-0.33450.1791-0.0662-0.41790.20370.47020.15220.14380.02750.02760.18030.10180.317735.0924-10.234514.4519
142.3905-0.1890.69971.9922-0.05361.6320.0220.1438-0.1948-0.0889-0.1333-0.06570.26160.09160.04090.13750.02390.03090.04730.01940.171225.6861-8.981310.3058
156.1867-1.43031.64215.22151.35693.0280.2753-0.7253-0.10260.6478-0.4543-0.102-0.016-0.16450.1530.3461-0.12950.0080.1972-0.00540.212529.2885-3.468649.6066
160.37431.27030.53344.61132.52532.4486-0.0733-0.50170.5250.1714-0.44110.99070.0096-0.85570.51250.2669-0.07990.09270.3464-0.16990.404718.80495.063745.4133
171.2974-0.3692-0.23021.2013-0.60891.98680.00030.1560.4949-0.115-0.09530.0556-0.299-0.03460.05290.2551-0.0198-0.04830.0850.00580.233527.21416.235232.3697
184.698-0.76160.73563.30550.83822.06150.0650.0880.19210.068-0.20960.0926-0.0213-0.11730.12210.2084-0.0154-0.02740.04950.00430.131228.58090.696737.877
192.8623-0.4541.52021.90191.51162.486-0.40390.4801-0.6102-1.23760.19450.30750.7173-0.04260.00280.5683-0.12660.05940.2856-0.15510.4649-4.9261-10.3845-32.391
206.33910.69050.36024.73-0.99899.0634-0.3170.8869-0.2559-0.2481-0.0932-0.71650.12611.12180.37480.43370.0610.10110.4071-0.0020.28478.943-8.3675-31.0286
211.9281-2.63540.44213.8177-0.52552.9776-0.20890.06350.4084-0.0017-0.095-0.2338-0.48170.71850.29830.3011-0.148-0.03290.30620.02140.22116.6531.0646-22.3665
221.5926-0.18490.71783.46571.2353.66-0.2947-0.02841.1571-0.1623-0.2563-0.2273-1.00930.46330.4250.4271-0.1242-0.06620.26250.03850.3240.61558.4458-22.5586
236.34290.62720.21657.19190.89323.88760.0454-0.0412-0.19010.13410.0336-0.23640.08360.4119-0.08670.1976-0.0555-0.02230.23910.06020.1556.1447-6.3372-18.8849
245.1116-0.8543-0.80952.54650.37633.4047-0.05230.3946-0.0713-0.16390.05080.13580.12270.33290.08620.1866-0.1043-0.01660.2341-0.02140.2032-0.962-5.0263-24.8673
258.327-0.9675-2.24762.63580.37944.2461-0.2675-0.24480.42290.04470.0949-0.1315-0.08520.35820.08310.252-0.0906-0.06030.18010.00820.17410.32350.1207-21.7313
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 14 )A3 - 14
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 20 )A15 - 20
3X-RAY DIFFRACTION3chain 'A' and (resid 21 through 32 )A21 - 32
4X-RAY DIFFRACTION4chain 'A' and (resid 33 through 42 )A33 - 42
5X-RAY DIFFRACTION5chain 'A' and (resid 43 through 54 )A43 - 54
6X-RAY DIFFRACTION6chain 'A' and (resid 55 through 68 )A55 - 68
7X-RAY DIFFRACTION7chain 'A' and (resid 69 through 88 )A69 - 88
8X-RAY DIFFRACTION8chain 'A' and (resid 89 through 108 )A89 - 108
9X-RAY DIFFRACTION9chain 'A' and (resid 109 through 119 )A109 - 119
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 14 )B3 - 14
11X-RAY DIFFRACTION11chain 'B' and (resid 15 through 20 )B15 - 20
12X-RAY DIFFRACTION12chain 'B' and (resid 21 through 54 )B21 - 54
13X-RAY DIFFRACTION13chain 'B' and (resid 55 through 68 )B55 - 68
14X-RAY DIFFRACTION14chain 'B' and (resid 69 through 119 )B69 - 119
15X-RAY DIFFRACTION15chain 'C' and (resid 3 through 14 )C3 - 14
16X-RAY DIFFRACTION16chain 'C' and (resid 15 through 32 )C15 - 32
17X-RAY DIFFRACTION17chain 'C' and (resid 33 through 68 )C33 - 68
18X-RAY DIFFRACTION18chain 'C' and (resid 69 through 119 )C69 - 119
19X-RAY DIFFRACTION19chain 'D' and (resid 3 through 14 )D3 - 14
20X-RAY DIFFRACTION20chain 'D' and (resid 15 through 32 )D15 - 32
21X-RAY DIFFRACTION21chain 'D' and (resid 33 through 42 )D33 - 42
22X-RAY DIFFRACTION22chain 'D' and (resid 43 through 54 )D43 - 54
23X-RAY DIFFRACTION23chain 'D' and (resid 55 through 76 )D55 - 76
24X-RAY DIFFRACTION24chain 'D' and (resid 77 through 97 )D77 - 97
25X-RAY DIFFRACTION25chain 'D' and (resid 98 through 119 )D98 - 119

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