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- PDB-7u0s: Crystal Structure of FK506-binding protein 1A from Aspergillus fu... -

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Basic information

Entry
Database: PDB / ID: 7u0s
TitleCrystal Structure of FK506-binding protein 1A from Aspergillus fumigatus Bound to Ascomycin
ComponentsFK506-binding protein 1A
KeywordsANTIFUNGAL PROTEIN / SSGCID / PPIase / Rapamycin-binding protein / FKBP / Peptidyl-prolyl cis-trans isomerase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / nucleus / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
ACETATE ION / Chem-KXX / FK506-binding protein 1A
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDeBouver, N.D. / Fox III, D. / Hoy, M.J. / Heitman, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mbio / Year: 2022
Title: Structure-Guided Synthesis of FK506 and FK520 Analogs with Increased Selectivity Exhibit In Vivo Therapeutic Efficacy against Cryptococcus.
Authors: Hoy, M.J. / Park, E. / Lee, H. / Lim, W.Y. / Cole, D.C. / DeBouver, N.D. / Bobay, B.G. / Pierce, P.G. / Fox 3rd, D. / Ciofani, M. / Juvvadi, P.R. / Steinbach, W. / Hong, J. / Heitman, J.
History
DepositionFeb 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: FK506-binding protein 1A
B: FK506-binding protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,47512
Polymers33,5372
Non-polymers2,93810
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.810, 91.470, 35.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FK506-binding protein 1A / FKBP / Peptidyl-prolyl cis-trans isomerase / PPIase / Rapamycin-binding protein


Mass: 16768.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: fpr1A, AFUA_6G12170 / Plasmid: AsfuA.18727.a.TM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4WLV6, peptidylprolyl isomerase

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Non-polymers , 7 types, 231 molecules

#2: Chemical ChemComp-KXX / (3S,4R,5S,8R,9E,12S,14S,15R,16S,18R,19R,22R,26aS)-8-ethyl-5,19-dihydroxy-3-{(1E)-1-[(1R,3R,4R)-4-hydroxy-3-methoxycyclohexyl]prop-1-en-2-yl}-14,16-dimethoxy-4,10,12,18-tetramethyl-5,6,8,11,12,13,14,15,16,17,18,19,24,25,26,26a-hexadecahydro-3H-15,19-epoxypyrido[2,1-c][1,4]oxazacyclotricosine-1,7,20,21(4H,23H)-tetrone / Ascomycin


Mass: 792.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C43H69NO12 / Feature type: SUBJECT OF INVESTIGATION / Comment: immunosuppressant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: [Barcode: 321029a1] [pin_id: kzq0-6] [collection: aps21idf 9/16/2021] [crystallization conditions: JCSG+ A1 - 0.2M lithium sulfate, pH 4.5, 50% (v/v) PEG 400] [cryo: direct]

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 16, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→40.75 Å / Num. obs: 32881 / % possible obs: 99.5 % / Redundancy: 4.846 % / Biso Wilson estimate: 19.13 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.075 / Χ2: 0.911 / Net I/σ(I): 13.78 / Num. measured all: 159338 / Scaling rejects: 9
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
1.7-1.744.9150.532.911535236523470.8820.59399.2
1.74-1.794.8790.4233.6111476237623520.9210.47499
1.79-1.844.9130.3374.4711050226722490.9510.37799.2
1.84-1.94.8650.255.7910785223022170.9730.2899.4
1.9-1.964.8930.2027.210480215721420.9810.22699.3
1.96-2.034.8740.1559.049997205920510.9870.17499.6
2.03-2.114.8670.13210.289860203820260.990.14899.4
2.11-2.194.8780.1111.979419194019310.9930.12399.5
2.19-2.294.8680.09813.289059186518610.9930.1199.8
2.29-2.44.8780.08714.938713179217860.9940.09899.7
2.4-2.534.880.07916.128310170717030.9950.08999.8
2.53-2.694.8610.06918.377817161416080.9950.07799.6
2.69-2.874.8520.06220.447361152115170.9960.06999.7
2.87-3.14.8320.05323.36881142714240.9970.05999.8
3.1-3.44.8190.04726.556400133113280.9970.05399.8
3.4-3.84.7870.04528.695725119811960.9970.05199.8
3.8-4.394.7520.04230.255127108010790.9970.04799.9
4.39-5.384.6670.04231.242709219150.9960.04799.3
5.38-7.64.5830.04329.5133237337250.9970.04998.9
7.6-40.754.1270.04429.3217504414240.9960.05196.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20-4438refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HWC

5hwc


Resolution: 1.7→40.75 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1921 1988 6.05 %
Rwork0.1683 30884 -
obs0.1697 32872 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.93 Å2 / Biso mean: 25.707 Å2 / Biso min: 12.96 Å2
Refinement stepCycle: final / Resolution: 1.7→40.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 194 227 2217
Biso mean--29.03 39.69 -
Num. residues----238
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 (%)
1.7-1.740.28491440.23642124226899
1.74-1.790.21931390.22342183232299
1.79-1.840.22821300.21042155228599
1.84-1.90.23971480.19292179232799
1.9-1.970.19041390.17392174231399
1.97-2.050.21371370.15762177231499
2.05-2.140.18091430.1612185232899
2.14-2.250.18871460.16421972343100
2.25-2.40.2031400.16121922332100
2.4-2.580.19151370.160322142351100
2.58-2.840.17631420.169822242366100
2.84-3.250.2251420.174422492391100
3.25-4.10.17861470.14922642411100
4.1-40.750.16411540.1662367252199
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)
15.70165.6289-5.965.5673-6.04359.33060.1893-0.4407-0.26120.8208-0.23110.56060.3802-0.44330.06330.2717-0.03990.12890.2114-0.00910.39376.33116.344823.51
22.4276-1.46913.96329.1093-0.97926.8341-0.0254-0.02080.28560.35050.0406-0.431-0.13180.2464-0.05940.1747-0.02620.04410.2092-0.01590.224618.825717.144719.3433
35.44840.4025-2.68542.1253-0.41032.81170.05040.18130.1073-0.1136-0.03840.12840.0396-0.0129-0.00820.14780.0057-0.040.1107-0.00220.113215.17987.94811.5868
45.70130.98311.2625.0059-1.95828.15490.15170.3997-0.4417-0.39110.07470.06380.6131-0.2686-0.20190.1520.04120.00640.1351-0.05590.196116.57340.549510.1234
59.0138-1.7162-2.98132.16460.31461.28750.0628-0.02750.0081-0.0055-0.0057-0.0431-0.01450.064-0.03680.1409-0.0145-0.01130.1334-0.02940.110123.72849.144414.2341
67.59925.6898-2.63387.709-3.24592.9869-0.22690.5540.1686-0.40760.36480.64570.266-0.3004-0.13770.1560.0051-0.0230.1434-0.01470.148710.11135.845212.5765
72.1373.0288-0.58524.3855-1.49854.1515-0.10960.4936-0.7273-0.1890.0627-0.30520.47640.00960.01050.2842-0.00960.05010.1825-0.04870.193237.0665-25.31738.9168
87.0717-4.3448-1.63127.29532.34414.82530.0106-0.48450.02010.87440.0716-0.39760.36540.1161-0.07790.2968-0.026-0.06270.2220.02630.180445.3836-18.400121.9913
96.30772.58424.69893.527-0.0166.6608-0.09950.341-0.1443-0.29620.266-0.2053-0.29990.3926-0.16010.1283-0.01980.0440.1356-0.01530.135941.1598-11.61547.7554
102.41111.59192.26523.06131.12332.3723-0.40810.7659-0.1282-0.67750.4166-0.2710.02640.1793-0.03670.2795-0.05050.0790.2695-0.03750.16139.2733-10.4916-0.3885
115.98536.335-6.11816.9967-6.60456.31930.0855-0.21130.44670.19940.00290.0131-0.18950.1637-0.13080.1729-0.0038-0.00720.22060.00110.196943.4613-4.833612.3354
127.4431-1.2552-1.63112.009-3.21567.1401-0.0745-0.77110.6440.5944-0.08320.1934-0.4966-0.55280.07250.23180.00020.03750.1757-0.06010.132732.7512-9.913818.1765
137.8931-3.43252.28143.65521.54324.2773-0.013-0.0588-0.03190.1780.0798-0.1710.08330.0823-0.03790.1724-0.03450.02010.09530.02530.150639.6878-18.73913.6576
148.88770.13580.93857.0634-5.42379.504-0.1342-0.08260.2832-0.1110.02650.1818-0.1913-0.37110.10130.1196-0.0072-0.02450.1324-0.04680.121425.2152-13.06056.0844
154.75181.10515.98141.58111.25957.55160.01530.2775-0.26-0.10540.0834-0.11550.12630.2499-0.06370.1746-0.02610.02580.1462-0.00280.113736.757-14.92516.7045
165.7048-1.0634-4.27652.7492-0.35523.77890.1055-1.01760.82730.8235-0.3324-0.3299-0.19390.7080.30290.3227-0.0231-0.01980.3514-0.04440.316950.963-10.042921.6858
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 20 )A15 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 38 )A21 - 38
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 68 )A39 - 68
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 86 )A69 - 86
5X-RAY DIFFRACTION5chain 'A' and (resid 87 through 126 )A87 - 126
6X-RAY DIFFRACTION6chain 'A' and (resid 127 through 141 )A127 - 141
7X-RAY DIFFRACTION7chain 'B' and (resid 28 through 38 )B28 - 38
8X-RAY DIFFRACTION8chain 'B' and (resid 39 through 50 )B39 - 50
9X-RAY DIFFRACTION9chain 'B' and (resid 51 through 60 )B51 - 60
10X-RAY DIFFRACTION10chain 'B' and (resid 61 through 72 )B61 - 72
11X-RAY DIFFRACTION11chain 'B' and (resid 73 through 79 )B73 - 79
12X-RAY DIFFRACTION12chain 'B' and (resid 80 through 86 )B80 - 86
13X-RAY DIFFRACTION13chain 'B' and (resid 87 through 106 )B87 - 106
14X-RAY DIFFRACTION14chain 'B' and (resid 107 through 120 )B107 - 120
15X-RAY DIFFRACTION15chain 'B' and (resid 121 through 136 )B121 - 136
16X-RAY DIFFRACTION16chain 'B' and (resid 137 through 141 )B137 - 141

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