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- PDB-8cu5: Crystal Structure of Putative Cyclophilin B from Brugia malayi -

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Basic information

Entry
Database: PDB / ID: 8cu5
TitleCrystal Structure of Putative Cyclophilin B from Brugia malayi
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / SSGCID / peptidyl-prolyl cis-trans isomerase / rotamase / structural genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesBrugia malayi (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Crystal Structure of Putative Cyclophilin B from Brugia malayi
Authors: DeBouver, N.D. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMay 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 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: Peptidyl-prolyl cis-trans isomerase
B: Peptidyl-prolyl cis-trans isomerase
C: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,29113
Polymers64,5343
Non-polymers75710
Water9,458525
1
A: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7945
Polymers21,5111
Non-polymers2824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6693
Polymers21,5111
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8285
Polymers21,5111
Non-polymers3164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.220, 137.220, 143.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-492-

HOH

21B-606-

HOH

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase / PPIase


Mass: 21511.359 Da / Num. of mol.: 3 / Fragment: BrmaA.00538.a.B2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis)
Gene: SM7 / Plasmid: BrmaA.00538.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6YNZ2, peptidylprolyl isomerase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 52.92 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: [Target: BrmaA.00538.a.B2.PD38321 - 20.5 mg/mL] [Barcode: 302391h9] [Pin: eko9-16] [Crystallization: sparse screen - JCSG+ H9 -100 mM Bis-Tris pH 5.5, 200 mM Lithium sulfate, 25% (w/v) PEG ...Details: [Target: BrmaA.00538.a.B2.PD38321 - 20.5 mg/mL] [Barcode: 302391h9] [Pin: eko9-16] [Crystallization: sparse screen - JCSG+ H9 -100 mM Bis-Tris pH 5.5, 200 mM Lithium sulfate, 25% (w/v) PEG 3550, 14C, 0.4:0.4 drop ratio] [Cryo: 15% EG]

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 1, 2018 / Details: hybrid photon counting
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.85→48.51 Å / Num. obs: 58246 / % possible obs: 100 % / Redundancy: 9.503 % / Biso Wilson estimate: 27.75 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.046 / Χ2: 1.015 / Net I/σ(I): 31.91 / Num. measured all: 553484 / Scaling rejects: 168
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
1.85-1.99.480.6083.940108423242310.9310.643100
1.9-1.959.4160.4815.1939133416141560.9570.50999.9
1.95-2.019.4680.3516.6238211403740360.9770.371100
2.01-2.079.7460.2868.3838204392039200.9830.302100
2.07-2.149.7030.20411.3136938380938070.9910.21699.9
2.14-2.219.3980.1561434671369036890.9950.165100
2.21-2.299.4340.13617.1233435355035440.9960.14499.8
2.29-2.399.5910.11119.6432994344034400.9970.118100
2.39-2.499.7120.09223.3631983329332930.9980.097100
2.49-2.629.9060.07827.4331293315931590.9980.082100
2.62-2.769.5270.0635.0728648300730070.9990.063100
2.76-2.939.3430.04840.7126618284928490.9990.051100
2.93-3.139.5360.03851.71256152687268610.04100
3.13-3.389.5810.0364.56240002505250510.031100
3.38-3.79.5330.02577.45220872317231710.026100
3.7-4.148.9650.02380.62190062120212010.024100
4.14-4.789.3010.01992.06173841869186910.02100
4.78-5.859.6270.01990.23154131601160110.02100
5.85-8.279.0130.01888.84114291268126810.019100
8.27-48.518.430.01497.06631475774910.01598.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FRU

4fru


Resolution: 1.85→48.51 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1964 2023 3.48 %
Rwork0.1701 56192 -
obs0.1711 58215 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.05 Å2 / Biso mean: 35.5165 Å2 / Biso min: 17.73 Å2
Refinement stepCycle: final / Resolution: 1.85→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4236 0 44 533 4813
Biso mean--41.72 40.93 -
Num. residues----549
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.85-1.90.34151180.28439644082
1.9-1.950.26951210.246139984119
1.95-20.22111390.195839734112
2-2.070.21031340.172439724106
2.07-2.140.19631600.163439494109
2.14-2.230.22281250.17140114136
2.23-2.330.23421210.186539924113
2.33-2.450.22021360.192940134149
2.45-2.610.2171470.189439854132
2.61-2.810.24231590.185339984157
2.81-3.090.19951410.187140314172
3.09-3.540.18981840.160340074191
3.54-4.460.16571670.13440684235
4.46-48.510.1691710.158542314402
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)
15.91954.2722-1.54817.5451-2.50742.35610.08720.00620.11120.17640.03860.15110.10010.055-0.16830.23360.0332-0.01390.205-0.04090.1079-19.9128-20.536125.3283
25.7414.12561.39854.3361.80172.6078-0.1068-0.0374-0.023-0.0869-0.08280.05330.14280.00290.1980.23010.0641-0.01370.1125-0.00080.1232-20.791-22.61320.6137
36.729-2.6865-1.03282.7677-0.16171.9403-0.1432-0.01220.2398-0.14160.0963-0.0502-0.03480.09410.03870.2321-0.0143-0.01660.17-0.03450.1547-21.3565-11.978316.0207
44.04773.2022-0.02222.9106-0.78843.021-0.48240.6140.2238-1.37680.41170.4937-0.31220.18550.07480.55330.0137-0.02540.31980.02210.2516-23.0635-17.58646.2469
52.3478-0.35510.30022.73280.01451.89390.01030.01070.0066-0.1608-0.10480.4010.0626-0.22390.08250.25230.0139-0.0360.2041-0.05220.2087-32.3676-17.875619.2455
62.4078-0.73470.8794.627-4.34295.285-0.1855-0.09340.35130.1548-0.0539-0.2114-0.29180.03590.20630.2790.0034-0.06670.2037-0.07310.3377-21.4244-2.292322.5068
72.92390.5477-0.1563.3754-1.02120.58730.0619-0.3264-0.18980.2734-0.0637-0.15060.02270.061-0.01460.32680.0015-0.04420.2451-0.04150.1121-20.7541-22.385427.2655
84.2751-1.9779-0.95843.5114.0426.1556-0.1009-0.0668-0.05150.2315-0.0530.38450.18230.05720.0990.1694-0.02210.01260.16750.03280.1771-8.4994-13.691838.7326
92.56661.80461.44735.78973.29513.73490.09150.01730.0149-0.0923-0.15660.0283-0.05210.02730.06070.19150.0068-0.02270.18320.04190.1886-2.8392-11.747338.6361
103.16352.3356-2.23767.4374-5.16554.87840.1471-0.0802-0.3351-0.0646-0.2805-0.31760.12590.34050.15730.1654-0.0182-0.04040.2239-0.01840.24761.5933-22.44339.4633
113.56172.27612.0696.32942.26864.25470.20260.1883-0.25480.00630.0224-1.09530.30570.3411-0.26990.19280.0307-0.01570.30750.05820.39611.392-16.924141.1517
122.00820.24770.2192.5313-0.14731.42370.0988-0.2876-0.12580.3245-0.1042-0.1706-0.00430.04310.00370.2132-0.0356-0.03740.22020.03290.2085-1.8952-16.359950.2256
134.7988-5.9730.5188.5007-1.68063.02280.06290.0338-0.2843-0.147-0.01550.11080.37060.007-0.04070.2627-0.0403-0.05760.2017-0.05580.3193-4.6596-31.79639.6957
142.4519-1.426-1.48994.72880.84843.68370.1129-0.01160.0153-0.1549-0.10840.2244-0.1457-0.1310.00050.0758-0.0386-0.08390.1823-0.03470.1802-9.341-12.09738.2596
152.33890.7979-1.38276.9216-1.41775.8779-0.2395-0.81520.8271-0.3344-0.06750.9250.0998-0.90880.32090.26710.0898-0.0160.7406-0.39130.6244-42.885313.481838.3291
163.3226-1.3988-0.00873.91131.15010.5131-0.111-1.12230.7875-0.0248-0.09290.2774-0.0532-0.23110.11430.33320.0577-0.03040.5501-0.29930.5074-37.790112.434741.1847
170.90650.6670.66285.10453.66766.6957-0.0591-0.31910.8116-0.3086-0.2220.0849-0.34720.01340.33590.20310.0441-0.05020.3136-0.16730.5274-32.994912.403230.175
182.1348-0.26210.58493.69163.56013.7648-0.10720.18061.5731-0.46310.3461-1.4483-0.63611.8553-0.03770.4289-0.07370.10630.7177-0.14440.7343-23.592612.826129.5108
195.9224.39180.06519.1345-3.89176.2793-0.4923-0.66220.1016-0.07630.2045-1.07450.1570.66850.31290.30110.0809-0.04150.585-0.19450.4824-23.58967.326441.5814
209.4744-1.92273.77265.68370.43065.94040.0185-1.004-0.20.4353-0.07530.32450.5736-0.57850.10440.3263-0.02770.05790.4696-0.1350.3059-38.9234-0.125738.3667
210.1677-0.1545-0.14163.82891.20073.7503-0.0051-0.48940.04530.2687-0.13790.25340.184-0.02540.12340.23910.03380.01380.3492-0.09990.3211-36.0912.170233.7514
226.9665-4.325-6.47517.16563.78829.14770.32240.48240.6156-0.6274-0.34440.1279-0.7456-0.84040.11040.39910.1007-0.15130.3243-0.10240.4543-38.916113.328220.5401
230.98760.1209-1.14464.13791.88282.6953-0.063-0.62840.8480.2967-0.15810.9078-0.1657-0.5920.1370.31010.086-0.01380.759-0.29580.7556-44.38413.144840.4166
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 38 )A21 - 38
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 65 )A39 - 65
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 88 )A66 - 88
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 108 )A89 - 108
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 159 )A109 - 159
6X-RAY DIFFRACTION6chain 'A' and (resid 160 through 180 )A160 - 180
7X-RAY DIFFRACTION7chain 'A' and (resid 181 through 203 )A181 - 203
8X-RAY DIFFRACTION8chain 'B' and (resid 21 through 38 )B21 - 38
9X-RAY DIFFRACTION9chain 'B' and (resid 39 through 65 )B39 - 65
10X-RAY DIFFRACTION10chain 'B' and (resid 66 through 88 )B66 - 88
11X-RAY DIFFRACTION11chain 'B' and (resid 89 through 108 )B89 - 108
12X-RAY DIFFRACTION12chain 'B' and (resid 109 through 159 )B109 - 159
13X-RAY DIFFRACTION13chain 'B' and (resid 160 through 180 )B160 - 180
14X-RAY DIFFRACTION14chain 'B' and (resid 181 through 203 )B181 - 203
15X-RAY DIFFRACTION15chain 'C' and (resid 21 through 38 )C21 - 38
16X-RAY DIFFRACTION16chain 'C' and (resid 39 through 65 )C39 - 65
17X-RAY DIFFRACTION17chain 'C' and (resid 66 through 88 )C66 - 88
18X-RAY DIFFRACTION18chain 'C' and (resid 89 through 98 )C89 - 98
19X-RAY DIFFRACTION19chain 'C' and (resid 99 through 108 )C99 - 108
20X-RAY DIFFRACTION20chain 'C' and (resid 109 through 124 )C109 - 124
21X-RAY DIFFRACTION21chain 'C' and (resid 125 through 159 )C125 - 159
22X-RAY DIFFRACTION22chain 'C' and (resid 160 through 180 )C160 - 180
23X-RAY DIFFRACTION23chain 'C' and (resid 181 through 203 )C181 - 203

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