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- PDB-10af: Crystal Structure of cyclophilin B, from Brugia malayi (K5H/S166A... -

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Basic information

Entry
Database: PDB / ID: 10af
TitleCrystal Structure of cyclophilin B, from Brugia malayi (K5H/S166A mutant)
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / cyclophilin B
Function / homology
Function and homology information


cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / cytoplasm
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: 1.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of cyclophilin B, from Brugia malayi (K5H/S166A mutant)
Authors: Dunham, J. / Lyons, R. / Xidas, P. / Meagher, L. / Meagher, A. / Seibold, S. / Lovell, S. / Battaile, K.P. / Bolen, R. / Mackey, K. / Stojanoff, V. / Pepenella, S. / Pinto, M.
History
DepositionJan 8, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9307
Polymers19,5351
Non-polymers3956
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.614, 57.614, 97.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 19535.158 Da / Num. of mol.: 1 / Mutation: K5H, S166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis)
Gene: Bm1_55850, Bm7143, BM_BM7143, BM_Bm7143 / Plasmid: BrmaA.01375.b.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0J9XUF2, peptidylprolyl isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Index A5: 2.0 M Ammonium sulfate, 0.1 M HEPES pH 7.5. BrmaA.01375.b.B1.PS01744 at 31 mg/mL. plate 14177 A4 drop 2, Puck: BNL-OEP 001-008, Cryo: 80% crystallant + 20% PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 14, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.25→48.63 Å / Num. obs: 50888 / % possible obs: 97.1 % / Redundancy: 17.1 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.013 / Rrim(I) all: 0.056 / Net I/σ(I): 28
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.456 / Num. unique obs: 1939 / CC1/2: 0.914 / Rpim(I) all: 0.172 / Rrim(I) all: 0.49 / % possible all: 76.4

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Processing

Software
NameVersionClassification
PHENIX(2.0_5896: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→44.39 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 10.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1348 2610 5.13 %
Rwork0.1148 --
obs0.1158 50833 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→44.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1288 0 18 245 1551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071390
X-RAY DIFFRACTIONf_angle_d11882
X-RAY DIFFRACTIONf_dihedral_angle_d15.133518
X-RAY DIFFRACTIONf_chiral_restr0.087193
X-RAY DIFFRACTIONf_plane_restr0.01254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.19981260.17711929X-RAY DIFFRACTION76
1.27-1.30.18451280.15412121X-RAY DIFFRACTION83
1.3-1.320.18721370.13832292X-RAY DIFFRACTION89
1.32-1.350.14761350.12032454X-RAY DIFFRACTION95
1.35-1.380.1541430.12568X-RAY DIFFRACTION99
1.38-1.420.12641140.09312598X-RAY DIFFRACTION100
1.42-1.460.12241560.09192583X-RAY DIFFRACTION100
1.46-1.50.11841480.09022574X-RAY DIFFRACTION100
1.5-1.550.13521370.09612620X-RAY DIFFRACTION100
1.55-1.60.11651670.10152578X-RAY DIFFRACTION100
1.6-1.670.1251310.09582585X-RAY DIFFRACTION100
1.67-1.740.11341380.09212629X-RAY DIFFRACTION100
1.74-1.840.11551340.09362608X-RAY DIFFRACTION100
1.84-1.950.12211300.09462630X-RAY DIFFRACTION100
1.95-2.10.11791360.10072623X-RAY DIFFRACTION100
2.1-2.310.13461260.10422667X-RAY DIFFRACTION100
2.31-2.650.14341130.11462678X-RAY DIFFRACTION100
2.65-3.330.15081230.13552717X-RAY DIFFRACTION100
3.34-44.390.13491880.13592769X-RAY DIFFRACTION100

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