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- PDB-4j4o: Crystal structure of FK506 binding domain of plasmodium VIVAX FKB... -

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Basic information

Entry
Database: PDB / ID: 4j4o
TitleCrystal structure of FK506 binding domain of plasmodium VIVAX FKBP35 in complex with D44
Components70 kDa peptidylprolyl isomerase, putative
KeywordsISOMERASE/ISOMERASE INHIBITOR / D44 / FKBP35 / FK506 / ISOMERASE-ISOMERASE INHIBITOR complex
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 domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat ...: / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / 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 / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-D44 / peptidylprolyl isomerase
Similarity search - Component
Biological speciesPlasmodium vivax SaI-1 (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsSreekanth, R. / Harikishore, A. / Yoon, H.S.
CitationJournal: Sci Rep / Year: 2013
Title: Small molecule Plasmodium FKBP35 inhibitor as a potential antimalaria agent.
Authors: Harikishore, A. / Niang, M. / Rajan, S. / Preiser, P.R. / Yoon, H.S.
History
DepositionFeb 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 70 kDa peptidylprolyl isomerase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6526
Polymers13,9721
Non-polymers6815
Water3,603200
1
A: 70 kDa peptidylprolyl isomerase, putative
hetero molecules

A: 70 kDa peptidylprolyl isomerase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,30512
Polymers27,9432
Non-polymers1,36210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area3480 Å2
ΔGint-9 kcal/mol
Surface area11560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.259, 68.259, 74.116
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-205-

GOL

21A-354-

HOH

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Components

#1: Protein 70 kDa peptidylprolyl isomerase, putative


Mass: 13971.687 Da / Num. of mol.: 1 / Fragment: FK506 BINDING DOMAIN, UNP RESIDUES 1-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax SaI-1 (eukaryote) / Strain: Salvador I / Gene: PVX_101260 / Plasmid: PETSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5K8X6, peptidylprolyl isomerase
#2: Chemical ChemComp-D44 / N-(2-ethylphenyl)-2-(3H-imidazo[4,5-b]pyridin-2-ylsulfanyl)acetamide


Mass: 312.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16N4OS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 3.57 Å3/Da / Density % sol: 65.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 3.0M AMMONIUM SULPHATE, 0.1M BICINE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 26, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.73→33.5 Å / Num. obs: 21268 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 10.32 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 22.4
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 7.93 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 6.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IHZ

3ihz


Resolution: 1.73→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.561 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1088 5.2 %RANDOM
Rwork0.177 ---
obs0.179 20015 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.73→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 46 200 1189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221031
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9991382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5085129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30725.20848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86715185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.665155
X-RAY DIFFRACTIONr_chiral_restr0.1090.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02773
X-RAY DIFFRACTIONr_mcbond_it0.9451.5608
X-RAY DIFFRACTIONr_mcangle_it1.7112980
X-RAY DIFFRACTIONr_scbond_it2.6073423
X-RAY DIFFRACTIONr_scangle_it4.4914.5398
LS refinement shellResolution: 1.73→1.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 85 -
Rwork0.271 1431 -
obs--98.31 %

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