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- PDB-2haq: Crystal Structure of Cyclophilin A from Leishmania Donovani -

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Basic information

Entry
Database: PDB / ID: 2haq
TitleCrystal Structure of Cyclophilin A from Leishmania Donovani
ComponentsCyclophilin
KeywordsISOMERASE / CYCLOPHILIN / ROTAMASE / PROLINE / CIS-TRANS / PROTOZOA / LEISHMANIA / DONOVANI / KALA-AZAR.
Function / homology
Function and homology information


cyclosporin A binding / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / protein folding / intracellular membrane-bounded organelle / cytoplasm
Similarity search - Function
Cyclophilin-like / Cyclophilin / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsVenugopal, V. / Sen, B. / Datta, A.K. / Banerjee, R.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Structure of cyclophilin from Leishmania donovani at 1.97 A resolution.
Authors: Venugopal, V. / Sen, B. / Datta, A.K. / Banerjee, R.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Lack of Abundance of Cytoplasmic Cyclosporin A Bind Protein Renders Free Living Leishmania Donovani Resistant to Cyclosporin A
Authors: Dutta, M. / Delhi, P. / Sinha, K.M. / Banerjee, R. / Datta, A.K.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallisation and Preliminary X-Ray Analysis of Cyclophilin from Leishmania Donovani
Authors: Banerjee, R. / Dutta, M. / Sen, M. / Datta, A.K.
#3: Journal: Curr.Sci. / Year: 2004
Title: Crystal Structure of Cyclophilin from Leishmania Donovani at 3.5 A Resolution
Authors: Banerjee, R. / Dutta, M. / Sen, M. / Datta, A.K.
History
DepositionJun 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Aug 30, 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

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Assembly

Deposited unit
A: Cyclophilin


Theoretical massNumber of molelcules
Total (without water)19,0911
Polymers19,0911
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.590, 48.590, 141.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe protein is a monomer

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Components

#1: Protein Cyclophilin


Mass: 19090.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: CYP / Plasmid: pQE32 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9U9R3, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.3 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.01M TRIS, 7.5% PEG3350, 0.005M IMID 0.02% AZIDE, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE RESERVOIR CONTAINING 40% PEG3350 IN THE SAME BUFFER. PROTEIN CONCENTRATION: 10 MG/ML, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 8, 2004 / Details: OSMIC MAXFLUX CONFOCAL MULTILAY
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→14.93 Å / Num. all: 12644 / Num. obs: 12516 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.1 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 30.1
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 4.5 / % possible all: 86.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XO7.PDB

1xo7


Resolution: 1.97→14.93 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.197 735 6.1 %RANDOM
Rwork0.178 ---
obs0.178 12137 96.1 %-
all-12644 --
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.94 Å20 Å20 Å2
2--2.94 Å20 Å2
3----5.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-15 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.97→14.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 0 102 1376
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 1.97→2.09 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.239 120 6.6 %
Rwork0.221 1702 -
obs--89.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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