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- PDB-7a73: Crystal structure of the two-domain cyclophilinA from Anabaena sp. -

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Basic information

Entry
Database: PDB / ID: 7a73
TitleCrystal structure of the two-domain cyclophilinA from Anabaena sp.
ComponentsAlr5059 protein
KeywordsPLANT PROTEIN / immunophilin
Function / homology
Function and homology information


thylakoid / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / metal ion binding
Similarity search - Function
: / Peptidyl-prolyl cis-trans isomerase CYP38-like, PsbQ-like domain / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, E. coli cyclophilin A-like / PsbQ-like domain superfamily / 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
peptidylprolyl isomerase
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsYadav, S. / Schleiff, E. / Yildiz, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)DFG SCHL585/7-2) Germany
CitationJournal: To Be Published
Title: The two-domain cyclophilin family protein anaCyp40 of Anabaena sp. regulates photosystem assembly and phycobilisome association
Authors: Yadav, S. / Schleiff, E. / Yildiz, O.
History
DepositionAug 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

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Assembly

Deposited unit
A: Alr5059 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3752
Polymers41,3351
Non-polymers401
Water10,611589
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-11 kcal/mol
Surface area17070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.120, 103.060, 44.170
Angle α, β, γ (deg.)90.000, 114.740, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Alr5059 protein


Mass: 41335.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: alr5059 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YM80
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.06 Å3/Da / Density % sol: 40.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 200mM ammonium citrate 20% PEG 3350 10% Morpheus additive screen

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2018
RadiationMonochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.14→37.38 Å / Num. obs: 115078 / % possible obs: 94.99 % / Redundancy: 19.8 % / Biso Wilson estimate: 14.78 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.04 / Rrim(I) all: 0.2 / Net I/σ(I): 8.1
Reflection shellResolution: 1.14→1.18 Å / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 11028 / CC1/2: 0.98 / Rpim(I) all: 1 / Rrim(I) all: 1 / % possible all: 91.14

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
DIALSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3rfy

3rfy


Resolution: 1.14→37.38 Å / SU ML: 0.1231 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 21.8212
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1981 11031 4.85 %
Rwork0.1791 216475 -
obs0.1801 115074 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.12 Å2
Refinement stepCycle: LAST / Resolution: 1.14→37.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 1 589 3198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712654
X-RAY DIFFRACTIONf_angle_d1.10363597
X-RAY DIFFRACTIONf_chiral_restr0.0796409
X-RAY DIFFRACTIONf_plane_restr0.0077474
X-RAY DIFFRACTIONf_dihedral_angle_d14.3678362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.150.29583840.29616778X-RAY DIFFRACTION89.79
1.15-1.170.283560.28116902X-RAY DIFFRACTION90.22
1.17-1.180.25343780.25876885X-RAY DIFFRACTION90.37
1.18-1.20.2893670.25386877X-RAY DIFFRACTION91.15
1.2-1.210.25393250.24497010X-RAY DIFFRACTION91.2
1.21-1.230.23533080.23237004X-RAY DIFFRACTION92.25
1.23-1.250.24763910.23557071X-RAY DIFFRACTION91.67
1.25-1.260.23493570.23026970X-RAY DIFFRACTION92.56
1.26-1.280.24123630.23247074X-RAY DIFFRACTION92.01
1.28-1.30.27213500.23097104X-RAY DIFFRACTION93.29
1.3-1.330.23843630.21637083X-RAY DIFFRACTION93.06
1.33-1.350.22363920.21287115X-RAY DIFFRACTION94.11
1.35-1.380.22453240.20997212X-RAY DIFFRACTION93.91
1.38-1.410.22663790.21197179X-RAY DIFFRACTION94.46
1.41-1.440.23513450.20857306X-RAY DIFFRACTION94.78
1.44-1.470.22313550.20427201X-RAY DIFFRACTION94.79
1.47-1.510.21693450.19747232X-RAY DIFFRACTION95.22
1.51-1.550.19353600.19227282X-RAY DIFFRACTION95.76
1.55-1.590.21533640.19017419X-RAY DIFFRACTION95.79
1.59-1.640.21913340.18957379X-RAY DIFFRACTION95.99
1.64-1.70.21244180.19547272X-RAY DIFFRACTION96.33
1.7-1.770.21843200.19587392X-RAY DIFFRACTION96.68
1.77-1.850.22613280.20237431X-RAY DIFFRACTION96.89
1.85-1.950.21094090.19597359X-RAY DIFFRACTION97.17
1.95-2.070.21784310.19147380X-RAY DIFFRACTION97.7
2.07-2.230.20213810.18067466X-RAY DIFFRACTION97.82
2.23-2.460.18683710.18017534X-RAY DIFFRACTION98.32
2.46-2.810.2123860.17737480X-RAY DIFFRACTION98.57
2.81-3.540.1813950.15637536X-RAY DIFFRACTION99.09
3.54-37.380.15144520.13147542X-RAY DIFFRACTION99.5
Refinement TLS params.Method: refined / Origin x: 33.3983170096 Å / Origin y: 39.4622726279 Å / Origin z: 44.3890157532 Å
111213212223313233
T0.0651080765559 Å20.0153928791145 Å20.000401509073383 Å2-0.129604978507 Å2-0.00842378850809 Å2--0.0943281615405 Å2
L0.580995704465 °2-0.0633033909461 °20.106958313177 °2-1.19764042788 °20.433299962421 °2--0.793026895199 °2
S-0.0308628078768 Å °-0.0704242081517 Å °0.0585056220524 Å °0.0361850230216 Å °-0.0136051989367 Å °-0.00761494503303 Å °-0.0493041344482 Å °-0.049542192491 Å °0.037260868063 Å °
Refinement TLS groupSelection details: (chain A and resseq 42:375)

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