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- PDB-6lkb: Crystal Structure of the peptidylprolyl isomerase domain of Arabi... -

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Basic information

Entry
Database: PDB / ID: 6lkb
TitleCrystal Structure of the peptidylprolyl isomerase domain of Arabidopsis thaliana CYP71.
ComponentsPeptidyl-prolyl cis-trans isomerase CYP71
KeywordsISOMERASE / PPIASE / CYP71 / cyclophilin / chromatin remodelling
Function / homology
Function and homology information


: / carpel development / sepal formation / meristem structural organization / leaf formation / regulation of root meristem growth / leaf shaping / stamen development / regulation of flower development / leaf vascular tissue pattern formation ...: / carpel development / sepal formation / meristem structural organization / leaf formation / regulation of root meristem growth / leaf shaping / stamen development / regulation of flower development / leaf vascular tissue pattern formation / protein peptidyl-prolyl isomerization / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / histone binding / chromatin binding / nucleus
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / : / 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 / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat ...Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / : / 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 / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / PHOSPHATE ION / Peptidyl-prolyl cis-trans isomerase CYP71
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.651 Å
AuthorsLakhanpal, S. / Jobichen, C. / Swaminathan, K.
CitationJournal: Febs Lett. / Year: 2021
Title: Structural and functional analyses of the PPIase domain of Arabidopsis thaliana CYP71 reveal its catalytic activity toward histone H3.
Authors: Lakhanpal, S. / Fan, J.S. / Luan, S. / Swaminathan, K.
History
DepositionDec 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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: Peptidyl-prolyl cis-trans isomerase CYP71
B: Peptidyl-prolyl cis-trans isomerase CYP71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8549
Polymers36,2992
Non-polymers5557
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-12 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.954, 60.928, 127.044
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Peptidyl-prolyl cis-trans isomerase CYP71 / PPIase CYP71 / Cyclophilin of 71 kDa / Cyclophilin-71


Mass: 18149.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CYP71, At3g44600, F14L2.150 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8W4D0, peptidylprolyl isomerase

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Non-polymers , 5 types, 321 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Co
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.25 Å3/Da / Density % sol: 62.15 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES (pH 6.5), 1.5M ammonium sulphate, 0.02M cobalt chloride hexahydrate

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→30.48 Å / Num. obs: 57328 / % possible obs: 99 % / Redundancy: 4 % / Biso Wilson estimate: 19.41 Å2 / CC1/2: 0.85 / Net I/σ(I): 5
Reflection shellResolution: 1.65→1.69 Å / Num. unique obs: 3778 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2a2n

2a2n


Resolution: 1.651→30.477 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2128 2005 3.5 %
Rwork0.189 55233 -
obs0.1899 57238 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.61 Å2 / Biso mean: 24.4805 Å2 / Biso min: 13.97 Å2
Refinement stepCycle: final / Resolution: 1.651→30.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 32 314 2888
Biso mean--44.18 34.49 -
Num. residues----320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.651-1.6920.30291330.3063364593
1.692-1.73780.29981420.2802388999
1.7378-1.78890.28811430.24283911100
1.7889-1.84660.25151430.2313911100
1.8466-1.91260.2671440.22193900100
1.9126-1.98920.19741370.19983916100
1.9892-2.07970.23421420.18573928100
2.0797-2.18930.21091440.18083966100
2.1893-2.32640.2491400.1823964100
2.3264-2.5060.20661440.18583936100
2.506-2.7580.20151440.18413995100
2.758-3.15670.19561470.18344000100
3.1567-3.97580.16811500.16224051100
3.9758-30.470.21541520.18214221100

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