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- PDB-1y0o: crystal structure of reduced AtFKBP13 -

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Basic information

Entry
Database: PDB / ID: 1y0o
Titlecrystal structure of reduced AtFKBP13
ComponentsFKBP-type peptidyl-prolyl cis-trans isomerase 3
KeywordsISOMERASE / Reduced AtFKBP13 / FK-506 binding protein
Function / homology
Function and homology information


thylakoid lumen / chloroplast thylakoid lumen / plastid / chloroplast / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity
Similarity search - Function
Photosynthetic NDH subunit of lumenal location 4-like / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase FKBP13, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsGayathri, G. / Swaminathan, K.
Citation
Journal: to be published
Title: Crystal structure of reduced AtFKBP13
Authors: Gopalan, G. / Swaminthan, K. / Luan, S. / Battaile, K.P.
#1: Journal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: Structural analysis uncovers a role for redox in regulating FKBP13, an immunophilin of the chloroplast thylakoid lumen
Authors: Gopalan, G. / He, Z. / Balmer, Y. / Romano, P. / Gupta, R. / Heroux, A. / Buchanan, B.B. / Swaminathan, K. / Luan, S.
History
DepositionNov 15, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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

Downloads & links

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Assembly

Deposited unit
A: FKBP-type peptidyl-prolyl cis-trans isomerase 3
B: FKBP-type peptidyl-prolyl cis-trans isomerase 3
C: FKBP-type peptidyl-prolyl cis-trans isomerase 3
D: FKBP-type peptidyl-prolyl cis-trans isomerase 3
E: FKBP-type peptidyl-prolyl cis-trans isomerase 3


Theoretical massNumber of molelcules
Total (without water)68,0435
Polymers68,0435
Non-polymers00
Water5,639313
1
A: FKBP-type peptidyl-prolyl cis-trans isomerase 3


Theoretical massNumber of molelcules
Total (without water)13,6091
Polymers13,6091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: FKBP-type peptidyl-prolyl cis-trans isomerase 3


Theoretical massNumber of molelcules
Total (without water)13,6091
Polymers13,6091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: FKBP-type peptidyl-prolyl cis-trans isomerase 3


Theoretical massNumber of molelcules
Total (without water)13,6091
Polymers13,6091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: FKBP-type peptidyl-prolyl cis-trans isomerase 3


Theoretical massNumber of molelcules
Total (without water)13,6091
Polymers13,6091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: FKBP-type peptidyl-prolyl cis-trans isomerase 3


Theoretical massNumber of molelcules
Total (without water)13,6091
Polymers13,6091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
B: FKBP-type peptidyl-prolyl cis-trans isomerase 3

B: FKBP-type peptidyl-prolyl cis-trans isomerase 3

A: FKBP-type peptidyl-prolyl cis-trans isomerase 3
D: FKBP-type peptidyl-prolyl cis-trans isomerase 3

A: FKBP-type peptidyl-prolyl cis-trans isomerase 3
D: FKBP-type peptidyl-prolyl cis-trans isomerase 3

C: FKBP-type peptidyl-prolyl cis-trans isomerase 3
E: FKBP-type peptidyl-prolyl cis-trans isomerase 3

C: FKBP-type peptidyl-prolyl cis-trans isomerase 3
E: FKBP-type peptidyl-prolyl cis-trans isomerase 3


Theoretical massNumber of molelcules
Total (without water)136,08610
Polymers136,08610
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
crystal symmetry operation6_654-x+3/2,-y+1/2,z-1/21
crystal symmetry operation7_645-x+3/2,y-1/2,-z+1/21
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_545x+1/2,y-1/2,z1
crystal symmetry operation8_555x+1/2,-y+1/2,-z1
Buried area18680 Å2
ΔGint-111 kcal/mol
Surface area47660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.898, 125.753, 119.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
FKBP-type peptidyl-prolyl cis-trans isomerase 3 / AtFKBP13 / PPIase / Rotamase / FK506 binding protein 1


Mass: 13608.647 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AtFKBP13 / Plasmid: PGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)LYS-S / References: UniProt: Q9SCY2, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.450949 Å3/Da / Density % sol: 50 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97879 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 13, 2004
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978791
20.9791
ReflectionResolution: 1.89→99 Å / Num. obs: 54269 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.08 / Net I/σ(I): -3
Reflection shellResolution: 1.89→2 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.621 / % possible all: 98.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
CNS1.1refinement
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U79

1u79


Resolution: 1.89→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 327978.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4568 10.1 %RANDOM
Rwork0.203 ---
all-53841 --
obs-45249 84.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 87.6493 Å2 / ksol: 0.493847 e/Å3
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--2.51 Å20 Å2
3----2.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.132 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.89→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 0 0 313 4943
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it1.611.5
X-RAY DIFFRACTIONc_mcangle_it2.632
X-RAY DIFFRACTIONc_scbond_it2.532
X-RAY DIFFRACTIONc_scangle_it3.832.5
LS refinement shellResolution: 1.89→2 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 462 10 %
Rwork0.21 4167 -
obs--51.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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