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- PDB-1u79: Crystal structure of AtFKBP13 -

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Basic information

Entry
Database: PDB / ID: 1u79
TitleCrystal structure of AtFKBP13
ComponentsFKBP-type peptidyl-prolyl cis-trans isomerase 3
KeywordsISOMERASE / tFKBP13 / 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: 1.85 Å
AuthorsGopalan, G. / Swaminathan, K.
Citation
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. / Buchanan, B.B. / Swaminathan, K. / Luan, S.
#1: Journal: Proc.Natl.Acad.Sci.Usa / Year: 2002
Title: A chloroplast FKBP interacts with and affects the accumulation of Rieske subunit of cytochrome bf complex
Authors: Gupta, R. / Mould, R.M. / He, Z. / Luan, S.
History
DepositionAug 3, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 28, 2004Provider: 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
Water8,341463
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_554-x+1/2,-y+1/2,z-1/21
crystal symmetry operation7_555-x+1/2,y+1/2,-z+1/21
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
crystal symmetry operation5_455x-1/2,y+1/2,z1
crystal symmetry operation8_455x-1/2,-y+1/2,-z1
Buried area18870 Å2
ΔGint-96 kcal/mol
Surface area47180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.026, 126.606, 119.404
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.: 463 / 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: 2.8 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 8-11% PEG 550MME, 2.5M ammonium sulfate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.97879 / Wavelength: 0.979 Å
DetectorType: BRANDEIS / Detector: CCD / Date: Mar 5, 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: 1.8→99 Å / Num. obs: 44839 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): -3
Reflection shellResolution: 1.8→1.95 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.22 / Rsym value: 0.25 / % possible all: 43.7

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Processing

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

1yat


Resolution: 1.85→8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 307661.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.232 4530 10.1 %RANDOM
Rwork0.212 ---
obs0.212 44839 78.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 93.7859 Å2 / ksol: 0.547019 e/Å3
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 0 0 463 5093
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.462
X-RAY DIFFRACTIONc_scangle_it3.652.5
LS refinement shellResolution: 1.85→1.96 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.251 403 9.8 %
Rwork0.223 3701 -
obs--43.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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