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- PDB-4nnr: FKBP13-FK506 Complex -

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Basic information

Entry
Database: PDB / ID: 4nnr
TitleFKBP13-FK506 Complex
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP2
Keywordsisomerase/isomerase inhibitor / loop crossing / immunophilin / FKBP / peptidyl-prolyl isomerase / Isomerase / isomerase-isomerase inhibitor complex
Function / homology
Function and homology information


FK506 binding / chaperone-mediated protein folding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase FKBP2/11 / 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
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / Peptidyl-prolyl cis-trans isomerase FKBP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsSchultz, L.W. / Martin, P.K. / Liang, J. / Schreiber, S.L. / Clardy, J.
CitationJournal: J.Am.Chem.Soc. / Year: 1994
Title: Atomic structure of the Immunophilin FKBP13-FK506 Complex: Insights into the Composite Binding Surface for Calcineurin
Authors: Schultz, L.W. / Martin, P.K. / Liang, J. / Schreiber, S.L. / Clardy, J.
History
DepositionNov 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP2
B: Peptidyl-prolyl cis-trans isomerase FKBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9554
Polymers31,3472
Non-polymers1,6082
Water2,018112
1
A: Peptidyl-prolyl cis-trans isomerase FKBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4772
Polymers15,6731
Non-polymers8041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase FKBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4772
Polymers15,6731
Non-polymers8041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.260, 74.060, 39.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP2 / PPIase FKBP2 / 13 kDa FK506-binding protein / 13 kDa FKBP / FKBP-13 / FK506-binding protein 2 / ...PPIase FKBP2 / 13 kDa FK506-binding protein / 13 kDa FKBP / FKBP-13 / FK506-binding protein 2 / FKBP-2 / Immunophilin FKBP13 / Rotamase


Mass: 15673.282 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP2, FKBP13 / Production host: Escherichia coli (E. coli) / References: UniProt: P26885, peptidylprolyl isomerase
#2: Chemical ChemComp-FK5 / 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / K506


Mass: 804.018 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H69NO12 / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.72 Å3/Da / Density % sol: 28.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: VAPOR DIFFUSION, HANGING DROP, pH 7, temperature 298K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: UCSD MARK II / Detector: AREA DETECTOR / Date: Jul 17, 1993
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.98→18 Å / Num. all: 13559 / Num. obs: 13559 / % possible obs: 87.05 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.98-2.13153
2.13-2.34194
2.35-2.68194
2.69-3.38195

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Processing

Software
NameClassification
SDMSdata collection
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→17.3 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.221 680 5% phenix
Rwork0.159 --
obs0.159 13559 -
all-13559 -
Refinement stepCycle: LAST / Resolution: 1.98→17.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1574 0 114 112 1800
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONo_angle_deg1.653
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.98-2.130.2904930.2302X-RAY DIFFRACTION152353
2.13-2.350.27631370.2012X-RAY DIFFRACTION274293
2.35-2.680.25491390.1842X-RAY DIFFRACTION275794
2.68-3.380.22831530.1637X-RAY DIFFRACTION283595
3.38-17.30.16591580.1168X-RAY DIFFRACTION302298

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