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- PDB-1d7h: FKBP COMPLEXED WITH DMSO -

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Basic information

Entry
Database: PDB / ID: 1d7h
TitleFKBP COMPLEXED WITH DMSO
ComponentsPROTEIN (FK506-BINDING PROTEIN)
KeywordsISOMERASE / IMMUNOPHILIN / DMSO / FKBP
Function / homology
Function and homology information


macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / I-SMAD binding ...macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / I-SMAD binding / signaling receptor inhibitor activity / regulation of amyloid precursor protein catabolic process / terminal cisterna / ryanodine receptor complex / : / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / FK506 binding / channel regulator activity / protein peptidyl-prolyl isomerization / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / regulation of immune response / heart morphogenesis / supramolecular fiber organization / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / peptidyl-prolyl cis-trans isomerase activity / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / T cell activation / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / negative regulation of transforming growth factor beta receptor signaling pathway / calcium ion transmembrane transport / Z disc / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of protein binding / protein folding / regulation of protein localization / protein refolding / positive regulation of canonical NF-kappaB signal transduction / amyloid fibril formation / transmembrane transporter binding / Potential therapeutics for SARS / membrane / cytosol / cytoplasm
Similarity search - Function
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
AMMONIUM ION / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBurkhard, P. / Taylor, P. / Walkinshaw, M.D.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: X-ray structures of small ligand-FKBP complexes provide an estimate for hydrophobic interaction energies.
Authors: Burkhard, P. / Taylor, P. / Walkinshaw, M.D.
#1: Journal: J.Am.Chem.Soc. / Year: 1991
Title: Atomic Structure of the Rapamycin Human Immunophilin FKBP-12 Complex
Authors: Van Duyne, G.D. / Standaert, R.F. / Schreiber, S.L. / Clardy, J.
History
DepositionOct 18, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Derived calculations / Refinement description / Category: software / struct_conf / struct_conf_type / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (FK506-BINDING PROTEIN)
B: PROTEIN (FK506-BINDING PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0578
Polymers23,6732
Non-polymers3846
Water2,702150
1
A: PROTEIN (FK506-BINDING PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0294
Polymers11,8371
Non-polymers1923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (FK506-BINDING PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0294
Polymers11,8371
Non-polymers1923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: PROTEIN (FK506-BINDING PROTEIN)
hetero molecules

A: PROTEIN (FK506-BINDING PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0578
Polymers23,6732
Non-polymers3846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area1980 Å2
ΔGint-40 kcal/mol
Surface area10570 Å2
MethodPISA, PQS
4
B: PROTEIN (FK506-BINDING PROTEIN)
hetero molecules

B: PROTEIN (FK506-BINDING PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0578
Polymers23,6732
Non-polymers3846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,y,-z-11
MethodPQS
Unit cell
Length a, b, c (Å)102.800, 36.450, 56.000
Angle α, β, γ (deg.)90.00, 96.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-401-

NH4

21A-403-

SO4

31B-402-

NH4

41B-404-

SO4

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Components

#1: Protein PROTEIN (FK506-BINDING PROTEIN) / FKBP-12


Mass: 11836.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62942, peptidylprolyl isomerase
#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 56 % SAT. AMMONIUM SULFATE 5 % DMSO, 100 MM TRIS (PH 8.0), VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.6 mMprotein1drop
2340 mMDMSO1drop
350 mMTris-HCl1drop
428 %(w/v)ammonium sulfate1drop
71 MTris-HCl1reservoir
5ammonium sulfate1reservoir
6DMSO1reservoir

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS / Detector: AREA DETECTOR / Date: Jan 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 14868 / % possible obs: 97 % / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
MADNESSdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cross valid method: A POSTERIORI / σ(F): 3 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.273 488 3 %RANDOM
Rwork0.213 ---
obs0.213 12997 97 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 20 150 1834
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.627
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Type: x_dihedral_angle_deg / Dev ideal: 27.221

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