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- PDB-1pbk: HOMOLOGOUS DOMAIN OF HUMAN FKBP25 -

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Basic information

Entry
Database: PDB / ID: 1pbk
TitleHOMOLOGOUS DOMAIN OF HUMAN FKBP25
ComponentsFKBP25
KeywordsISOMERASE / FKBP12 HOMOLOGOUS DOMAIN OF HFKBP25
Function / homology
Function and homology information


FK506 binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / signaling receptor activity / RNA binding / nucleus
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase FKBP3 / FKBP3, basic tilted helix bundle domain / Basic tilted helix bundle domain / 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
RAPAMYCIN IMMUNOSUPPRESSANT DRUG / Peptidyl-prolyl cis-trans isomerase FKBP3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsLiang, J. / Hung, D.T. / Schreiber, S.L. / Clardy, J.
Citation
Journal: J.Am.Chem.Soc. / Year: 1996
Title: Structure of the human 25 kDa FK506 binding protein complexed with rapamycin.
Authors: Liang, J. / Hung, D.T. / Schreiber, S.L. / Clardy, J.
#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. / Karplus, P.A. / Schreiber, S.L. / Clardy, J.
History
DepositionSep 1, 1995Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: FKBP25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8742
Polymers12,9601
Non-polymers9141
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.000, 86.000, 55.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein FKBP25 / FKBP25 C-TERMINAL DOMAIN / EC 5.2.1.8


Mass: 12959.964 Da / Num. of mol.: 1
Fragment: FKBP12 HOMOLOGOUS DOMAIN, RESIDUES PRO 109 - ASP 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21(DE3) / Gene: HUMAN HIPPOCAMPAL CDNA LIBRARY / Plasmid: PGEX-3X
Gene (production host): HUMAN HIPPOCAMPAL CDNA LIBRARY (CLONTECH, PALO ALTO,CA)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) (NOVAGEN) / References: UniProt: Q00688
#2: Chemical ChemComp-RAP / RAPAMYCIN IMMUNOSUPPRESSANT DRUG / Sirolimus


Mass: 914.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H79NO13 / Comment: immunosuppressant, antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRECOMBINANT HFKBP25 IS AN UNSTABLE PROTEIN AND DEGRADED RAPIDLY FOLLOWING THE PURIFICATION. WITH ...RECOMBINANT HFKBP25 IS AN UNSTABLE PROTEIN AND DEGRADED RAPIDLY FOLLOWING THE PURIFICATION. WITH TIME, ONLY A MIXTURE OF FRAGMENTS WITH MOLECULAR WEIGHTS RANGING FROM 13.7KDA TO 15KDA (MASS RESULT) COULD BE IDENTIFIED IN THE ORIGINAL FKBP25 SAMPLE. HOWEVER, THE HETEROGENEOUS SAMPLE OF THE FRAGMENT FKBP25 COULD BE CRYSTALLIZED AFTER COMPLEXING IT WITH RAPAMYCIN (KD=0.9 NM) AND THE ELECTRON DENSITY IS COMPOSED OF RESIDUES FROM PRO 109 TO ASP 224. RESIDUES FROM GLN 150 TO ALA 159 ARE COMPLETELY DISORDERED; THEREFORE THE MODEL OF THIS REGION IS ONLY RESTRICTED BY THE DYNAMICS FORCE FIELD AND HAS RELATIVELY HIGH THERMAL FACTORS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.96 Å3/Da / Density % sol: 63 %
Crystal grow
*PLUS
pH: 8.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130-35 %(w/v)ammonium sulfate1reservoir
2100 mMHEPES1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Dec 28, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→8 Å / Num. obs: 7539 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.065
Reflection
*PLUS
Lowest resolution: 100 Å / Num. obs: 7520 / % possible obs: 98.1 % / Num. measured all: 24730
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 99.4 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.5→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.243 -5 %
Rwork0.185 --
obs0.185 7539 99 %
Displacement parametersBiso mean: 21.9 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms913 0 65 50 1028
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg2.89
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.29
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.906
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 7334 / Rfactor obs: 0.191 / Rfactor Rfree: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.88
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.29
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.906

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