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- PDB-4iq2: P21 crystal form of FKBP12.6 -

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Basic information

Entry
Database: PDB / ID: 4iq2
TitleP21 crystal form of FKBP12.6
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP1B
KeywordsISOMERASE / FKBP12.6
Function / homology
Function and homology information


positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of release of sequestered calcium ion into cytosol / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / response to redox state / protein maturation by protein folding / 'de novo' protein folding ...positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of release of sequestered calcium ion into cytosol / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / response to redox state / protein maturation by protein folding / 'de novo' protein folding / negative regulation of heart rate / FK506 binding / positive regulation of axon regeneration / channel regulator activity / smooth muscle contraction / response to vitamin E / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / T cell proliferation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / release of sequestered calcium ion into cytosol / regulation of cytosolic calcium ion concentration / calcium channel complex / sarcoplasmic reticulum membrane / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium-mediated signaling / response to hydrogen peroxide / Stimuli-sensing channels / Z disc / positive regulation of cytosolic calcium ion concentration / protein refolding / transmembrane transporter binding / signaling receptor binding / 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
MALONIC ACID / Peptidyl-prolyl cis-trans isomerase FKBP1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChen, H. / Mustafi, S.M. / Li, H.M. / LeMaster, D.M. / Hernandez, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Crystal structure and conformational flexibility of the unligated FK506-binding protein FKBP12.6.
Authors: Chen, H. / Mustafi, S.M. / LeMaster, D.M. / Li, Z. / Heroux, A. / Li, H. / Hernandez, G.
History
DepositionJan 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Apr 29, 2015Group: Non-polymer description
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP1B
B: Peptidyl-prolyl cis-trans isomerase FKBP1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4513
Polymers23,3472
Non-polymers1041
Water4,342241
1
A: Peptidyl-prolyl cis-trans isomerase FKBP1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7772
Polymers11,6731
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase FKBP1B


Theoretical massNumber of molelcules
Total (without water)11,6731
Polymers11,6731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.061, 49.346, 50.980
Angle α, β, γ (deg.)90.00, 101.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP1B / PPIase FKBP1B / 12.6 kDa FK506-binding protein / 12.6 kDa FKBP / FKBP-12.6 / FK506-binding protein ...PPIase FKBP1B / 12.6 kDa FK506-binding protein / 12.6 kDa FKBP / FKBP-12.6 / FK506-binding protein 1B / FKBP-1B / Immunophilin FKBP12.6 / Rotamase / h-FKBP-12


Mass: 11673.307 Da / Num. of mol.: 2 / Mutation: C22V, C76I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1B, FKBP12.6, FKBP1L, FKBP9, OTK4 / Production host: Escherichia coli (E. coli) / References: UniProt: P68106, peptidylprolyl isomerase
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0 M malonic acid, pH 7.0, 4% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 2, 2012
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→38.232 Å / Num. all: 20138 / Num. obs: 20138 / % possible obs: 95.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 4.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1549 / Rsym value: 0.51 / % possible all: 77.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C9H

1c9h


Resolution: 1.7→38.232 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 2000 9.94 %RANDOM
Rwork0.2261 ---
obs0.2285 20126 95.77 %-
all-20138 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.081 Å2 / ksol: 0.419 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.4301 Å2-0 Å20.7531 Å2
2---2.9927 Å20 Å2
3----0.4374 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 7 241 1892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031682
X-RAY DIFFRACTIONf_angle_d0.8492267
X-RAY DIFFRACTIONf_dihedral_angle_d11.839642
X-RAY DIFFRACTIONf_chiral_restr0.056248
X-RAY DIFFRACTIONf_plane_restr0.003302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74260.45781090.4363987X-RAY DIFFRACTION75
1.7426-1.78970.40591330.40331212X-RAY DIFFRACTION90
1.7897-1.84240.41051430.35691289X-RAY DIFFRACTION96
1.8424-1.90180.34131420.33241286X-RAY DIFFRACTION96
1.9018-1.96980.35421440.3061310X-RAY DIFFRACTION97
1.9698-2.04870.33231450.2631317X-RAY DIFFRACTION97
2.0487-2.14190.26891430.24911298X-RAY DIFFRACTION97
2.1419-2.25480.26081460.22631318X-RAY DIFFRACTION98
2.2548-2.39610.24531460.22341322X-RAY DIFFRACTION98
2.3961-2.5810.24591480.22621336X-RAY DIFFRACTION98
2.581-2.84070.27071470.22581347X-RAY DIFFRACTION99
2.8407-3.25160.21181500.20511346X-RAY DIFFRACTION99
3.2516-4.09590.19641500.17051364X-RAY DIFFRACTION100
4.0959-38.2420.19341540.17841394X-RAY DIFFRACTION99

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