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- PDB-9w8p: Isomerase at 260K -

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Basic information

Entry
Database: PDB / ID: 9w8p
TitleIsomerase at 260K
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP1A
KeywordsISOMERASE / Immunophilin
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 / regulation of amyloid precursor protein catabolic process / terminal cisterna / ryanodine receptor complex / signaling receptor inhibitor activity / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / FK506 binding / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / regulation of ryanodine-sensitive calcium-release channel activity / Calcineurin activates NFAT / regulation of immune response / heart morphogenesis / supramolecular fiber organization / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / sarcoplasmic reticulum membrane / T cell activation / sarcoplasmic reticulum / protein maturation / peptidylprolyl isomerase / calcium channel regulator activity / peptidyl-prolyl cis-trans isomerase activity / negative regulation of transforming growth factor beta receptor signaling pathway / SARS-CoV-1 activates/modulates innate immune responses / Z disc / protein folding / regulation of protein localization / protein refolding / amyloid fibril formation / Potential therapeutics for SARS / transmembrane transporter binding / positive regulation of canonical NF-kappaB signal transduction / membrane / cytosol / cytoplasm
Similarity search - Function
: / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGuven, O. / DeMirci, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Isomerase at 260K
Authors: Guven, O. / DeMirci, H.
History
DepositionAug 7, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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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 FKBP1A
B: Peptidyl-prolyl cis-trans isomerase FKBP1A


Theoretical massNumber of molelcules
Total (without water)23,9352
Polymers23,9352
Non-polymers00
Water2,414134
1
A: Peptidyl-prolyl cis-trans isomerase FKBP1A


Theoretical massNumber of molelcules
Total (without water)11,9681
Polymers11,9681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase FKBP1A


Theoretical massNumber of molelcules
Total (without water)11,9681
Polymers11,9681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.380, 36.344, 55.467
Angle α, β, γ (deg.)90.00, 95.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-88-

HIS

21A-229-

HOH

31B-221-

HOH

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP1A


Mass: 11967.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1A
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P62942
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.14 Å3/Da / Density % sol: 42.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: NaCl, Ammonium Sulfate, TRIS

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Data collection

DiffractionMean temperature: 260 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Oct 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→18.39 Å / Num. obs: 13924 / % possible obs: 96.73 % / Redundancy: 1.9 % / CC1/2: 0.97 / Net I/σ(I): 27.33
Reflection shellResolution: 2→2.071 Å / Num. unique obs: 1294 / CC1/2: 0.989

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
CrysalisPro1.171.42.35adata reduction
CrysalisPro1.171.42.35adata scaling
PHENIX1.20.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→18.39 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 30.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2463 1354 10.01 %
Rwork0.2172 --
obs0.2202 13533 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→18.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 0 134 1814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041716
X-RAY DIFFRACTIONf_angle_d0.7042314
X-RAY DIFFRACTIONf_dihedral_angle_d11.344652
X-RAY DIFFRACTIONf_chiral_restr0.048246
X-RAY DIFFRACTIONf_plane_restr0.005304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.30331300.23031164X-RAY DIFFRACTION95
2.07-2.150.28421310.21691190X-RAY DIFFRACTION95
2.15-2.250.2461360.2171216X-RAY DIFFRACTION97
2.25-2.370.27841340.21391203X-RAY DIFFRACTION97
2.37-2.520.25871320.22331194X-RAY DIFFRACTION97
2.52-2.710.29241360.24551228X-RAY DIFFRACTION97
2.71-2.980.29551380.25391240X-RAY DIFFRACTION99
2.98-3.410.23551370.22881228X-RAY DIFFRACTION97
3.41-4.290.20261380.19911246X-RAY DIFFRACTION98
4.3-18.390.20681420.18951270X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.1321-1.5533-1.99725.09782.4364.8861-0.6243-0.6532-0.15971.00150.51510.20020.75810.20430.03750.21-0.03870.02750.20510.02960.1995-19.5068-20.248310.0944
23.13791.0501-1.51750.793-0.76315.0132-0.34750.3342-0.5353-0.0589-0.11260.34060.12260.05140.04040.08280.0011-0.03480.1615-0.03070.2008-27.8394-15.0815-3.0476
32.1457-0.10340.35642.0386-0.10781.9826-0.0384-0.00580.14580.1212-0.0533-0.0281-0.07230.16640.00470.1138-0.00210.02570.07580.00360.1039-12.5825-11.831.7694
43.8916-1.81570.62371.4806-0.47110.42820.01190.09330.00450.0533-0.084-0.051-0.03770.04130.03010.0681-0.001-0.00120.04280.00460.0821-13.9064-18.8255.2603
52.25321.51820.4691.7173-0.65081.33760.69250.25490.37-0.48560.456-0.9487-1.75851.08220.041-1.5516-0.84430.2829-0.14610.12860.48762.6552-15.04774.282
61.926-0.68520.52631.7445-0.09820.7785-0.0156-0.02910.1080.0767-0.1072-0.0179-0.15780.07660.09390.089-0.01940.03520.0960.0360.0717-12.9426-13.93994.5133
73.9499-0.611-1.81734.64342.32335.6802-0.4777-0.9025-0.67961.25210.5009-0.12040.683-0.2458-0.04740.3487-0.0554-0.02790.35850.09980.2563-22.4301-4.365837.5033
82.29070.13720.04360.533-0.44041.72570.07680.34-0.1334-0.1566-0.09230.24410.0777-0.1663-0.07190.12740.0098-0.00430.1377-0.03390.1874-24.22853.468527.5932
92.73160.486-0.27631.00821.11871.8923-0.1979-0.70780.64371.04140.1674-0.2659-0.15890.4904-0.16350.4249-0.04850.00630.5072-0.01460.3408-10.4737.429437.3952
103.87290.0444-0.65251.6122-0.87562.22170.0870.3196-0.074-0.1085-0.1919-0.1086-0.0755-0.00190.03740.19890.0173-00.18630.02230.113-17.56951.416824.3037
114.1123-1.5720.54551.4449-0.18140.98790.0657-0.396-0.19920.0742-0.02160.10660.0239-0.00950.02070.1424-0.0461-0.00560.19790.01050.1265-16.7883-2.911532.7804
120.7093-0.68030.29853.01473.23175.33710.11770.1073-0.0123-0.36460.2506-0.458-0.95751.1092-0.01950.2406-0.0929-0.03980.33240.01820.2169-0.42740.836931.7964
132.6311-0.8520.74642.0091-0.00711.6493-0.0418-0.13730.26860.1699-0.1233-0.0665-0.15840.20130.04180.1534-0.01550.02450.21040.04080.1429-15.80532.014532.0771
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 9 )
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 21 )
3X-RAY DIFFRACTION3chain 'A' and (resid 22 through 66 )
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 86 )
5X-RAY DIFFRACTION5chain 'A' and (resid 87 through 91 )
6X-RAY DIFFRACTION6chain 'A' and (resid 92 through 108 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 9 )
8X-RAY DIFFRACTION8chain 'B' and (resid 10 through 31 )
9X-RAY DIFFRACTION9chain 'B' and (resid 32 through 43 )
10X-RAY DIFFRACTION10chain 'B' and (resid 44 through 66 )
11X-RAY DIFFRACTION11chain 'B' and (resid 67 through 86 )
12X-RAY DIFFRACTION12chain 'B' and (resid 87 through 91 )
13X-RAY DIFFRACTION13chain 'B' and (resid 92 through 108 )

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