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- PDB-8x6p: Isomerase Protein -

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Basic information

Entry
Database: PDB / ID: 8x6p
TitleIsomerase Protein
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP1A
KeywordsISOMERASE / Proline
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 / 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 / calcium channel regulator activity / protein maturation / T cell activation / peptidyl-prolyl cis-trans isomerase activity / sarcoplasmic reticulum / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / 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 / Z disc / SARS-CoV-1 activates/modulates innate immune responses / 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 domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / 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: 1.05 Å
AuthorsGuven, O. / Demirci, H.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other government Turkey
CitationJournal: To Be Published
Title: Isomerase Protein
Authors: Guven, O. / Demirci, H.
History
DepositionNov 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1284
Polymers23,9352
Non-polymers1922
Water5,873326
1
A: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules

A: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1284
Polymers23,9352
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1470 Å2
ΔGint-48 kcal/mol
Surface area11210 Å2
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules

B: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1284
Polymers23,9352
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1460 Å2
ΔGint-47 kcal/mol
Surface area11100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.850, 36.124, 54.499
Angle α, β, γ (deg.)90.00, 95.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21B-201-

SO4

31A-373-

HOH

41B-373-

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 (E. coli) / References: UniProt: P62942
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 40.95 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: NaCl, Ammonium Sulfate, TRIS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-Arc 150 / Detector: PIXEL / Date: Apr 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.05→53.9 Å / Num. obs: 101614 / % possible obs: 94.5 % / Redundancy: 3.7 % / CC1/2: 0.999 / CC star: 0.995 / Net I/σ(I): 16.16
Reflection shellResolution: 1.05→1.08 Å / Num. unique obs: 6791 / CC1/2: 0.075 / CC star: 0.373

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→22.08 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 28.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2237 2000 2.48 %
Rwork0.205 --
obs0.2054 80574 87.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.05→22.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 10 326 2016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081830
X-RAY DIFFRACTIONf_angle_d1.1322489
X-RAY DIFFRACTIONf_dihedral_angle_d13.129703
X-RAY DIFFRACTIONf_chiral_restr0.093260
X-RAY DIFFRACTIONf_plane_restr0.009336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.080.40291130.42484425X-RAY DIFFRACTION69
1.08-1.110.42891160.37294590X-RAY DIFFRACTION72
1.11-1.140.31531210.33214768X-RAY DIFFRACTION75
1.14-1.170.29341290.30525027X-RAY DIFFRACTION78
1.17-1.220.26531320.27265194X-RAY DIFFRACTION82
1.22-1.270.26191390.25575471X-RAY DIFFRACTION86
1.27-1.320.29911410.24145565X-RAY DIFFRACTION87
1.32-1.390.24521500.21455882X-RAY DIFFRACTION92
1.39-1.480.23511530.2025959X-RAY DIFFRACTION93
1.48-1.590.21821530.18756047X-RAY DIFFRACTION94
1.59-1.750.20231610.17666288X-RAY DIFFRACTION98
1.75-2.010.2181610.17086370X-RAY DIFFRACTION99
2.01-2.530.18941630.18296400X-RAY DIFFRACTION99
2.53-22.080.18641680.17326588X-RAY DIFFRACTION100
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)
12.885-1.1288-2.63195.12742.57914.1236-0.3315-0.3916-0.24610.41050.34530.08450.33070.2255-0.03450.1020.00270.01910.06820.01510.0623-19.0671-20.25819.9697
24.27170.2468-2.26231.0034-0.18235.6394-0.08030.2973-0.2018-0.14480.02140.13090.1594-0.06410.10870.06920.0039-0.01450.057-0.00570.0785-26.916-15.5425-3.7432
34.1551-1.24293.43811.8273-0.43773.2819-0.1109-0.04290.07850.04460.0959-0.0677-0.1838-0.00180.01150.065-0.01730.01380.06140.00130.0818-14.6312-8.76392.6474
44.8084-3.55543.17366.574-2.69116.2178-0.2117-0.07730.26680.4311-0.1134-0.2357-0.2530.1390.31310.091-0.0244-0.01260.0933-0.01170.0971-7.1821-8.81939.62
52.90250.26191.09622.33673.32625.5247-0.17910.16250.2442-0.72460.272-0.2149-0.69370.2694-0.10050.115-0.0126-0.00780.07670.00770.0987-14.2225-5.918-3.417
68.1936-0.22194.75354.6327-1.57857.90260.07390.5777-0.0338-0.3531-0.0534-0.00710.12130.4358-0.0060.07380.01130.01130.10460.00340.0739-12.0664-16.8288-7.0808
76.4596-1.7281-0.74360.70690.05161.0537-0.04880.1278-0.13110.0304-0.01810.03790.00850.00440.06450.0722-0.00480.00640.04170.00380.0638-19.7937-17.48590.9036
82.05761.6751-0.42662.05760.26041.1367-0.233-0.16530.14040.3050.1285-0.076-0.00750.12410.01260.07410.00860.0030.07090.00270.0511-16.8369-15.9729.2288
97.8366-2.27780.94230.6716-0.12172.03030.05410.0055-0.4273-0.0202-0.02560.00410.0998-0.0215-0.02350.0712-0.00090.00010.0667-0.00030.0797-5.6621-24.03063.695
106.55451.4492-1.82071.8377-0.80373.10670.0547-0.2645-0.06360.0567-0.0353-0.01440.02870.1149-0.02790.06490.00850.00010.0851-0.00280.05880.5383-18.88146.9123
114.6115-2.24382.46931.7677-1.35882.8718-0.03990.02220.0930.01760.05230.0649-0.18470.00090.0130.0649-0.01410.00590.03090.00650.0774-18.8151-9.66341.8973
123.16-0.9277-0.51691.67550.05113.05840.0077-0.08-0.25570.02820.01510.15620.0644-0.0058-0.02370.0637-0.03210.01370.0381-0.01040.0989-26.8169-0.477430.049
133.5241-0.91441.39573.3392-0.1683.1115-0.0903-0.16220.11090.19120.007-0.172-0.07030.13750.05890.0609-0.0160.010.09540.01710.0755-14.20326.803729.4245
144.02-0.9419-0.08060.64640.26470.1671-0.0142-0.2754-0.10170.06930.01970.00950.01560.0453-0.00460.0847-0.00510.00140.09820.01710.0537-15.1819-0.558230.9641
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 30 )
4X-RAY DIFFRACTION4chain 'A' and (resid 31 through 43 )
5X-RAY DIFFRACTION5chain 'A' and (resid 44 through 50 )
6X-RAY DIFFRACTION6chain 'A' and (resid 51 through 57 )
7X-RAY DIFFRACTION7chain 'A' and (resid 58 through 71 )
8X-RAY DIFFRACTION8chain 'A' and (resid 72 through 77 )
9X-RAY DIFFRACTION9chain 'A' and (resid 78 through 86 )
10X-RAY DIFFRACTION10chain 'A' and (resid 87 through 97 )
11X-RAY DIFFRACTION11chain 'A' and (resid 98 through 108 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 21 )
13X-RAY DIFFRACTION13chain 'B' and (resid 22 through 57 )
14X-RAY DIFFRACTION14chain 'B' and (resid 58 through 108 )

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