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- PDB-7dki: Silk worm FKBP, isoform-1 -

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Basic information

Entry
Database: PDB / ID: 7dki
TitleSilk worm FKBP, isoform-1
ComponentsPeptidylprolyl isomerase
KeywordsISOMERASE / FK506 binding / slikworm
Function / homology: / 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 / sarcoplasmic reticulum membrane / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / peptidylprolyl isomerase
Function and homology information
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYuchi, Z. / Nayak, B.C.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31972287 China
Ministry of Science and Technology (MoST, China)2017YFD0201400, 2017YFD0201403 China
National Natural Science Foundation of China (NSFC)2019B2-0017 China
CitationJournal: To Be Published
Title: Silk worm FKBP, isoform-1
Authors: Yuchi, Z. / Nayak, B.C.
History
DepositionNov 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidylprolyl isomerase
B: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1374
Polymers23,9532
Non-polymers1842
Water3,567198
1
A: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0692
Polymers11,9761
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5680 Å2
MethodPISA
2
B: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0692
Polymers11,9761
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-1 kcal/mol
Surface area5590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.409, 52.409, 77.109
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Peptidylprolyl isomerase / FK-506 binding protein / Isoform 1


Mass: 11976.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: 732917 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1HQ55, peptidylprolyl isomerase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.55 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1M sodium citrate tribasic dihydrate, 0.1M sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 193.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 16023 / % possible obs: 100 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.05 / Rrim(I) all: 0.111 / Χ2: 0.472 / Net I/σ(I): 4 / Num. measured all: 74774
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.20.4458020.8230.2860.5310.4599.8
2.03-2.073.50.387950.8490.2350.4490.455100
2.07-2.113.70.447810.8530.2610.5130.476100
2.11-2.153.90.3718030.9060.2140.430.458100
2.15-2.24.10.3078160.9470.170.3520.459100
2.2-2.254.20.317690.9330.170.3540.476100
2.25-2.314.20.2877990.9360.1570.3280.45899.9
2.31-2.374.70.2778410.950.1420.3120.461100
2.37-2.445.10.2697890.9560.1320.30.463100
2.44-2.525.20.2468230.9620.1190.2740.468100
2.52-2.615.10.2097680.9750.1020.2330.439100
2.61-2.7150.1838030.9820.0910.2050.445100
2.71-2.844.80.1618180.9830.0820.1810.451100
2.84-2.995.20.1247770.9880.060.1380.46100
2.99-3.175.30.0958180.9950.0450.1060.464100
3.17-3.425.20.0737900.9970.0350.0810.483100
3.42-3.764.90.068200.9970.030.0670.523100
3.76-4.315.40.0527970.9980.0250.0580.518100
4.31-5.435.10.0478030.9980.0230.0530.522100
5.43-505.20.058110.9980.0250.0560.485100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3247refinement
PDB_EXTRACT3.25data extraction
PHENIXmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1fkb

1fkb


Resolution: 2→45.388 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.2 / Phase error: 20.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1978 1512 9.92 %
Rwork0.1547 13729 -
obs0.1592 15241 95.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.93 Å2 / Biso mean: 22.7056 Å2 / Biso min: 11.49 Å2
Refinement stepCycle: final / Resolution: 2→45.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 28 198 1856
Biso mean--26.91 29.96 -
Num. residues----214
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.06440.24231280.1865117790
2.0644-2.13820.2361310.1832117390
2.1382-2.22380.24631430.1642118992
2.2238-2.3250.21331440.1598122793
2.325-2.44760.21141320.1587123594
2.4476-2.60090.21361340.1646128796
2.6009-2.80170.2191460.1779123296
2.8017-3.08360.23781370.165131698
3.0836-3.52970.22421350.1561128999
3.5297-4.44640.15911410.12821307100
4.4464-45.3880.14231410.1414129799

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