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- PDB-8z38: FK506 binding protein 1B (including FK506) -

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Basic information

Entry
Database: PDB / ID: 8z38
TitleFK506 binding protein 1B (including FK506)
Componentspeptidylprolyl isomerase
KeywordsPROTEIN BINDING / FK506 / FK506 binding protein 1B
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / 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
6-CARBOXYPIPERIDINE / peptidylprolyl isomerase
Similarity search - Component
Biological speciesPyricularia oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsLiu, X.H. / Zhao, W.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2023YFD1400202-3 China
CitationJournal: To Be Published
Title: High-resolution cocrystallized crystal structures of FK506 and FK506-binding proteins
Authors: Liu, X.H. / Zhao, W.H.
History
DepositionApr 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,1043
Polymers23,9752
Non-polymers1291
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-9 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.157, 59.382, 67.246
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein peptidylprolyl isomerase / FK506 binding protein 1B(including FK506)


Mass: 11987.425 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyricularia oryzae (rice blast fungus) / Gene: PoMZ_03707 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P7N8E2, peptidylprolyl isomerase
#2: Chemical ChemComp-CPI / 6-CARBOXYPIPERIDINE


Type: D-peptide linking / Mass: 129.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5, 1.4 M tri-Sodium Citrate dihydrate or 2.1 M DL-Malic Acid pH 7.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.17→42.65 Å / Num. obs: 10844 / % possible obs: 88.93 % / Redundancy: 5.6 % / Biso Wilson estimate: 26.41 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1712 / Rpim(I) all: 0.07119 / Rrim(I) all: 0.1866 / Net I/σ(I): 6.74
Reflection shellResolution: 2.17→2.248 Å / Rmerge(I) obs: 0.7258 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1114 / CC1/2: 0.758 / Rpim(I) all: 0.3117 / Rrim(I) all: 0.7951

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Processing

Software
NameVersionClassification
HKL-30007.21data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
HKL-30007.21data reduction
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→42.65 Å / SU ML: 0.2501 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.2621
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2586 522 4.82 %
Rwork0.1984 10319 -
obs0.2014 10841 88.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.64 Å2
Refinement stepCycle: LAST / Resolution: 2.17→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 9 76 1765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631721
X-RAY DIFFRACTIONf_angle_d0.82812329
X-RAY DIFFRACTIONf_chiral_restr0.0548258
X-RAY DIFFRACTIONf_plane_restr0.0058306
X-RAY DIFFRACTIONf_dihedral_angle_d13.2814631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.390.29881240.23832636X-RAY DIFFRACTION92.31
2.39-2.730.34211210.25382619X-RAY DIFFRACTION91.55
2.73-3.440.25011390.20132485X-RAY DIFFRACTION86.43
3.44-42.650.22521380.16522579X-RAY DIFFRACTION85.76

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