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- PDB-4ihr: Crystal structure of recombinant kirola (Act d 11) -

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Basic information

Entry
Database: PDB / ID: 4ihr
TitleCrystal structure of recombinant kirola (Act d 11)
ComponentsKirola
KeywordsALLERGEN / MLP/RRP family / PR-10 related
Function / homology
Function and homology information


activation of immune response / defense response
Similarity search - Function
: / Pathogenesis-related protein Bet v I family / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Kirola
Similarity search - Component
Biological speciesActinidia deliciosa (kiwifruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsOsinski, T. / Majorek, K.A. / Ciardiello, M.A. / Chruszcz, M. / Minor, W.
CitationJournal: Mol.Immunol. / Year: 2013
Title: Structural and bioinformatic analysis of the kiwifruit allergen Act d 11, a member of the family of ripening-related proteins.
Authors: Chruszcz, M. / Ciardiello, M.A. / Osinski, T. / Majorek, K.A. / Giangrieco, I. / Font, J. / Breiteneder, H. / Thalassinos, K. / Minor, W.
History
DepositionDec 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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
Revision 1.2Sep 20, 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

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Assembly

Deposited unit
A: Kirola
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7669
Polymers17,6951
Non-polymers718
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.060, 72.060, 113.585
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-208-

CL

21A-338-

HOH

31A-340-

HOH

41A-351-

HOH

51A-375-

HOH

61A-458-

HOH

71A-474-

HOH

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Components

#1: Protein Kirola / Act d 11


Mass: 17695.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinidia deliciosa (kiwifruit) / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3) RIL / References: UniProt: P85524
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 6 / Source method: obtained synthetically
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.15 M citric acid, 0.35 M magnesium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9772 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 6, 2011
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 23683 / Num. obs: 23683 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 20.9 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 55.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 17.2 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1141 / Rsym value: 0.834 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4IGV

4igv


Resolution: 1.6→34.37 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.809 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.086 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2123 1152 5.1 %RANDOM
Rwork0.17518 ---
all0.17703 21426 --
obs0.17703 21426 95.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.937 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.02 Å2-0 Å2
2---0.02 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 8 175 1362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021235
X-RAY DIFFRACTIONr_bond_other_d0.0050.021177
X-RAY DIFFRACTIONr_angle_refined_deg1.8241.9571684
X-RAY DIFFRACTIONr_angle_other_deg0.86432717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2825.6653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03415224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.826152
X-RAY DIFFRACTIONr_chiral_restr0.1230.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021374
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02264
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 35 -
Rwork0.191 875 -
obs--53.19 %
Refinement TLS params.Method: refined / Origin x: -17.237 Å / Origin y: -23.501 Å / Origin z: -14.506 Å
111213212223313233
T0.0304 Å20.0054 Å2-0.0162 Å2-0.0845 Å20.0327 Å2--0.0317 Å2
L0.5783 °2-0.2203 °20.1489 °2-1.1515 °20.0798 °2--1.5494 °2
S-0.0036 Å °0.0036 Å °-0.0135 Å °0.0219 Å °-0.084 Å °-0.1252 Å °-0.0485 Å °0.1807 Å °0.0875 Å °

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