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- PDB-4jp7: High resolution structure of a papaya barwin-like protein (crysta... -

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Basic information

Entry
Database: PDB / ID: 4jp7
TitleHigh resolution structure of a papaya barwin-like protein (crystal form 2)
Componentspapaya barwin-like protein
KeywordsUNKNOWN FUNCTION / pathogenesis-related protein of family 4 / barwin family / double-psi beta barrel
Function / homology
Function and homology information


RNA nuclease activity / defense response to fungus / defense response to bacterium
Similarity search - Function
Barwin domain / Barwin, conserved site / Pathogenesis-related protein-4 / Barwin family / Barwin domain signature 1. / Barwin domain signature 2. / Barwin domain profile. / RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases ...Barwin domain / Barwin, conserved site / Pathogenesis-related protein-4 / Barwin family / Barwin domain signature 1. / Barwin domain signature 2. / Barwin domain profile. / RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Papaya barwin-like protein
Similarity search - Component
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.05 Å
AuthorsWohlkonig, A. / Wintjens, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: High-resolution structure of a papaya plant-defence barwin-like protein solved by in-house sulfur-SAD phasing.
Authors: Huet, J. / Teinkela Mbosso, E.J. / Soror, S. / Meyer, F. / Looze, Y. / Wintjens, R. / Wohlkonig, A.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: papaya barwin-like protein
B: papaya barwin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4233
Polymers27,3302
Non-polymers921
Water3,819212
1
A: papaya barwin-like protein


Theoretical massNumber of molelcules
Total (without water)13,6651
Polymers13,6651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: papaya barwin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7572
Polymers13,6651
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.908, 56.964, 74.202
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein papaya barwin-like protein / papaya latex PR-4 protein


Mass: 13665.235 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: protein extracted from the latex of the plant Carica papaya
Source: (natural) Carica papaya (papaya) / References: UniProt: U5HK42*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 117408 / % possible obs: 94.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.98 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.25
Reflection shellResolution: 1→1.11 Å / Redundancy: 1.86 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 1.94 / % possible all: 92.8

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Processing

Software
NameVersionClassification
XDSdata scaling
SHELXSphasing
REFMAC5.7.0029refinement
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.05→39.53 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.977 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17011 5369 5 %RANDOM
Rwork0.14253 ---
obs0.14393 101997 98.51 %-
all-119633 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.857 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å20 Å2
2--0.03 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.05→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 6 212 2141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191988
X-RAY DIFFRACTIONr_bond_other_d0.0090.021784
X-RAY DIFFRACTIONr_angle_refined_deg2.0411.912703
X-RAY DIFFRACTIONr_angle_other_deg1.1033.0064060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9025242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.05122.70896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.62115294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1591516
X-RAY DIFFRACTIONr_chiral_restr0.1460.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022312
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02528
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr8.43633772
X-RAY DIFFRACTIONr_sphericity_free36.735583
X-RAY DIFFRACTIONr_sphericity_bonded22.49453842
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 387 -
Rwork0.215 7347 -
obs--96.8 %

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