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- PDB-7t9r: Crystal structure of Crocodile defensin CpoBD13:phosphatidic acid... -

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Basic information

Entry
Database: PDB / ID: 7t9r
TitleCrystal structure of Crocodile defensin CpoBD13:phosphatidic acid complex
ComponentsCpoBD13
KeywordsANTIMICROBIAL PROTEIN / Defensin / phosphatidic acid / complex / phospholipid
Function / homologyChem-PA6 / PHOSPHATE ION
Function and homology information
Biological speciesCrocodylus porosus (Australian saltwater crocodile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsKvansakul, M. / Williams, S. / Hulett, M.D.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP190103591 Australia
CitationJournal: Nat Commun / Year: 2023
Title: Crocodile defensin (CpoBD13) antifungal activity via pH-dependent phospholipid targeting and membrane disruption.
Authors: Williams, S.A. / Lay, F.T. / Bindra, G.K. / Banjara, S. / Poon, I.K.H. / Phan, T.K. / Kvansakul, M. / Hulett, M.D.
History
DepositionDec 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CpoBD13
B: CpoBD13
C: CpoBD13
D: CpoBD13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,03016
Polymers18,2334
Non-polymers1,79812
Water2,342130
1
A: CpoBD13
hetero molecules


  • defined by author&software
  • 5.47 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)5,4747
Polymers4,5581
Non-polymers9156
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CpoBD13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8422
Polymers4,5581
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CpoBD13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9994
Polymers4,5581
Non-polymers4413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CpoBD13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,7153
Polymers4,5581
Non-polymers1572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.056, 33.694, 36.642
Angle α, β, γ (deg.)90.093, 90.016, 90.014
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein/peptide
CpoBD13


Mass: 4558.144 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crocodylus porosus (Australian saltwater crocodile)
Production host: Komagataella pastoris (fungus)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PA6 / (R)-2-(FORMYLOXY)-3-(PHOSPHONOOXY)PROPYL PENTANOATE / PHOSPHATIDIC ACID / Phosphatidic acid


Mass: 284.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H17O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 1.83 Å3/Da / Density % sol: 32.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8M Sodium phosphate monobasic monohydrate, 0.8M Potassium phosphate monobasic, 0.1M sodium HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Aug 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.45→24.82 Å / Num. obs: 21344 / % possible obs: 99.9 % / Redundancy: 2.5 % / Biso Wilson estimate: 9.01 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.081 / Net I/σ(I): 6.5
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 2 / Num. unique obs: 1038 / CC1/2: 0.416 / % possible all: 90.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874+SVNrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7T9Q

7t9q


Resolution: 1.45→24.78 Å / SU ML: 0.1533 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.5849
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2151 916 4.31 %
Rwork0.1941 20351 -
obs0.195 21267 92.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.84 Å2
Refinement stepCycle: LAST / Resolution: 1.45→24.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 109 130 1503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621409
X-RAY DIFFRACTIONf_angle_d1.06371880
X-RAY DIFFRACTIONf_chiral_restr0.06160
X-RAY DIFFRACTIONf_plane_restr0.0038242
X-RAY DIFFRACTIONf_dihedral_angle_d17.1261503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.530.26521330.23672854X-RAY DIFFRACTION91.35
1.53-1.620.2661080.22192892X-RAY DIFFRACTION91.74
1.62-1.750.21291380.20822865X-RAY DIFFRACTION91.89
1.75-1.920.22761060.19772970X-RAY DIFFRACTION93.33
1.92-2.20.2231570.17872917X-RAY DIFFRACTION94.47
2.2-2.770.24381460.18782932X-RAY DIFFRACTION93.44
2.77-24.780.17341280.1852921X-RAY DIFFRACTION92.99

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