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- PDB-3a2e: Crystal structure of ginkbilobin-2, the novel antifungal protein ... -

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Basic information

Entry
Database: PDB / ID: 3a2e
TitleCrystal structure of ginkbilobin-2, the novel antifungal protein from Ginkgo biloba seeds
ComponentsGinkbilobin-2
KeywordsPLANT PROTEIN / DOMAIN 26 UNKNOWN FUNCTION (DUF26) / C-X8-C-X2-C MOTIF / ANTIFUNGAL PROTEIN / EMBRYO-ABUNDANT PROTEIN (EAP)
Function / homology
Function and homology information


induction of programmed cell death / aspartic-type endopeptidase inhibitor activity / D-mannose binding / defense response to fungus / actin binding / killing of cells of another organism / defense response to bacterium / extracellular space
Similarity search - Function
Gnk2 domain, C-X8-C-X2-C motif / Killer Toxin P4; Chain A / Gnk2-homologous domain / Gnk2-homologous domain superfamily / : / Salt stress response/antifungal / Gnk2-homologous domain profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Antifungal protein ginkbilobin-2
Similarity search - Component
Biological speciesGinkgo biloba (maidenhair tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.38 Å
AuthorsMiyakawa, T. / Miyazono, K. / Sawano, Y. / Hatano, K. / Tanokura, M.
CitationJournal: Proteins / Year: 2009
Title: Crystal structure of ginkbilobin-2 with homology to the extracellular domain of plant cysteine-rich receptor-like kinases
Authors: Miyakawa, T. / Miyazono, K. / Sawano, Y. / Hatano, K. / Tanokura, M.
History
DepositionMay 13, 2009Deposition site: PDBJ / Processing site: PDBJ
SupersessionJun 2, 2009ID: 2E79
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ginkbilobin-2
B: Ginkbilobin-2
C: Ginkbilobin-2
D: Ginkbilobin-2


Theoretical massNumber of molelcules
Total (without water)46,6844
Polymers46,6844
Non-polymers00
Water8,683482
1
A: Ginkbilobin-2


Theoretical massNumber of molelcules
Total (without water)11,6711
Polymers11,6711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ginkbilobin-2


Theoretical massNumber of molelcules
Total (without water)11,6711
Polymers11,6711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ginkbilobin-2


Theoretical massNumber of molelcules
Total (without water)11,6711
Polymers11,6711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ginkbilobin-2


Theoretical massNumber of molelcules
Total (without water)11,6711
Polymers11,6711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.169, 143.169, 143.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-267-

HOH

21A-388-

HOH

31D-376-

HOH

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Components

#1: Protein
Ginkbilobin-2


Mass: 11671.059 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ginkgo biloba (maidenhair tree) / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4ZDL6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
15.23832976.519234
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop6.621% polyacrylic acid 5100, 100 mM MES, 20 mM MgCl2, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2932vapor diffusion, sitting drop6.61.6 M ammonium sulfate, 12% dioxane, 100 mM MES, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
SYNCHROTRONPhoton Factory AR-NW12A20.97909, 0.97934, 0.96411
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDOct 28, 2006
ADSC QUANTUM 2102CCDDec 1, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979091
30.979341
40.964111
Reflection twinOperator: l,-k,h / Fraction: 0.485
ReflectionResolution: 2.38→50 Å / Num. obs: 39529 / % possible obs: 99.7 % / Redundancy: 15.2 % / Rsym value: 0.061 / Net I/σ(I): 61.2 / Num. measured all: 602150
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 8.2 / Rsym value: 0.375

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.38→43.17 Å / Occupancy max: 1 / Occupancy min: 0.98 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.09 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1981 5.02 %RANDOM
Rwork0.207 37489 --
obs0.208 39470 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 87.147 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 70.92 Å2 / Biso mean: 34.8 Å2 / Biso min: 25.03 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.38→43.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 0 482 3742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063320
X-RAY DIFFRACTIONf_angle_d1.0014468
X-RAY DIFFRACTIONf_chiral_restr0.071496
X-RAY DIFFRACTIONf_plane_restr0.004600
X-RAY DIFFRACTIONf_dihedral_angle_d17.981184
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.378-2.4190.273950.26118231918
2.419-2.4630.283770.24918831960
2.463-2.5110.283850.23718711956
2.511-2.5620.282830.23918931976
2.562-2.6180.273820.22318541936
2.618-2.6780.25880.22218671955
2.678-2.7450.2321070.22618601967
2.745-2.820.2281030.22418501953
2.82-2.9030.205930.21218701963
2.903-2.9960.255990.20218631962
2.996-3.1030.2081000.20718751975
3.103-3.2270.2221200.19618371957
3.227-3.3740.197980.19518751973
3.374-3.5520.2161360.18918401976
3.552-3.7750.1921150.18118561971
3.775-4.0660.179980.17518831981
4.066-4.4750.223940.17418971991
4.475-5.1210.246900.18618981988
5.121-6.4490.231080.22719142022
6.449-43.1740.3181100.26419802090

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