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- PDB-4xre: Crystal structure of Gnk2 complexed with mannose -

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Basic information

Entry
Database: PDB / ID: 4xre
TitleCrystal structure of Gnk2 complexed with mannose
ComponentsAntifungal protein ginkbilobin-2
KeywordsANTIFUNGAL PROTEIN / C-X8-C-X2-C MOTIF / ANTIFUNGAL ACTIVITY / LECTIN
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
alpha-D-mannopyranose / Antifungal protein ginkbilobin-2
Similarity search - Component
Biological speciesGinkgo biloba (maidenhair tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.597 Å
AuthorsMiyakawa, T. / Hatano, K. / Miyauchi, Y. / Suwa, Y. / Sawano, Y. / Tanokura, M.
CitationJournal: Plant Physiol. / Year: 2014
Title: A secreted protein with plant-specific cysteine-rich motif functions as a mannose-binding lectin that exhibits antifungal activity.
Authors: Miyakawa, T. / Hatano, K. / Miyauchi, Y. / Suwa, Y. / Sawano, Y. / Tanokura, M.
History
DepositionJan 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site ..._chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antifungal protein ginkbilobin-2
B: Antifungal protein ginkbilobin-2
C: Antifungal protein ginkbilobin-2
D: Antifungal protein ginkbilobin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5696
Polymers47,2094
Non-polymers3602
Water2,702150
1
A: Antifungal protein ginkbilobin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9822
Polymers11,8021
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5400 Å2
MethodPISA
2
B: Antifungal protein ginkbilobin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9822
Polymers11,8021
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint3 kcal/mol
Surface area5420 Å2
MethodPISA
3
C: Antifungal protein ginkbilobin-2


Theoretical massNumber of molelcules
Total (without water)11,8021
Polymers11,8021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5430 Å2
MethodPISA
4
D: Antifungal protein ginkbilobin-2


Theoretical massNumber of molelcules
Total (without water)11,8021
Polymers11,8021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.400, 143.400, 143.400
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-311-

HOH

21B-304-

HOH

31B-309-

HOH

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Components

#1: Protein
Antifungal protein ginkbilobin-2 /


Mass: 11802.254 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ginkgo biloba (maidenhair tree) / Gene: GNK2 / Production host: Escherichia coli (E. coli) / References: UniProt: A4ZDL6
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 5.2 Å3/Da / Density % sol: 76.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28% PEG MME 2000, 0.1M TRIS-HCL, 0.2M AMMONIUM SULFATE
PH range: 7.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.68
11K, H, -L20.32
ReflectionResolution: 2.597→20 Å / Num. obs: 30598 / % possible obs: 99.9 % / Redundancy: 21.5 % / Rsym value: 0.089 / Net I/σ(I): 74.7
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 20.2 % / Mean I/σ(I) obs: 9.9 / Rsym value: 0.491 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A2E

3a2e


Resolution: 2.597→19.886 Å / Cross valid method: THROUGHOUT / σ(F): 0.01 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2885 1496 5.64 %RANDOM
Rwork0.2492 ---
obs0.2511 26530 87.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.478 Å2 / ksol: 0.296 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.597→19.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 24 150 3434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073344
X-RAY DIFFRACTIONf_angle_d1.1324502
X-RAY DIFFRACTIONf_dihedral_angle_d17.9251198
X-RAY DIFFRACTIONf_chiral_restr0.075506
X-RAY DIFFRACTIONf_plane_restr0.003600

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