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- PDB-3psm: .98A crystal structure of a dimeric plant defensin SPE10 -

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Basic information

Entry
Database: PDB / ID: 3psm
Title.98A crystal structure of a dimeric plant defensin SPE10
ComponentsDefensin
KeywordsANTIMICROBIAL PROTEIN / dimer / defensin
Function / homology
Function and homology information


defense response to fungus / killing of cells of another organism
Similarity search - Function
Defensin, plant / Gamma-thionins family signature. / Gamma-thionin family / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPachyrhizus erosus (jicama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.98 Å
AuthorsZhou, H. / Song, X. / Gong, W.
CitationJournal: To be Published
Title: 0.98A crystal structure of a dimeric plant defensin SPE10
Authors: Zhou, H. / Song, X. / Gong, W.
History
DepositionDec 1, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 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

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Assembly

Deposited unit
A: Defensin
B: Defensin


Theoretical massNumber of molelcules
Total (without water)11,0222
Polymers11,0222
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.714, 28.111, 54.853
Angle α, β, γ (deg.)90.00, 103.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Defensin / SPE10


Mass: 5511.249 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pachyrhizus erosus (jicama) / References: UniProt: Q6B519
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 35% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.98 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 5, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 0.98→100 Å / Num. all: 55949 / Num. obs: 55557 / % possible obs: 99.3 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 18.2 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 31.83
Reflection shellResolution: 0.98→1.01 Å / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 4.48 / % possible all: 96.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
Shake& Bakemodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
Shake& Bakephasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.98→10 Å / Num. parameters: 9169 / Num. restraintsaints: 10500 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
RfactorNum. reflection% reflectionSelection details
Rfree0.1637 2635 5 %RANDOM
Rwork0.1198 ---
all0.125 52719 --
obs0.1248 52719 94.3 %-
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 657.62 / Occupancy sum non hydrogen: 997.37
Refinement stepCycle: LAST / Resolution: 0.98→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms758 0 0 183 941
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.032
X-RAY DIFFRACTIONs_zero_chiral_vol0.098
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.102
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.115
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.101

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