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- PDB-1du5: THE CRYSTAL STRUCTURE OF ZEAMATIN. -

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Basic information

Entry
Database: PDB / ID: 1du5
TitleTHE CRYSTAL STRUCTURE OF ZEAMATIN.
ComponentsZEAMATIN
KeywordsANTIFUNGAL PROTEIN / beta sandwich
Function / homology
Function and homology information


defense response to fungus / defense response / killing of cells of another organism
Similarity search - Function
Thaumatin / Thaumatin / Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBatalia, M.A. / Monzingo, A.F. / Ernst, S. / Roberts, W. / Robertus, J.D.
CitationJournal: Nat.Struct.Biol. / Year: 1996
Title: The crystal structure of the antifungal protein zeamatin, a member of the thaumatin-like, PR-5 protein family.
Authors: Batalia, M.A. / Monzingo, A.F. / Ernst, S. / Roberts, W. / Robertus, J.D.
History
DepositionJan 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 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: ZEAMATIN
B: ZEAMATIN


Theoretical massNumber of molelcules
Total (without water)44,1582
Polymers44,1582
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.490, 56.720, 47.720
Angle α, β, γ (deg.)90.00, 105.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ZEAMATIN


Mass: 22078.777 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: P33679
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.06 Å3/Da / Density % sol: 40.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, potassium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %PEG80001reservoir
20.2 Mpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: May 4, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 12577 / Num. obs: 12219 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 19.8
Reflection shellResolution: 2.5→2.69 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.152 / Num. unique all: 2306 / % possible all: 93.2
Reflection shell
*PLUS
% possible obs: 93.2 %

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Processing

Software
NameVersionClassification
SDMSdata collection
SDMSdata reduction
X-PLORmodel building
X-PLOR3.1refinement
SDMSdata scaling
X-PLORphasing
RefinementResolution: 2.5→5 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1222 -random
Rwork0.167 ---
all0.176 12219 --
obs0.176 12219 97.2 %-
Refinement stepCycle: LAST / Resolution: 2.5→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3086 0 0 39 3125
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg2.89
X-RAY DIFFRACTIONx_torsion_deg26.95
X-RAY DIFFRACTIONx_torsion_impr_deg1.23
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.95
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.23

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