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- PDB-7xc8: Crystal structure of cotton alpha-like expansin GhEXLA1 -

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Basic information

Entry
Database: PDB / ID: 7xc8
TitleCrystal structure of cotton alpha-like expansin GhEXLA1
ComponentsBeta-expansin
KeywordsPLANT PROTEIN / alpha-like expansin GhEXLA1 / cell wall
Function / homology
Function and homology information


sexual reproduction / anatomical structure morphogenesis / extracellular region
Similarity search - Function
Major pollen allergen Lol pI / Expansin/Lol pI / Rare lipoprotein A (RlpA)-like double-psi beta-barrel / Expansin, Cellulose-binding-like domain profile. / Expansin, cellulose-binding-like domain / Expansin C-terminal domain / Expansin/pollen allergen, DPBB domain / Expansin, family-45 endoglucanase-like domain profile. / RlpA-like protein, double-psi beta-barrel domain / Expansin, cellulose-binding-like domain superfamily ...Major pollen allergen Lol pI / Expansin/Lol pI / Rare lipoprotein A (RlpA)-like double-psi beta-barrel / Expansin, Cellulose-binding-like domain profile. / Expansin, cellulose-binding-like domain / Expansin C-terminal domain / Expansin/pollen allergen, DPBB domain / Expansin, family-45 endoglucanase-like domain profile. / RlpA-like protein, double-psi beta-barrel domain / Expansin, cellulose-binding-like domain superfamily / Lytic transglycolase / RlpA-like domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Beta-expansin
Similarity search - Component
Biological speciesGossypium hirsutum (cotton)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsZhao, F. / Men, S. / Xue, Y. / Tu, L.L. / Yin, P. / Zhang, X.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31671739 China
CitationJournal: To Be Published
Title: Crystal structure of cotton alpha-like expansin GhEXLA1
Authors: Zhao, F. / Men, S. / Xue, Y. / Tu, L.L. / Yin, P. / Zhang, X.L.
History
DepositionMar 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-expansin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3394
Polymers27,0491
Non-polymers2903
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-0 kcal/mol
Surface area10920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.273, 151.273, 61.026
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-462-

HOH

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Components

#1: Protein Beta-expansin / expansin-like A2


Mass: 27048.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gossypium hirsutum (cotton) / Gene: LOC107921049, EXPB-L3D / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A1U8L037
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.06 Å3/Da / Density % sol: 69.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PEG 3350, Tacsimate pH4.0 / PH range: 3.8-4.5

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.55→19.88 Å / Num. obs: 13869 / % possible obs: 99.8 % / Redundancy: 38 % / Biso Wilson estimate: 44.96 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.028 / Rrim(I) all: 0.127 / Χ2: 0.99 / Net I/σ(I): 33.3
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 39 % / Rmerge(I) obs: 0.867 / Mean I/σ(I) obs: 6.3 / Num. unique obs: 1663 / CC1/2: 0.963 / Rpim(I) all: 0.193 / Rrim(I) all: 0.888 / Χ2: 0.99 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19rc5_4047refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→19.88 Å / SU ML: 0.3007 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2791
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2393 1385 10 %
Rwork0.1913 12462 -
obs0.1961 13847 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.71 Å2
Refinement stepCycle: LAST / Resolution: 2.55→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 19 63 1818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821785
X-RAY DIFFRACTIONf_angle_d0.99392403
X-RAY DIFFRACTIONf_chiral_restr0.0573262
X-RAY DIFFRACTIONf_plane_restr0.0084306
X-RAY DIFFRACTIONf_dihedral_angle_d8.4398254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.640.36281340.25571212X-RAY DIFFRACTION100
2.64-2.750.29341350.24141212X-RAY DIFFRACTION100
2.75-2.870.31431360.23421220X-RAY DIFFRACTION100
2.87-3.020.27891370.21441232X-RAY DIFFRACTION100
3.02-3.210.23631360.2241230X-RAY DIFFRACTION100
3.21-3.460.30521370.2171226X-RAY DIFFRACTION100
3.46-3.80.25441390.1981254X-RAY DIFFRACTION100
3.8-4.350.21121380.15841244X-RAY DIFFRACTION100
4.35-5.460.1841420.15351277X-RAY DIFFRACTION100
5.46-19.880.20841510.17931355X-RAY DIFFRACTION99.74

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