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- PDB-1xd5: Crystal structures of novel monomeric monocot mannose-binding lec... -

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Basic information

Entry
Database: PDB / ID: 1xd5
TitleCrystal structures of novel monomeric monocot mannose-binding lectins from Gastrodia elata
Componentsantifungal protein GAFP-1
KeywordsANTIFUNGAL PROTEIN / monocot mannose binding lectin / monomer / homogeneous beta-sheet
Function / homology
Function and homology information


response to other organism
Similarity search - Function
Agglutinin, subunit A / Bulb-type lectin domain / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / Orthogonal Prism / Mainly Beta
Similarity search - Domain/homology
Biological speciesGastrodia elata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiu, W. / Yang, N. / Wang, M. / Huang, R.H. / Hu, Z. / Wang, D.C.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural Mechanism Governing the Quaternary Organization of Monocot Mannose-binding Lectin Revealed by the Novel Monomeric Structure of an Orchid Lectin
Authors: Liu, W. / Yang, N. / Ding, J. / Huang, R.H. / Hu, Z. / Wang, D.C.
History
DepositionSep 4, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: antifungal protein GAFP-1
B: antifungal protein GAFP-1
C: antifungal protein GAFP-1
D: antifungal protein GAFP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4226
Polymers49,2304
Non-polymers1922
Water4,774265
1
A: antifungal protein GAFP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5003
Polymers12,3071
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: antifungal protein GAFP-1


Theoretical massNumber of molelcules
Total (without water)12,3071
Polymers12,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: antifungal protein GAFP-1


Theoretical massNumber of molelcules
Total (without water)12,3071
Polymers12,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: antifungal protein GAFP-1


Theoretical massNumber of molelcules
Total (without water)12,3071
Polymers12,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
A: antifungal protein GAFP-1
B: antifungal protein GAFP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8074
Polymers24,6152
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-34 kcal/mol
Surface area10690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.087, 91.488, 81.132
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-195-

HOH

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Components

#1: Protein
antifungal protein GAFP-1 / gastrodianin-1


Mass: 12307.442 Da / Num. of mol.: 4 / Fragment: residues 1-112 / Source method: isolated from a natural source / Source: (natural) Gastrodia elata (plant) / Tissue: corms / References: UniProt: Q9AXZ2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.35 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, dioxane, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2002
RadiationMonochromator: Fixed-exit double-crystal monochromator with silicon (111) and germanium (220) crystals
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→24.7 Å / Num. all: 31377 / Num. obs: 31341 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.097 / Net I/σ(I): 6.7
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→24.69 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.088 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20606 1553 5 %RANDOM
Rwork0.16548 ---
all0.183 31339 --
obs0.16739 29785 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.265 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2→24.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 10 265 3717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213510
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.9064771
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1815441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022768
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21443
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2256
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6971.52176
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35623453
X-RAY DIFFRACTIONr_scbond_it1.77631334
X-RAY DIFFRACTIONr_scangle_it2.9254.51318
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.2 115
Rwork0.175 2145

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