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- PDB-3mez: X-ray structural analysis of a mannose specific lectin from dutch... -

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Basic information

Entry
Database: PDB / ID: 3mez
TitleX-ray structural analysis of a mannose specific lectin from dutch crocus (crocus vernus)
Components
  • Mannose-specific lectin 3 chain 1
  • Mannose-specific lectin 3 chain 2
KeywordsSUGAR BINDING PROTEIN / Lectin / Crocus / Heterotetramer
Function / homology
Function and homology information


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
FORMIC ACID / Mannose-specific lectin 3
Similarity search - Component
Biological speciesCrocus vernus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.94 Å
AuthorsAkrem, A. / Meyer, A. / Perbandt, M. / Voelter, W. / Buck, F. / Betzel, C.
CitationJournal: To be Published
Title: X-ray structural analysis of a mannose specific lectin from dutch crocus (crocus vernus)
Authors: Akrem, A.
History
DepositionApr 1, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 25, 2019Group: Data collection / Category: diffrn_source / reflns / reflns_shell
Item: _diffrn_source.pdbx_synchrotron_site / _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Mannose-specific lectin 3 chain 1
B: Mannose-specific lectin 3 chain 2
C: Mannose-specific lectin 3 chain 1
D: Mannose-specific lectin 3 chain 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,62915
Polymers48,9844
Non-polymers64411
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-52 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.422, 98.154, 105.827
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Mannose-specific lectin 3 chain 1


Mass: 12013.144 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Bulb / Source: (natural) Crocus vernus (plant) / References: UniProt: P86626
#2: Protein Mannose-specific lectin 3 chain 2


Mass: 12478.987 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Bulb / Source: (natural) Crocus vernus (plant) / References: UniProt: P86626
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR WILL CONTACT UNIPROT FOR MODIFICATION ON DATABASE P86626 (LEC3_CROVR).

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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: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4M Sodium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. obs: 48106 / Observed criterion σ(I): 3.84 / Redundancy: 4.3 % / Rmerge(I) obs: 0.098
Reflection shellResolution: 1.94→2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.33

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Processing

Software
NameVersionClassification
DENZOdata reduction
SOLVEphasing
REFMAC5.5.0109refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1MSA

1msa


Resolution: 1.94→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.405 / SU ML: 0.098 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22504 1647 5 %RANDOM
Rwork0.17773 ---
obs0.18015 30977 85.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.909 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2---1.42 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.94→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 42 295 3765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0213529
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1421.9284797
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3085442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.79524.483174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.64915528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3461524
X-RAY DIFFRACTIONr_chiral_restr0.2640.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212718
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3821.52216
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.30623546
X-RAY DIFFRACTIONr_scbond_it3.57231313
X-RAY DIFFRACTIONr_scangle_it4.9114.51251
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 100 -
Rwork0.22 2255 -
obs--85.92 %

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