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- PDB-6s3f: Moringa seed protein Mo-CBP3-4 -

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Basic information

Entry
Database: PDB / ID: 6s3f
TitleMoringa seed protein Mo-CBP3-4
Components(2S albumin) x 2
KeywordsANTIFUNGAL PROTEIN
Function / homology
Function and homology information


nutrient reservoir activity
Similarity search - Function
Napin/ 2S seed storage protein/Conglutin / Plant lipid-transfer and hydrophobic proteins / Hydrophobic Seed Protein / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / 2S albumin
Similarity search - Component
Biological speciesMoringa oleifera (horseradish tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.68 Å
AuthorsMoulin, M. / Mossou, E. / Mitchell, E.P. / Haertlein, M. / Forsyth, V.T. / Rennie, A.R.
CitationJournal: J Colloid Interface Sci / Year: 2019
Title: Towards a molecular understanding of the water purification properties of Moringa seed proteins.
Authors: Moulin, M. / Mossou, E. / Signor, L. / Kieffer-Jaquinod, S. / Kwaambwa, H.M. / Nermark, F. / Gutfreund, P. / Mitchell, E.P. / Haertlein, M. / Forsyth, V.T. / Rennie, A.R.
History
DepositionJun 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2S albumin
B: 2S albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9358
Polymers10,6232
Non-polymers3126
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-23 kcal/mol
Surface area5570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.070, 108.070, 43.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-101-

CL

21A-103-

FMT

31A-103-

FMT

41B-102-

FMT

51A-201-

HOH

61A-211-

HOH

71A-225-

HOH

81A-232-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein 2S albumin / CBP3


Mass: 7374.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Moringa oleifera (horseradish tree) / References: UniProt: W5S2D2
#2: Protein/peptide 2S albumin / CBP3


Mass: 3248.731 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Moringa oleifera (horseradish tree) / References: UniProt: W5S2D2

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Non-polymers , 4 types, 51 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M citic acid 2.4M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 16, 2013
RadiationMonochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.68→54.45 Å / Num. obs: 15156 / % possible obs: 99.6 % / Redundancy: 7.1 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.02 / Net I/σ(I): 24.7
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 741 / Rpim(I) all: 0.411 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.68→19.37 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.803 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.1 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23093 720 5 %RANDOM
Rwork0.18147 ---
obs0.18392 13557 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.791 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0 Å2
2---0.06 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.68→19.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms736 0 19 45 800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.019808
X-RAY DIFFRACTIONr_bond_other_d0.0030.02793
X-RAY DIFFRACTIONr_angle_refined_deg2.3061.9321086
X-RAY DIFFRACTIONr_angle_other_deg1.18631803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5365100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.35621.52246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77615149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3321516
X-RAY DIFFRACTIONr_chiral_restr0.1410.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021942
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02234
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_it4.4793.353370
X-RAY DIFFRACTIONr_mcbond_other4.4733.353371
X-RAY DIFFRACTIONr_mcangle_it6.394.992462
X-RAY DIFFRACTIONr_mcangle_other6.3935.005463
X-RAY DIFFRACTIONr_scbond_it6.1984.266437
X-RAY DIFFRACTIONr_scbond_other6.1554.268437
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.7136.117618
X-RAY DIFFRACTIONr_long_range_B_refined13.07427.982955
X-RAY DIFFRACTIONr_long_range_B_other13.0627.989955
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.723 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 48 -
Rwork0.205 820 -
obs--80.37 %

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