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- PDB-6km8: Crystal Structure of Momordica charantia 7S globulin -

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Basic information

Entry
Database: PDB / ID: 6km8
TitleCrystal Structure of Momordica charantia 7S globulin
Components7S globulin
KeywordsPLANT PROTEIN / 7S globulin bi-cupin fold / Glycosylated / Copper-ion
Function / homologyJelly Rolls / Jelly Rolls / Sandwich / Mainly Beta / ACETATE ION / COPPER (II) ION
Function and homology information
Biological speciesMomordica charantia (bitter melon)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.099 Å
AuthorsKesari, P. / Pratap, S. / Dhankhar, P. / Dalal, V. / Kumar, P.
CitationJournal: Sci Rep / Year: 2020
Title: Structural characterization and in-silico analysis of Momordica charantia 7S globulin for stability and ACE inhibition.
Authors: Kesari, P. / Pratap, S. / Dhankhar, P. / Dalal, V. / Mishra, M. / Singh, P.K. / Chauhan, H. / Kumar, P.
History
DepositionJul 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 7S globulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1193
Polymers42,9961
Non-polymers1232
Water1267
1
A: 7S globulin
hetero molecules

A: 7S globulin
hetero molecules

A: 7S globulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,3579
Polymers128,9893
Non-polymers3686
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area14790 Å2
ΔGint-99 kcal/mol
Surface area38150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.765, 90.765, 68.476
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein 7S globulin


Mass: 42996.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Momordica charantia (bitter melon)
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 1.89 Å3/Da / Density % sol: 35.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Sodium acetate trihydrate pH 4.6, 2M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.099→50 Å / Num. obs: 5314 / % possible obs: 89.52 % / Redundancy: 2.8 % / Biso Wilson estimate: 53.8 Å2 / Rsym value: 0.12 / Net I/σ(I): 11.17
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.29 / Num. unique obs: 397 / Rsym value: 0.407 / % possible all: 66.44

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E1R

5e1r


Resolution: 3.099→45.383 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.8
RfactorNum. reflection% reflection
Rfree0.278 251 4.73 %
Rwork0.1908 --
obs0.1952 5306 89.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.91 Å2 / Biso mean: 53.54 Å2 / Biso min: 12.63 Å2
Refinement stepCycle: final / Resolution: 3.099→45.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2741 0 5 7 2753
Biso mean--44.62 29.97 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012800
X-RAY DIFFRACTIONf_angle_d1.5033779
X-RAY DIFFRACTIONf_chiral_restr0.107405
X-RAY DIFFRACTIONf_plane_restr0.007505
X-RAY DIFFRACTIONf_dihedral_angle_d18.281041
LS refinement shellResolution: 3.1→3.15 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3231 111 -
Rwork0.2143 2208 -
obs--79 %

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