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- PDB-7bkx: Diploptera punctata inspired lipocalin-like Milk protein expresse... -

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Basic information

Entry
Database: PDB / ID: 7bkx
TitleDiploptera punctata inspired lipocalin-like Milk protein expressed in Saccharomyces cerevisiae
ComponentsMilk protein
KeywordsLIPID BINDING PROTEIN / Lipocalin-like protein / Milk protein / Beta-barrel / N-glycosylation
Function / homologyCalycin / metal ion binding / PALMITOLEIC ACID / Milk protein
Function and homology information
Biological speciesDiploptera punctata (Pacific beetle cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBanerjee, S. / Kanagavijayan, D. / Subramanian, R. / Santhakumari, P.R. / Chavas, L.M.G. / Ramaswamy, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR5801/INF/22/156/2012 India
Citation
Journal: Biochim Biophys Acta Gen Subj / Year: 2022
Title: Structure of recombinantly expressed cockroach Lili-Mip protein in glycosylated and deglycosylated forms.
Authors: KanagaVijayan, D. / Subramanian, R. / Santhakumari, P.R. / Chavas, L.M.G. / Banerjee, S.
#1: Journal: IUCrJ / Year: 2016
Title: Structure of a heterogeneous, glycosylated, lipid-bound, in vivo-grown protein crystal at atomic resolution from the viviparous cockroach Diploptera punctata.
Authors: Banerjee, S. / Coussens, N.P. / Gallat, F.X. / Sathyanarayanan, N. / Srikanth, J. / Yagi, K.J. / Gray, J.S. / Tobe, S.S. / Stay, B. / Chavas, L.M. / Ramaswamy, S.
History
DepositionJan 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Milk protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,26810
Polymers20,6371
Non-polymers1,6319
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-76 kcal/mol
Surface area8280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.610, 135.662, 39.654
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11AAA-208-

ZN

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Milk protein


Mass: 20637.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Diploptera punctata (Pacific beetle cockroach)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q6SVB5

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 31 molecules

#4: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30O2 / Feature type: SUBJECT OF INVESTIGATION
#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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.36 Å3/Da / Density % sol: 63.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 15% of PEG MME 550, 100 mM MES pH 6.5, and 10 mM ZnSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.35→20.612 Å / Num. obs: 12200 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rrim(I) all: 0.073 / Net I/σ(I): 18.1
Reflection shellResolution: 2.35→2.39 Å / Num. unique obs: 1224 / CC1/2: 0.3 / Rrim(I) all: 0.836

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Processing

Software
NameVersionClassification
xia25.8.0258data reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.18.2-3874refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NYQ

4nyq


Resolution: 2.35→20.6 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / SU B: 18.065 / SU ML: 0.207 / Cross valid method: FREE R-VALUE / ESU R: 0.251 / ESU R Free: 0.228
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2782 573 4.712 %
Rwork0.2222 11588 -
all0.225 --
obs-12161 99.77 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 58.393 Å2
Baniso -1Baniso -2Baniso -3
1--2.572 Å20 Å2-0 Å2
2--1.942 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1234 0 97 26 1357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131380
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171182
X-RAY DIFFRACTIONr_angle_refined_deg2.1011.7391888
X-RAY DIFFRACTIONr_angle_other_deg1.351.642753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.4015156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27222.17469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.23615185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.394156
X-RAY DIFFRACTIONr_chiral_restr0.0830.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021523
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02296
X-RAY DIFFRACTIONr_nbd_refined0.2540.2307
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.21185
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2641
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.2649
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.251
X-RAY DIFFRACTIONr_metal_ion_refined0.3020.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2830.27
X-RAY DIFFRACTIONr_nbd_other0.1830.214
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0630.22
X-RAY DIFFRACTIONr_mcbond_it3.1214.17624
X-RAY DIFFRACTIONr_mcbond_other3.1124.171623
X-RAY DIFFRACTIONr_mcangle_it4.7936.263780
X-RAY DIFFRACTIONr_mcangle_other4.796.262781
X-RAY DIFFRACTIONr_scbond_it3.5194.899756
X-RAY DIFFRACTIONr_scbond_other3.5174.903757
X-RAY DIFFRACTIONr_scangle_it5.7677.21108
X-RAY DIFFRACTIONr_scangle_other5.7647.2051109
X-RAY DIFFRACTIONr_lrange_it8.87652.3731501
X-RAY DIFFRACTIONr_lrange_other8.86452.3691500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.4110.3390.3814X-RAY DIFFRACTION100
2.411-2.4770.292330.281843X-RAY DIFFRACTION100
2.477-2.5490.405310.302774X-RAY DIFFRACTION100
2.549-2.6270.322450.289786X-RAY DIFFRACTION100
2.627-2.7130.278420.26764X-RAY DIFFRACTION100
2.713-2.8080.432430.28703X-RAY DIFFRACTION99.8661
2.808-2.9140.349520.266683X-RAY DIFFRACTION100
2.914-3.0330.398260.254701X-RAY DIFFRACTION99.8626
3.033-3.1670.38280.262648X-RAY DIFFRACTION100
3.167-3.3210.26250.256635X-RAY DIFFRACTION100
3.321-3.5010.281340.242597X-RAY DIFFRACTION100
3.501-3.7120.25350.215567X-RAY DIFFRACTION100
3.712-3.9680.276220.191551X-RAY DIFFRACTION100
3.968-4.2850.262280.176497X-RAY DIFFRACTION100
4.285-4.6920.178180.15471X-RAY DIFFRACTION100
4.692-5.2420.165190.164427X-RAY DIFFRACTION100
5.242-6.0470.237140.204382X-RAY DIFFRACTION100
6.047-7.3920.322160.257334X-RAY DIFFRACTION100
7.392-10.3920.272140.22272X-RAY DIFFRACTION100
10.392-20.60.3190.237139X-RAY DIFFRACTION85.5491
Refinement TLS params.Method: refined / Origin x: 3.1056 Å / Origin y: 21.3104 Å / Origin z: 17.965 Å
111213212223313233
T0.1738 Å2-0.0326 Å2-0.026 Å2-0.0318 Å2-0.0158 Å2--0.046 Å2
L1.4963 °21.414 °2-0.1814 °2-7.9653 °23.0573 °2--1.6309 °2
S-0.186 Å °-0.1009 Å °0.258 Å °-0.1264 Å °0.1641 Å °0.3363 Å °0.1231 Å °0.1126 Å °0.0219 Å °
Refinement TLS groupSelection: ALL

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