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- PDB-8f0v: Lipocalin-like Milk protein-2 - E38A mutant -

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Basic information

Entry
Database: PDB / ID: 8f0v
TitleLipocalin-like Milk protein-2 - E38A mutant
ComponentsMilk protein
KeywordsLIPID BINDING PROTEIN / Lipocalin / Mutation / cockroach milk / Lili Mip.
Function / homologyCalycin / metal ion binding / Milk protein
Function and homology information
Biological speciesDiploptera punctata (Pacific beetle cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.951 Å
AuthorsSubramanian, R. / KanagaVijayan, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Plos One / Year: 2023
Title: Variability in phenylalanine side chain conformations facilitates broad substrate tolerance of fatty acid binding in cockroach milk proteins.
Authors: Santhakumari, P.R. / Dhanabalan, K. / Virani, S. / Hopf-Jannasch, A.S. / Benoit, J.B. / Chopra, G. / Subramanian, R.
#1: 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. / Subramanian, R. / Banerjee, S.
#2: 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
DepositionNov 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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
A: Milk protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8187
Polymers17,9581
Non-polymers8606
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.771, 52.337, 136.348
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-206-

ZN

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Components

#1: Protein Milk protein


Mass: 17958.211 Da / Num. of mol.: 1 / Mutation: E38A
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
#2: 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
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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: 1

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Sample preparation

CrystalDensity Matthews: 3.95 Å3/Da / Density % sol: 69 % / Description: diamond shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0 (0.002 M Zinc sulfate heptahydrate; 0.08 M HEPES pH 7.0; 25 % v/v Jeffamine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.07 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: May 7, 2022 / Details: double crystal
RadiationMonochromator: Rosenbaum-Rock monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.95→38.18 Å / Num. obs: 6461 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 76 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.054 / Net I/σ(I): 11.5
Reflection shellResolution: 2.95→3.13 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2 / Mean I/σ(I) obs: 1 / Num. unique obs: 1021 / CC1/2: 0.58 / Rpim(I) all: 0.83 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BKX

7bkx


Resolution: 2.951→38.18 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.907 / SU B: 22.75 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R: 0.806 / ESU R Free: 0.404
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2936 323 5.023 %
Rwork0.2345 6107 -
all0.237 --
obs-6430 99.798 %
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: 98.323 Å2
Baniso -1Baniso -2Baniso -3
1-6.649 Å2-0 Å20 Å2
2--0.7 Å2-0 Å2
3----7.349 Å2
Refinement stepCycle: LAST / Resolution: 2.951→38.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1235 0 45 2 1282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121329
X-RAY DIFFRACTIONr_bond_other_d0.0040.0161107
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.6881816
X-RAY DIFFRACTIONr_angle_other_deg0.4321.5662584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4585154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.29355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.41410180
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.731062
X-RAY DIFFRACTIONr_chiral_restr0.0540.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021493
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02270
X-RAY DIFFRACTIONr_nbd_refined0.2150.2290
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.21169
X-RAY DIFFRACTIONr_nbtor_refined0.190.2639
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2692
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1220.220
X-RAY DIFFRACTIONr_nbd_other0.0930.28
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0330.22
X-RAY DIFFRACTIONr_mcbond_it7.83610.196619
X-RAY DIFFRACTIONr_mcbond_other7.83510.197619
X-RAY DIFFRACTIONr_mcangle_it12.30615.255772
X-RAY DIFFRACTIONr_mcangle_other12.29815.254773
X-RAY DIFFRACTIONr_scbond_it7.74711.045710
X-RAY DIFFRACTIONr_scbond_other7.74211.051711
X-RAY DIFFRACTIONr_scangle_it11.96716.3211044
X-RAY DIFFRACTIONr_scangle_other11.96216.3251045
X-RAY DIFFRACTIONr_lrange_it17.344129.2671460
X-RAY DIFFRACTIONr_lrange_other17.345129.3031461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.951-3.0270.418250.402444X-RAY DIFFRACTION99.7872
3.027-3.1090.531210.392430X-RAY DIFFRACTION100
3.109-3.1990.251170.379409X-RAY DIFFRACTION100
3.199-3.2960.433300.331413X-RAY DIFFRACTION100
3.296-3.4040.289190.316372X-RAY DIFFRACTION100
3.404-3.5220.338170.271394X-RAY DIFFRACTION100
3.522-3.6540.205230.242367X-RAY DIFFRACTION100
3.654-3.8020.247270.243334X-RAY DIFFRACTION100
3.802-3.9690.311200.209354X-RAY DIFFRACTION100
3.969-4.160.473130.183323X-RAY DIFFRACTION99.7033
4.16-4.3830.275150.201329X-RAY DIFFRACTION100
4.383-4.6450.285120.191292X-RAY DIFFRACTION100
4.645-4.960.201170.162283X-RAY DIFFRACTION100
4.96-5.350.254130.163263X-RAY DIFFRACTION100
5.35-5.8490.297100.211258X-RAY DIFFRACTION100
5.849-6.520.202140.234226X-RAY DIFFRACTION100
6.52-7.4930.289110.251195X-RAY DIFFRACTION99.5169
7.493-9.090.36680.2176X-RAY DIFFRACTION100
9.09-12.5060.2870.221148X-RAY DIFFRACTION99.359
12.506-38.180.33340.3197X-RAY DIFFRACTION95.283

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