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- PDB-8f0y: Lipocalin-like Milk protein-1 -

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Basic information

Entry
Database: PDB / ID: 8f0y
TitleLipocalin-like Milk protein-1
ComponentsMilk protein
KeywordsLIPID BINDING PROTEIN / Lipocalin / Mutation / cockroach milk / Lili Mip.Sequence 1
Function / homologyCalycin / Milk protein
Function and homology information
Biological speciesDiploptera punctata (Pacific beetle cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSubramanian, R. / KanagaVijayan, D. / Shantakumar, R.P.S.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Milk protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5764
Polymers17,9121
Non-polymers6643
Water1267
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)32.672, 33.038, 38.640
Angle α, β, γ (deg.)100.765, 99.681, 103.599
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Milk protein


Mass: 17912.180 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: Q6SVB6
#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: Water ChemComp-HOH / 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: 2.19 Å3/Da / Density % sol: 43.74 % / Description: Rod shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 0.2M Potassium Nitrate, pH 6.9, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2022
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.1→37.02 Å / Num. obs: 8498 / % possible obs: 96.7 % / Redundancy: 2.6 % / CC1/2: 0.98 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.112 / Rrim(I) all: 0.158 / Net I/σ(I): 3.5
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.6 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
8.91-37.010.0681130.9920.0680.09696.7
2.1-2.160.627040.4830.620.87795.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NYQ

4nyq


Resolution: 2.1→37.012 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.06 / SU ML: 0.225 / Cross valid method: FREE R-VALUE / ESU R: 0.277 / ESU R Free: 0.216
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2523 433 5.095 %
Rwork0.1962 8065 -
all0.199 --
obs-8498 96.689 %
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: 40.13 Å2
Baniso -1Baniso -2Baniso -3
1--2.312 Å21.22 Å20.946 Å2
2---0.371 Å22.202 Å2
3---0.257 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1221 0 42 7 1270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0121306
X-RAY DIFFRACTIONr_bond_other_d0.0030.0161145
X-RAY DIFFRACTIONr_angle_refined_deg2.5971.6911782
X-RAY DIFFRACTIONr_angle_other_deg0.8621.5782680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1065148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.60156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.6110199
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.181059
X-RAY DIFFRACTIONr_chiral_restr0.1240.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021445
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02266
X-RAY DIFFRACTIONr_nbd_refined0.2210.2240
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.21119
X-RAY DIFFRACTIONr_nbtor_refined0.2040.2624
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1020.2708
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0870.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2720.211
X-RAY DIFFRACTIONr_nbd_other0.2520.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1380.22
X-RAY DIFFRACTIONr_mcbond_it4.7853.428598
X-RAY DIFFRACTIONr_mcbond_other4.7863.429598
X-RAY DIFFRACTIONr_mcangle_it6.6745.116744
X-RAY DIFFRACTIONr_mcangle_other6.6725.123745
X-RAY DIFFRACTIONr_scbond_it7.9094.522708
X-RAY DIFFRACTIONr_scbond_other7.9034.524709
X-RAY DIFFRACTIONr_scangle_it11.8156.4121038
X-RAY DIFFRACTIONr_scangle_other11.816.4131039
X-RAY DIFFRACTIONr_lrange_it14.13951.751405
X-RAY DIFFRACTIONr_lrange_other14.13551.7931406
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.1-2.1540.299310.2895920.296520.9340.93895.55210.291
2.154-2.2130.439250.2565680.2636240.8690.95295.03210.256
2.213-2.2770.305280.2615670.2636190.9310.94996.12280.255
2.277-2.3470.246220.2455600.2456100.9610.95795.40980.242
2.347-2.4240.327190.2485450.2515760.9210.95797.91670.243
2.424-2.5080.284240.2375030.2395520.9350.95995.4710.238
2.508-2.6030.345280.2064970.2135360.9150.97197.94780.207
2.603-2.7080.269430.24790.2055420.9610.97396.310.21
2.708-2.8280.313270.2034280.214650.9290.97197.84950.213
2.828-2.9650.264210.1534650.1574990.9590.98697.39480.163
2.965-3.1250.208280.1683960.1714330.9750.98397.92150.18
3.125-3.3130.239300.1674020.1724430.960.98397.51690.187
3.313-3.5390.226310.1553670.1614050.960.98798.27160.177
3.539-3.820.1880.1543500.1553680.9870.98797.28260.175
3.82-4.180.205200.1583260.1613590.9740.98496.37880.184
4.18-4.6660.186130.1452880.1473130.9820.98696.16610.168
4.666-5.3740.248110.1872480.192710.9780.98295.5720.225
5.374-6.5470.25840.2082320.2092430.9080.97897.11930.249
6.547-9.1170.29190.2431570.2461700.980.9797.64710.302
9.117-37.0120.202110.254940.2481080.9840.94797.22220.31

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