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- PDB-7q02: Zn-free structure of lipocalin-like Milk protein, inspired from D... -

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Basic information

Entry
Database: PDB / ID: 7q02
TitleZn-free structure of lipocalin-like Milk protein, inspired from Diploptera punctata, expressed in Saccharomyces cerevisiae
ComponentsMilk protein
KeywordsLIPID BINDING PROTEIN / Lipocalin / Milk Protein / Dipolptera punctata
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: 1.45 Å
AuthorsBanerjee, S. / Dhanabalan, K.V. / Ramaswamy, S.
Funding support India, 3items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR5801/INF/22/156/2012 India
Department of Biotechnology (DBT, India)DBT-RA fellowship India
Science and Engineering Research Board (SERB)postdoc fellowship India
CitationJournal: 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.
History
DepositionOct 14, 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)19,1082
Polymers18,8531
Non-polymers2541
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint1 kcal/mol
Surface area7770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.362, 47.692, 97.612
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Milk protein


Mass: 18853.268 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
#2: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.26 % / Description: Plate-like crystals.
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M Sodium Acetate, HCl, pH 4.5; 25 % (w/v) PEG 3350
Temp details: Controlled room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.45→48.81 Å / Num. obs: 28438 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 12.79 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.046 / Rrim(I) all: 0.117 / Net I/σ(I): 10.7 / Num. measured all: 180115 / Scaling rejects: 137
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.45-1.485.50.771774614070.7580.3590.8532.1100
7.81-48.815.30.05212432360.9980.0250.05825.199.9

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NYQ

4nyq


Resolution: 1.45→48.81 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1945 1402 4.94 %
Rwork0.1498 26970 -
obs0.1519 28372 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.2 Å2 / Biso mean: 18.435 Å2 / Biso min: 7.62 Å2
Refinement stepCycle: final / Resolution: 1.45→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 18 224 1490
Biso mean--31.36 35.25 -
Num. residues----153
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.45-1.50.28681530.219226012754
1.5-1.560.22291410.1726532794
1.56-1.630.2221360.160326562792
1.63-1.720.19231300.156526832813
1.72-1.830.21361540.159526472801
1.83-1.970.17331520.141826732825
1.97-2.170.20171420.134826862828
2.17-2.480.18861210.143727182839
2.48-3.120.19381260.156127692895
3.12-48.810.17621470.141428843031

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