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- PDB-5wd6: bovine salivary protein form 30b -

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Basic information

Entry
Database: PDB / ID: 5wd6
Titlebovine salivary protein form 30b
ComponentsShort palate, lung and nasal epithelium carcinoma-associated protein 2B
KeywordsLIPID BINDING PROTEIN / Hydrophobic channel
Function / homologyLipid-binding serum glycoprotein, N-terminal / Bactericidal permeability-increasing protein, alpha/beta domain superfamily / LBP / BPI / CETP family, N-terminal domain / secretory granule / lipopolysaccharide binding / extracellular region / Short palate, lung and nasal epithelium carcinoma-associated protein 2B
Function and homology information
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsZhang, H. / Arcus, V.L.
CitationJournal: Plos One / Year: 2019
Title: The three dimensional structure of Bovine Salivary Protein 30b (BSP30b) and its interaction with specific rumen bacteria.
Authors: Zhang, H. / Burrows, J. / Card, G.L. / Attwood, G. / Wheeler, T.T. / Arcus, V.L.
History
DepositionJul 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short palate, lung and nasal epithelium carcinoma-associated protein 2B
B: Short palate, lung and nasal epithelium carcinoma-associated protein 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2134
Polymers56,1332
Non-polymers802
Water3,675204
1
A: Short palate, lung and nasal epithelium carcinoma-associated protein 2B
hetero molecules

B: Short palate, lung and nasal epithelium carcinoma-associated protein 2B


Theoretical massNumber of molelcules
Total (without water)56,2134
Polymers56,1332
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area1370 Å2
ΔGint-26 kcal/mol
Surface area18100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.650, 59.570, 89.940
Angle α, β, γ (deg.)90.00, 106.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Short palate, lung and nasal epithelium carcinoma-associated protein 2B / BSP30b / Common salivary protein form b


Mass: 28066.619 Da / Num. of mol.: 2 / Fragment: UNP residues 20-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: SPLUNC2B, BSP30B / Production host: Escherichia coli (E. coli) / References: UniProt: P79125
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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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: 1.88 Å3/Da / Density % sol: 34.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 0.2M CaCl2, 9% PEG 3350, 5% IPA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→47.43 Å / Num. obs: 28136 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 28.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.04 / Net I/σ(I): 11.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.662 / Num. unique obs: 4080 / CC1/2: 0.922 / Rpim(I) all: 0.245 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
MOSFLM7.2.1data reduction
SCALAdata scaling
AutoSolphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: SAD / Resolution: 2→47.429 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2514 1999 7.11 %
Rwork0.2051 --
obs0.2084 28121 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→47.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2840 0 2 204 3046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072877
X-RAY DIFFRACTIONf_angle_d0.8053917
X-RAY DIFFRACTIONf_dihedral_angle_d8.2232089
X-RAY DIFFRACTIONf_chiral_restr0.053514
X-RAY DIFFRACTIONf_plane_restr0.005500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.05010.29651420.2321852X-RAY DIFFRACTION100
2.0501-2.10550.27671420.2271869X-RAY DIFFRACTION100
2.1055-2.16750.27661410.22491833X-RAY DIFFRACTION100
2.1675-2.23740.30131410.2311840X-RAY DIFFRACTION100
2.2374-2.31740.28451430.23731867X-RAY DIFFRACTION100
2.3174-2.41020.28141430.22791884X-RAY DIFFRACTION100
2.4102-2.51990.29041420.21911848X-RAY DIFFRACTION100
2.5199-2.65270.29671420.22231866X-RAY DIFFRACTION100
2.6527-2.81890.23081430.21671868X-RAY DIFFRACTION100
2.8189-3.03650.29651420.22081846X-RAY DIFFRACTION100
3.0365-3.3420.26151430.21341873X-RAY DIFFRACTION100
3.342-3.82540.22491440.18071871X-RAY DIFFRACTION100
3.8254-4.81890.22361430.16711878X-RAY DIFFRACTION99
4.8189-47.44210.21681480.20631927X-RAY DIFFRACTION99

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