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- PDB-6pxz: Crystal Structure of mouse Serum Amyloid A3 (SAA3) in the trimeri... -

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Basic information

Entry
Database: PDB / ID: 6pxz
TitleCrystal Structure of mouse Serum Amyloid A3 (SAA3) in the trimeric form
ComponentsSerum amyloid A-3 protein
KeywordsTRANSPORT PROTEIN / Retinol binding / Asymmetric / Trimer
Function / homology
Function and homology information


response to stilbenoid / Toll-like receptor 4 binding / high-density lipoprotein particle / chemoattractant activity / cellular response to interleukin-1 / cell chemotaxis / acute-phase response / response to bacterium / extracellular space
Similarity search - Function
Serum amyloid A protein / Serum amyloid A protein / Serum amyloid A proteins signature. / Serum amyloid A proteins
Similarity search - Domain/homology
Serum amyloid A-3 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsHu, Z. / Hooper, L.V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Molecular basis for retinol binding by serum amyloid A during infection.
Authors: Hu, Z. / Bang, Y.J. / Ruhn, K.A. / Hooper, L.V.
History
DepositionJul 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum amyloid A-3 protein
B: Serum amyloid A-3 protein
C: Serum amyloid A-3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2284
Polymers35,7463
Non-polymers4831
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-34 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.317, 74.882, 89.940
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 Serum amyloid A-3 protein /


Mass: 11915.195 Da / Num. of mol.: 3 / Fragment: UNP residues 19-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Saa3 / Production host: Escherichia coli (E. coli) / References: UniProt: P04918
#2: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M trisodium citrate, 0.1 M HEPES, pH 7.5, 6% PEG6000, 10% isopropanol

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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 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 39758 / % possible obs: 99.9 % / Redundancy: 8.4 % / Biso Wilson estimate: 28.53 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.026 / Rrim(I) all: 0.075 / Χ2: 1.123 / Net I/σ(I): 7.7 / Num. measured all: 333363
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.738.11.46119450.5690.5441.5610.688100
1.73-1.768.41.41719580.6490.5171.5090.644100
1.76-1.798.50.97419640.7640.3541.0370.658100
1.79-1.838.50.80819520.8360.2930.860.698100
1.83-1.878.60.66419790.8830.240.7060.737100
1.87-1.918.50.66519350.9210.2420.7080.952100
1.91-1.968.40.45419610.9290.1660.4841.296100
1.96-2.028.60.31719870.9640.1140.3370.848100
2.02-2.078.50.29319530.9620.1070.3121.186100
2.07-2.148.50.2119740.9830.0760.2241.02899.9
2.14-2.228.60.14819850.990.0530.1570.955100
2.22-2.318.30.16819730.9870.0620.1791.674100
2.31-2.418.50.09819690.9960.0350.1040.973100
2.41-2.548.50.08719950.9970.0310.0921.203100
2.54-2.78.50.07219870.9980.0260.0771.222100
2.7-2.918.50.06120080.9980.0220.0651.253100
2.91-3.28.40.05919950.9980.0210.0631.622100
3.2-3.668.20.0520330.9990.0180.0531.886100
3.66-4.6180.03920600.9990.0140.0421.555100
4.61-507.80.03621450.9980.0140.0391.38898.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-3000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q5G

4q5g


Resolution: 1.7→28.84 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.58
RfactorNum. reflection% reflection
Rfree0.2519 1975 5 %
Rwork0.2172 --
obs0.219 39535 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.66 Å2 / Biso mean: 37.55 Å2 / Biso min: 21.94 Å2
Refinement stepCycle: final / Resolution: 1.7→28.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2429 0 22 302 2753
Biso mean--40.96 44.84 -
Num. residues----305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072524
X-RAY DIFFRACTIONf_angle_d0.8933391
X-RAY DIFFRACTIONf_chiral_restr0.063289
X-RAY DIFFRACTIONf_plane_restr0.004458
X-RAY DIFFRACTIONf_dihedral_angle_d13.964937
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.74250.30231410.29912654100
1.7425-1.78960.31491380.27142641100
1.7896-1.84230.27671380.24932629100
1.8423-1.90170.30131400.27352653100
1.9017-1.96970.33231390.30942644100
1.9697-2.04850.32091400.2422667100
2.0485-2.14170.29561400.24382660100
2.1417-2.25460.27371390.23592666100
2.2546-2.39580.24611380.212265499
2.3958-2.58070.27081420.21232686100
2.5807-2.84020.25711410.21182692100
2.8402-3.25070.24611440.21172728100
3.2507-4.09370.2261430.18372724100
4.0937-28.840.22291520.212286299

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