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- PDB-4q5g: Crystal Structure of mouse Serum Amyloid A3 -

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Basic information

Entry
Database: PDB / ID: 4q5g
TitleCrystal Structure of mouse Serum Amyloid A3
ComponentsSerum amyloid A-3 protein
KeywordsPROTEIN BINDING / four helix bundle / serum amyloid A3 / retinol binding / retinol transport / acute phase response
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 protein / Serum amyloid A proteins signature. / Serum amyloid A proteins / Topoisomerase I; Chain A, domain 4 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Serum amyloid A-3 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.057 Å
AuthorsDerebe, M.G. / Hooper, L.V.
CitationJournal: elife / Year: 2014
Title: Biochemical and structural analysis reveals a retinol binding function for serum amyloid A proteins
Authors: Derebe, M.G. / Zlatkov, C.M. / Gattu, S. / Ruhn, K.A. / Vaishnava, S. / Diehl, G.E. / MacMillan, J.B. / Williams, N.S. / Hooper, L.V.
History
DepositionApr 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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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


Theoretical massNumber of molelcules
Total (without water)24,1122
Polymers24,1122
Non-polymers00
Water1,44180
1
A: Serum amyloid A-3 protein
B: Serum amyloid A-3 protein

A: Serum amyloid A-3 protein
B: Serum amyloid A-3 protein


Theoretical massNumber of molelcules
Total (without water)48,2244
Polymers48,2244
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area6060 Å2
ΔGint-78 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.327, 78.327, 62.319
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Serum amyloid A-3 protein


Mass: 12055.880 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 75-80% MPD, 0.1M sodium acetate , pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 12206 / Num. obs: 12206 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
JBluIce-EPICSdata collection
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 2.057→39.163 Å / SU ML: 0.16 / σ(F): 0 / Phase error: 19.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2135 1196 9.8 %
Rwork0.1667 11010 -
obs0.1712 12206 89.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.82 Å2 / Biso mean: 32.1953 Å2 / Biso min: 10.82 Å2
Refinement stepCycle: LAST / Resolution: 2.057→39.163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1608 0 0 80 1688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071654
X-RAY DIFFRACTIONf_angle_d0.92214
X-RAY DIFFRACTIONf_chiral_restr0.036190
X-RAY DIFFRACTIONf_plane_restr0.005296
X-RAY DIFFRACTIONf_dihedral_angle_d13.31612
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0574-2.13980.2238900.166487696664
2.1398-2.23720.22181030.1622991109473
2.2372-2.35510.2311240.15911085120981
2.3551-2.50270.20551350.16211241137692
2.5027-2.69580.20611500.1571348149899
2.6958-2.96710.21821520.16091342149499
2.9671-3.39620.20031440.15413661510100
3.3962-4.2780.18751480.150813631511100
4.278-39.17060.24281500.198813981548100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.769-1.78992.15832.7703-0.77186.2434-0.2072-0.3493-1.1247-0.11520.0420.7053-0.4798-1.0717-0.92650.1652-0.0146-0.02960.23080.02670.375416.59816.21337.559
25.8004-1.91831.93624.9276-3.82153.7238-0.09660.0738-0.6702-0.1173-0.10460.12280.2517-0.1631-0.06170.14080.00240.05530.106-0.00840.257726.58714.84839.531
33.52780.78480.7422.5728-0.54783.61710.34430.0586-1.01360.22280.29770.0324-0.0146-0.1396-0.29730.1724-0.0172-0.02010.14950.06740.310732.6919.84442.837
44.3441-0.60951.83983.72691.05258.05150.0657-0.1695-1.11610.3335-0.33771.09051.08930.2972-1.02430.21820.01710.02720.17690.09790.36045.3823.43637.781
57.4807-1.16122.72294.17690.65874.67910.00320.0142-0.48560.1360.01880.47810.16690.0142-0.00230.0736-0.00520.00430.1452-0.00660.2502-0.48931.71535.192
64.43850.0110.25044.8649-0.38087.9360.2780.61010.0968-0.42970.24510.3343-0.84590.1468-0.1920.17250.0347-0.04030.21160.00970.121311.52631.43533.055
76.3034-0.0639-4.0414.5951.16897.85490.12850.8697-0.1023-0.8655-0.7153-0.4768-0.01990.98780.05890.25010.0770.0130.38550.07010.21316.85438.82529.994
83.5048-0.33712.34892.73480.16133.98210.1803-0.1992-0.2481-0.0107-0.09750.55940.1837-0.385-0.11150.1042-0.0067-0.0120.16040.02110.2095-7.93534.28632.3
96.37110.64330.49515.17861.48968.6384-0.0609-0.41030.16980.48070.16270.1216-0.66640.1184-0.14810.23020.0484-0.00940.16120.00190.14721.60825.84440.566
104.2973-2.0787-0.53816.93253.63739.3499-0.12750.12050.4672-0.0120.1079-0.0194-0.21440.28840.00570.08810.0055-0.03140.16430.03580.225831.44623.38740.452
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 6:31 )A6 - 31
2X-RAY DIFFRACTION2( CHAIN A AND RESID 36:51 )A36 - 51
3X-RAY DIFFRACTION3( CHAIN A AND RESID 92:108 )A92 - 108
4X-RAY DIFFRACTION4( CHAIN B AND RESID 6:31 )B6 - 31
5X-RAY DIFFRACTION5( CHAIN B AND RESID 36:51 )B36 - 51
6X-RAY DIFFRACTION6( CHAIN B AND RESID 53:71 )B53 - 71
7X-RAY DIFFRACTION7( CHAIN B AND RESID 72:91 )B72 - 91
8X-RAY DIFFRACTION8( CHAIN B AND RESID 92:108 )B92 - 108
9X-RAY DIFFRACTION9( CHAIN A AND RESID 53:71 )A53 - 71
10X-RAY DIFFRACTION10( CHAIN A AND RESID 80:91 )A80 - 91

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