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- PDB-7ecq: Crystal structure of FAM3A -

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Basic information

Entry
Database: PDB / ID: 7ecq
TitleCrystal structure of FAM3A
ComponentsProtein FAM3A
KeywordsCYTOKINE / regulator
Function / homologyFAM3C (ILEI) domain / FAM3 family / ILEI/PANDER domain / Interleukin-like EMT inducer / GG-type lectin domain profile. / carbohydrate binding / extracellular space / Chem-J0R / Protein FAM3A
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.381 Å
AuthorsChang, Z. / Shi, C.
CitationJournal: To Be Published
Title: High Resolution Crystal Structure of FAM3A shed lights on its function on beta-oxidation
Authors: Chang, Z. / Shi, C.
History
DepositionMar 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein FAM3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7403
Polymers19,4831
Non-polymers2562
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-12 kcal/mol
Surface area9080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.186, 60.782, 78.907
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 Protein FAM3A


Mass: 19483.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fam3a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9D8T0
#2: Chemical ChemComp-J0R / [(2R)-1-(trimethyl-$l^4-azanyl)propan-2-yl] ethanoate


Mass: 160.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 289.15 K / Method: evaporation
Details: 0.2 M Ammonium Sulfate, 0.1 M MES pH6.5, 30% w/v Polyethylene Glycol Monomethyl Ether 5000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.968 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. obs: 39780 / % possible obs: 95.44 % / Redundancy: 14.4 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 44.35
Reflection shellResolution: 1.38→1.43 Å / Rmerge(I) obs: 0.394 / Num. unique obs: 3768

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
Adxvdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2yoq

2yoq


Resolution: 1.381→39.453 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 15.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1713 1971 4.96 %
Rwork0.1632 37728 -
obs0.1636 39699 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.01 Å2 / Biso mean: 17.6911 Å2 / Biso min: 6.7 Å2
Refinement stepCycle: final / Resolution: 1.381→39.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1364 0 16 257 1637
Biso mean--29.29 29.85 -
Num. residues----175
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3815-1.4160.2081400.1878249994
1.39-1.430.15421680.15290099
1.416-1.45430.18731480.1711264997
1.4543-1.49710.1621420.16260598
1.4971-1.54540.16591330.1564267998
1.5454-1.60070.18881300.1648265398
1.6007-1.66470.19021330.1592266299
1.6647-1.74050.19481440.1655265998
1.7405-1.83230.18931420.1682269499
1.8323-1.94710.17521210.1547272399
1.9471-2.09740.18331420.1565272399
2.0974-2.30840.14361340.14271599
2.3084-2.64240.17611500.17072764100
2.6424-3.32890.17891440.16762803100

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