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- PDB-3mx7: Crystal Structure Analysis of Human FAIM-NTD -

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Basic information

Entry
Database: PDB / ID: 3mx7
TitleCrystal Structure Analysis of Human FAIM-NTD
ComponentsFas apoptotic inhibitory molecule 1
KeywordsAPOPTOSIS / Beta Sheet
Function / homology
Function and homology information


negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / apoptotic process / cytoplasm
Similarity search - Function
Lipocalin - #180 / Fas apoptotic inhibitory molecule 1 / FAIM1 domain superfamily / Fas apoptotic inhibitory molecule (FAIM1) / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fas apoptotic inhibitory molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsLi, G. / Qu, L. / Meng, G. / Zheng, X.
CitationJournal: To be Published
Title: The structure of human Fas apoptotic inhibitory molecule
Authors: Li, G. / Qu, L. / Meng, G. / Bai, X. / Dai, K. / Zheng, X.
History
DepositionMay 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fas apoptotic inhibitory molecule 1


Theoretical massNumber of molelcules
Total (without water)10,1841
Polymers10,1841
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.170, 57.170, 69.946
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Fas apoptotic inhibitory molecule 1


Mass: 10183.710 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, UNP residues 1-90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAIM, FAIM1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NVQ4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.67M sodium phosphate, 0.73M potassium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.04361 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jan 16, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04361 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 14391 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 17.267
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 5 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 11.041 / Num. unique all: 2521 / Rsym value: 0.187 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.76→28.57 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.687 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0.16 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20045 663 4.9 %RANDOM
Rwork0.17645 ---
all0.179 ---
obs0.17759 12781 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.386 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.76→28.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms716 0 0 104 820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022730
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.944981
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.74324.33330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32715137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.126152
X-RAY DIFFRACTIONr_chiral_restr0.1550.2109
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.02526
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2981.5441
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4442708
X-RAY DIFFRACTIONr_scbond_it3.433289
X-RAY DIFFRACTIONr_scangle_it5.6954.5273
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.805 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 56 -
Rwork0.194 909 -
obs-1018 99.18 %

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