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- PDB-2ilr: Crystal structure of human Fanconi Anemia protein E C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2ilr
TitleCrystal structure of human Fanconi Anemia protein E C-terminal domain
ComponentsFanconi anemia group E protein
KeywordsONCOPROTEIN / antiparallel helical hairpin / helical repeat / FANC repeat
Function / homology
Function and homology information


Fanconi anaemia nuclear complex / interstrand cross-link repair / Fanconi Anemia Pathway / PKR-mediated signaling / chromosome / centrosome / chromatin / nucleoplasm / nucleus / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #480 / Fanconi Anaemia group E protein, C-terminal / Fanconi anemia group E protein / Fanconi Anaemia group E protein FANCE / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Fanconi anemia group E protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsPellegrini, L. / Nookala, R.K.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Insights into Fanconi Anaemia from the structure of human FANCE
Authors: Nookala, R.K. / Hussain, S. / Pellegrini, L.
History
DepositionOct 3, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fanconi anemia group E protein


Theoretical massNumber of molelcules
Total (without water)28,9861
Polymers28,9861
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.291, 59.291, 140.249
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe asymmetric unit of the crystal contains one chain of the FANCE protein. This corresponds to the biological unit of the protein.

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Components

#1: Protein Fanconi anemia group E protein / Protein FACE


Mass: 28986.127 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 273-536 / Mutation: C391A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCE / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HB96
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.085M TrisCl, 0.170M Sodium Acetate, 25.5% PEG 4000, 15% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.9794, 0.9798, 0.9764
SYNCHROTRONESRF ID2920.9794
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDMay 17, 2006
ADSC QUANTUM 2102CCDMay 17, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97981
30.97641
ReflectionResolution: 2→18.75 Å / Num. all: 17665 / Num. obs: 17665 / % possible obs: 98.9 % / Redundancy: 8.6 % / Biso Wilson estimate: 27.8 Å2 / Rsym value: 0.05 / Net I/σ(I): 8.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 8.9 % / Num. unique all: 2470 / Rsym value: 0.195 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→18.75 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.9 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24356 888 5.1 %RANDOM
Rwork0.19409 ---
obs0.19648 16512 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.895 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2→18.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 0 144 2066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221970
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7762.0322675
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4485250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76325.30366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56315382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.612159
X-RAY DIFFRACTIONr_chiral_restr0.1130.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021380
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.2992
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21409
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2121
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3551.51315
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.11122043
X-RAY DIFFRACTIONr_scbond_it3.2893747
X-RAY DIFFRACTIONr_scangle_it4.9584.5632
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 67 -
Rwork0.2 1183 -
obs--98.27 %

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