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- PDB-3u9j: Crystal structure of oxidized human FBXL5 hemerythrin like domain -

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Basic information

Entry
Database: PDB / ID: 3u9j
TitleCrystal structure of oxidized human FBXL5 hemerythrin like domain
ComponentsF-box/LRR-repeat protein 5
KeywordsPROTEIN BINDING / FBOX / LRR / Ubiquitin ligase E3 / iron sensor
Function / homology
Function and homology information


SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Association of TriC/CCT with target proteins during biosynthesis / ubiquitin ligase complex / Iron uptake and transport / 2 iron, 2 sulfur cluster binding / multicellular organismal-level iron ion homeostasis / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation ...SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Association of TriC/CCT with target proteins during biosynthesis / ubiquitin ligase complex / Iron uptake and transport / 2 iron, 2 sulfur cluster binding / multicellular organismal-level iron ion homeostasis / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / intracellular iron ion homeostasis / protein ubiquitination / iron ion binding / perinuclear region of cytoplasm / nucleus / cytosol
Similarity search - Function
nmb1532 protein domain like / FBXL5-like, hemerythrin-like domain / Hemerythrin-like / Hemerythrin HHE cation binding domain / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like ...nmb1532 protein domain like / FBXL5-like, hemerythrin-like domain / Hemerythrin-like / Hemerythrin HHE cation binding domain / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / F-box domain / Leucine Rich repeat / Four Helix Bundle (Hemerythrin (Met), subunit A) / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / F-box/LRR-repeat protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.603 Å
AuthorsLi, P.
CitationJournal: Chembiochem / Year: 2012
Title: The Structural Basis of Iron Sensing by the Human F-box Protein FBXL5.
Authors: Shu, C. / Sung, M.W. / Stewart, M.D. / Igumenova, T.I. / Tan, X. / Li, P.
History
DepositionOct 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F-box/LRR-repeat protein 5
B: F-box/LRR-repeat protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3406
Polymers39,1172
Non-polymers2234
Water7,080393
1
A: F-box/LRR-repeat protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6703
Polymers19,5581
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: F-box/LRR-repeat protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6703
Polymers19,5581
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.082, 77.343, 78.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-312-

HOH

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Components

#1: Protein F-box/LRR-repeat protein 5 / F-box and leucine-rich repeat protein 5 / F-box protein FBL4/FBL5 / p45SKP2-like protein


Mass: 19558.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBXL5, FBL4, FBL5, FLR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKA1
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2011
RadiationMonochromator: Si-Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→32 Å / Num. all: 44592 / Num. obs: 44325 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.6→1.63 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX1.7_650model building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: SAD / Resolution: 1.603→31.881 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 27.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 3485 4.5 %random
Rwork0.1666 ---
all0.1689 84753 --
obs0.1689 -91.28 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.531 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.4021 Å2-0 Å2-0 Å2
2---4.2199 Å20 Å2
3----2.1822 Å2
Refinement stepCycle: LAST / Resolution: 1.603→31.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2660 0 4 393 3057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032718
X-RAY DIFFRACTIONf_angle_d0.7543648
X-RAY DIFFRACTIONf_dihedral_angle_d12.5221046
X-RAY DIFFRACTIONf_chiral_restr0.061382
X-RAY DIFFRACTIONf_plane_restr0.003470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.603-1.62470.29831150.23832568X-RAY DIFFRACTION79
1.6247-1.64790.3371150.22612659X-RAY DIFFRACTION83
1.6479-1.67250.28541250.23492681X-RAY DIFFRACTION83
1.6725-1.69870.31451330.21012740X-RAY DIFFRACTION85
1.6987-1.72650.26981200.18992736X-RAY DIFFRACTION84
1.7265-1.75630.27351470.17752750X-RAY DIFFRACTION85
1.7563-1.78820.22131170.18162764X-RAY DIFFRACTION85
1.7882-1.82260.24381350.16582731X-RAY DIFFRACTION85
1.8226-1.85980.22041220.15262771X-RAY DIFFRACTION85
1.8598-1.90020.22991340.14932752X-RAY DIFFRACTION85
1.9002-1.94440.20181470.14953085X-RAY DIFFRACTION96
1.9444-1.9930.24051340.14852987X-RAY DIFFRACTION92
1.993-2.04690.23191600.15473033X-RAY DIFFRACTION94
2.0469-2.10710.22391410.15153109X-RAY DIFFRACTION96
2.1071-2.17510.23261440.14593062X-RAY DIFFRACTION96
2.1751-2.25290.22051510.153155X-RAY DIFFRACTION98
2.2529-2.3430.18321410.14453115X-RAY DIFFRACTION96
2.343-2.44960.24621500.13993108X-RAY DIFFRACTION96
2.4496-2.57870.17011580.14373131X-RAY DIFFRACTION97
2.5787-2.74020.18441420.14963160X-RAY DIFFRACTION98
2.7402-2.95170.21881600.16033151X-RAY DIFFRACTION98
2.9517-3.24840.22831560.16663227X-RAY DIFFRACTION99
3.2484-3.71790.17811510.15453190X-RAY DIFFRACTION99
3.7179-4.68180.18271480.1623179X-RAY DIFFRACTION98
4.6818-31.88730.25241390.23473034X-RAY DIFFRACTION93

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