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- PDB-2lxw: The solution structure of XIAP(RING)-binding domain of human XAF1 -

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Basic information

Entry
Database: PDB / ID: 2lxw
TitleThe solution structure of XIAP(RING)-binding domain of human XAF1
ComponentsXIAP-associated factor 1
KeywordsAPOPTOSIS / XAF1 / XIAP(RING)-binding domain
Function / homology
Function and homology information


response to interferon-beta / molecular sequestering activity / negative regulation of type I interferon production / Interferon alpha/beta signaling / apoptotic process / mitochondrion / zinc ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1730 / XIAP-associated factor 1 / XIAP-associated factor 1, C-terminal / XIAP-associated factor 1 C-terminal domain / : / : / TRAFD1/XAF1, zinc finger / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1730 / XIAP-associated factor 1 / XIAP-associated factor 1, C-terminal / XIAP-associated factor 1 C-terminal domain / : / : / TRAFD1/XAF1, zinc finger / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
XIAP-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model1
AuthorsTse, M. / Cho, C. / Guan, X. / Sze, K.
CitationJournal: To be Published
Title: The solution structure of XIAP(RING)-binding domain of human XAF1
Authors: Tse, M. / Cho, C. / Guan, X. / Sze, K.
History
DepositionSep 3, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: XIAP-associated factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2682
Polymers6,2021
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 300structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein XIAP-associated factor 1 / BIRC4-binding protein


Mass: 6202.118 Da / Num. of mol.: 1 / Fragment: UNP residues 251-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XAF1, BIRC4BP, XIAPAF1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6GPH4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H NOESY
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HNCA
1713D HN(CO)CA
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11113D 1H-15N TOCSY
11213D HNCO

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Sample preparation

DetailsContents: 1.2 mM [U-100% 13C; U-100% 15N] protein_1-1, 20 mM BisTris-HCl-2, 150 mM sodium chloride-3, 5 mM D10 DTT-4, 1 mM PMSF-5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMprotein_1-1[U-100% 13C; U-100% 15N]1
20 mMBisTris-HCl-21
150 mMsodium chloride-31
5 mMDTT-4D101
1 mMPMSF-51
Sample conditionsIonic strength: 0.15 / pH: 6.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichautomated peak assignments
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
Amberrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 15 / Representative conformer: 1

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