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- PDB-3ux2: Crystal Structure of Domain-Swapped Fam96a Major dimer -

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Basic information

Entry
Database: PDB / ID: 3ux2
TitleCrystal Structure of Domain-Swapped Fam96a Major dimer
ComponentsMIP18 family protein FAM96A
KeywordsIMMUNE SYSTEM / DUF59 / 3D domain swapping / protein-protein interaction / Alpha and beta protein (a+b) / Cytosolic iron-sulfur protein assembly 1
Function / homology
Function and homology information


cytosolic [4Fe-4S] assembly targeting complex / protein maturation / chromosome segregation / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
MIP18 family / MIP18 family-like / Iron-sulfur cluster assembly protein / Fe-S cluster assembly domain superfamily
Similarity search - Domain/homology
Cytosolic iron-sulfur assembly component 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsChen, K.-E. / Kobe, B. / Martin, J.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: The mammalian DUF59 protein Fam96a forms two distinct types of domain-swapped dimer.
Authors: Chen, K.E. / Richards, A.A. / Ariffin, J.K. / Ross, I.L. / Sweet, M.J. / Kellie, S. / Kobe, B. / Martin, J.L.
History
DepositionDec 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Advisory / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Oct 16, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MIP18 family protein FAM96A


Theoretical massNumber of molelcules
Total (without water)15,1191
Polymers15,1191
Non-polymers00
Water2,306128
1
A: MIP18 family protein FAM96A

A: MIP18 family protein FAM96A


Theoretical massNumber of molelcules
Total (without water)30,2382
Polymers30,2382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area6750 Å2
ΔGint-65 kcal/mol
Surface area14050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.411, 90.961, 34.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein MIP18 family protein FAM96A


Mass: 15119.002 Da / Num. of mol.: 1 / Fragment: DUF59 Domain, UNP residues 31-157
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM96A / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H5X1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 1.99 Å3/Da / Density % sol: 38.3 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 7.5
Details: HEPES, ammonium acetate, PEG 3350, pH 7.5, VAPOR DIFFUSION, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2010
RadiationMonochromator: Sagitally focused Si / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→58.507 Å / Num. all: 11602 / Num. obs: 11601 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 14 Å2 / Limit h max: 42 / Limit h min: 0 / Limit k max: 50 / Limit k min: 0 / Limit l max: 19 / Limit l min: 0 / Rmerge(I) obs: 0.06 / Net I/σ(I): 33.9
Reflection scaleGroup code: 1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 15.5 / Num. unique all: 1659 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SHELXphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
Blu-IceGUIdata collection
XDSdata reduction
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→19.541 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8779 / SU ML: 0.14 / σ(F): 1.97 / Phase error: 18.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1977 554 4.78 %Random
Rwork0.1613 ---
obs0.1631 11587 99.98 %-
all-11602 --
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.013 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 61.22 Å2 / Biso mean: 19.6894 Å2 / Biso min: 4.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.8824 Å20 Å20 Å2
2--0.7337 Å2-0 Å2
3---0.1487 Å2
Refine analyzeLuzzati coordinate error obs: 0.14 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 0 128 1128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161024
X-RAY DIFFRACTIONf_angle_d1.5821386
X-RAY DIFFRACTIONf_chiral_restr0.104166
X-RAY DIFFRACTIONf_plane_restr0.007180
X-RAY DIFFRACTIONf_dihedral_angle_d13.254410
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8003-1.98130.21261390.157526982837
1.9813-2.26760.2061340.1527212855
2.2676-2.85550.21231370.158127612898
2.8555-19.54190.18291440.168728532997

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