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- PDB-8sv7: The 1.53 Angstrom structure of human Tango2 -

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Basic information

Entry
Database: PDB / ID: 8sv7
TitleThe 1.53 Angstrom structure of human Tango2
ComponentsTransport and Golgi organization protein 2 homolog
KeywordsTRANSPORT PROTEIN / Heme / Transport / Transport and Golgi organization 2 (TANGO2) protein / AKA heme-responsive gene 9 (HRG-9) / high resolution apo structure
Function / homologyTransport and Golgi organisation protein 2 / Transport and Golgi organisation 2 / Golgi organization / protein secretion / Golgi apparatus / mitochondrion / cytosol / cytoplasm / Transport and Golgi organization protein 2 homolog
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsZhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: The crystal structure of human Tango2, a heme transport protein determined to 1.53 Angstroms resolution
Authors: Zhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
History
DepositionMay 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transport and Golgi organization protein 2 homolog
B: Transport and Golgi organization protein 2 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1284
Polymers61,9362
Non-polymers1922
Water9,530529
1
A: Transport and Golgi organization protein 2 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0642
Polymers30,9681
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transport and Golgi organization protein 2 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0642
Polymers30,9681
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.730, 49.960, 241.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Transport and Golgi organization protein 2 homolog


Mass: 30968.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TANGO2, C22orf25 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PlysE / References: UniProt: Q6ICL3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Equal parts of protein solution 25 mg/ml and a precipitate cocktail consisting of 1.0 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 1% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2023 / Details: KB mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→48.71 Å / Num. obs: 84855 / % possible obs: 94.2 % / Redundancy: 13.6 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.13 / Rrim(I) all: 0.049 / Net I/σ(I): 28.14
Reflection shellResolution: 1.53→1.57 Å / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 3.97 / Num. unique obs: 4390 / CC1/2: 0.967 / CC star: 0.989 / Rrim(I) all: 0.525 / % possible all: 65.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSV. 220110data scaling
XDSV. 220110data reduction
PHENIX(1.20.1_4487: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→48.71 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / Phase error: 21.17
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1957 2019 2.38 %Random
Rwork0.1676 ---
obs-84823 92.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.13 Å2
Refinement stepCycle: LAST / Resolution: 1.53→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4237 0 10 529 4776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00544340
X-RAY DIFFRACTIONf_angle_d0.79625897
X-RAY DIFFRACTIONf_chiral_restr0.0534655
X-RAY DIFFRACTIONf_plane_restr0.0053759
X-RAY DIFFRACTIONf_dihedral_angle_d16.84321565
LS refinement shellResolution: 1.53→1.57 Å
RfactorNum. reflection% reflection
Rfree0.2681 --
Rwork0.2017 --
obs-3694 58 %

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