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- PDB-5gu5: Crystal structure of p24gamma2 GOLD domain determined by sulfur-SAD -

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Basic information

Entry
Database: PDB / ID: 5gu5
TitleCrystal structure of p24gamma2 GOLD domain determined by sulfur-SAD
ComponentsTransmembrane emp24 domain-containing protein 5
KeywordsTRANSPORT PROTEIN / GPI-anchored protein / p24 protein family
Function / homology
Function and homology information


WNT ligand biogenesis and trafficking / Golgi ribbon formation / cis-Golgi network / COPII-coated ER to Golgi transport vesicle / Golgi organization / endoplasmic reticulum exit site / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / intracellular protein transport ...WNT ligand biogenesis and trafficking / Golgi ribbon formation / cis-Golgi network / COPII-coated ER to Golgi transport vesicle / Golgi organization / endoplasmic reticulum exit site / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / intracellular protein transport / membrane => GO:0016020 / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum
Similarity search - Function
Transmembrane emp24 domain-containing protein 5 / emp24/gp25L/p24 family/GOLD / emp24/gp25L/p24 family/GOLD / Transmembrane emp24 domain-containing protein / GOLD domain superfamily / GOLD domain / GOLD domain profile.
Similarity search - Domain/homology
BROMIDE ION / Transmembrane emp24 domain-containing protein 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsNagae, M. / Yamaguchi, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Takeda Science Foundation Japan
MEXT25121738 Japan
CitationJournal: Proteins / Year: 2017
Title: Crystallographic analysis of murine p24 gamma 2 Golgi dynamics domain
Authors: Nagae, M. / Liebschner, D. / Yamada, Y. / Morita-Matsumoto, K. / Matsugaki, N. / Senda, T. / Fujita, M. / Kinoshita, T. / Yamaguchi, Y.
History
DepositionAug 25, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transmembrane emp24 domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2943
Polymers13,1351
Non-polymers1602
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-1 kcal/mol
Surface area6650 Å2
2
A: Transmembrane emp24 domain-containing protein 5
hetero molecules

A: Transmembrane emp24 domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5896
Polymers26,2692
Non-polymers3204
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/31
Buried area2500 Å2
ΔGint-10 kcal/mol
Surface area11380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.410, 79.410, 125.948
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Transmembrane emp24 domain-containing protein 5 / p24 family protein gamma-2 / p24gamma2


Mass: 13134.519 Da / Num. of mol.: 1 / Fragment: UNP residues 33-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tmed5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CXE7
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br

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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: 4.36 Å3/Da / Density % sol: 71.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 60% (v/v) Tascimate (pH 8.0)

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 12, 2013
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 6265 / % possible obs: 99 % / Redundancy: 12.8 % / Rsym value: 0.083 / Net I/σ(I): 72.1
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: 000)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(1.10_2155: 000)phasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→35.833 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.21
RfactorNum. reflection% reflection
Rfree0.2739 282 4.57 %
Rwork0.224 --
obs0.2261 6165 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→35.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms871 0 2 0 873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004891
X-RAY DIFFRACTIONf_angle_d0.731200
X-RAY DIFFRACTIONf_dihedral_angle_d15.063527
X-RAY DIFFRACTIONf_chiral_restr0.05126
X-RAY DIFFRACTIONf_plane_restr0.004158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8002-3.52750.37731310.30212876X-RAY DIFFRACTION100
3.5275-35.83620.24671510.20113007X-RAY DIFFRACTION98

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