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- PDB-5h11: Crystal structure of Zebrafish Sec10 -

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Basic information

Entry
Database: PDB / ID: 5h11
TitleCrystal structure of Zebrafish Sec10
ComponentsUncharacterized protein
KeywordsEXOCYTOSIS / helical protein / exocyst complex / membrane traffic
Function / homology
Function and homology information


pronephros development / photoreceptor cell development / exocyst / photoreceptor cell outer segment organization / retina layer formation / retinal pigment epithelium development / melanosome transport / Golgi to plasma membrane transport / photoreceptor cell maintenance / determination of left/right symmetry ...pronephros development / photoreceptor cell development / exocyst / photoreceptor cell outer segment organization / retina layer formation / retinal pigment epithelium development / melanosome transport / Golgi to plasma membrane transport / photoreceptor cell maintenance / determination of left/right symmetry / exocytosis / outflow tract morphogenesis / cilium assembly / kidney development / retina development in camera-type eye
Similarity search - Function
Exocyst complex component Sec10-like / : / : / Exocyst complex component Sec10-like, alpha-helical bundle / Exocyst complex component Sec10, N-terminal
Similarity search - Domain/homology
BROMIDE ION / Exocyst complex component 5
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.732 Å
AuthorsChen, J. / Yamagata, A. / Fukai, S.
Funding support Japan, 5items
OrganizationGrant numberCountry
JSPS22121003 Japan
JSPS24570126 Japan
JSPS25650018 Japan
JSPS24687012 Japan
JSTCREST Japan
CitationJournal: Sci Rep / Year: 2017
Title: Crystal structure of Sec10, a subunit of the exocyst complex
Authors: Chen, J. / Yamagata, A. / Kubota, K. / Sato, Y. / Goto-Ito, S. / Fukai, S.
History
DepositionOct 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,14911
Polymers58,3501
Non-polymers79910
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-1 kcal/mol
Surface area26740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.693, 162.652, 45.572
Angle α, β, γ (deg.)90.00, 95.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Uncharacterized protein / Sec10 / exocyst complex


Mass: 58349.824 Da / Num. of mol.: 1 / Fragment: UNP residues 195-708 / Mutation: 385-394 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: exoc5 / Production host: Escherichia coli (E. coli) / References: UniProt: B0BLY0
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 4.68 Å3/Da / Density % sol: 73.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES-Na buffer, 0.57 M K Na tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9185 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: CMOS / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9185 Å / Relative weight: 1
ReflectionResolution: 2.73→50 Å / Num. obs: 26989 / % possible obs: 95.3 % / Redundancy: 8.2 % / Net I/σ(I): 10.7
Reflection shellResolution: 2.73→2.78 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.5 / % possible all: 75.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.732→46.917 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 31.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 1384 5.13 %
Rwork0.2363 --
obs0.2378 26977 95.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.732→46.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3991 0 10 2 4003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034058
X-RAY DIFFRACTIONf_angle_d0.6075472
X-RAY DIFFRACTIONf_dihedral_angle_d15.6731534
X-RAY DIFFRACTIONf_chiral_restr0.023619
X-RAY DIFFRACTIONf_plane_restr0.002707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7317-2.82930.37751080.34072137X-RAY DIFFRACTION78
2.8293-2.94260.34371230.33582370X-RAY DIFFRACTION90
2.9426-3.07650.36571520.32012556X-RAY DIFFRACTION95
3.0765-3.23860.3071490.29742541X-RAY DIFFRACTION95
3.2386-3.44150.32691470.27682627X-RAY DIFFRACTION98
3.4415-3.70710.28211430.23852652X-RAY DIFFRACTION99
3.7071-4.080.26261400.21272678X-RAY DIFFRACTION99
4.08-4.66990.23921400.19862648X-RAY DIFFRACTION98
4.6699-5.88180.22211360.20522694X-RAY DIFFRACTION100
5.8818-46.92420.20361460.18892690X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 41.2126 Å / Origin y: 1.4728 Å / Origin z: 20.3488 Å
111213212223313233
T0.7503 Å2-0.0905 Å2-0.0799 Å2-0.3913 Å2-0.0432 Å2--0.1475 Å2
L0.2168 °20.4567 °20.3814 °2-0.9271 °20.6582 °2--0.5307 °2
S0.0135 Å °0.0204 Å °-0.0053 Å °0.0587 Å °0.0123 Å °-0.01 Å °0.1053 Å °-0.059 Å °-0.0103 Å °
Refinement TLS groupSelection details: all

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