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- PDB-6lii: A quinone oxidoreductase -

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Basic information

Entry
Database: PDB / ID: 6lii
TitleA quinone oxidoreductase
ComponentsSynaptic vesicle membrane protein VAT-1 homolog
KeywordsOXIDOREDUCTASE / Quinone / NADPH / NADP
Function / homology
Function and homology information


negative regulation of mitochondrial fusion / Oxidoreductases / azurophil granule lumen / oxidoreductase activity / mitochondrial outer membrane / Neutrophil degranulation / extracellular exosome / extracellular region / zinc ion binding / membrane
Similarity search - Function
: / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Synaptic vesicle membrane protein VAT-1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHakoshima, T. / Kim, S.-Y. / Mori, T.
CitationJournal: Sci Rep / Year: 2021
Title: Structural insights into vesicle amine transport-1 (VAT-1) as a member of the NADPH-dependent quinone oxidoreductase family.
Authors: Kim, S.-Y. / Mori, T. / Chek, M.F. / Furuya, S. / Matsumoto, K. / Yajima, T. / Ogura, T. / Hakoshima, T.
History
DepositionDec 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptic vesicle membrane protein VAT-1 homolog
B: Synaptic vesicle membrane protein VAT-1 homolog
C: Synaptic vesicle membrane protein VAT-1 homolog
D: Synaptic vesicle membrane protein VAT-1 homolog


Theoretical massNumber of molelcules
Total (without water)152,2164
Polymers152,2164
Non-polymers00
Water4,053225
1
A: Synaptic vesicle membrane protein VAT-1 homolog
B: Synaptic vesicle membrane protein VAT-1 homolog


Theoretical massNumber of molelcules
Total (without water)76,1082
Polymers76,1082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-22 kcal/mol
Surface area26200 Å2
MethodPISA
2
C: Synaptic vesicle membrane protein VAT-1 homolog
D: Synaptic vesicle membrane protein VAT-1 homolog


Theoretical massNumber of molelcules
Total (without water)76,1082
Polymers76,1082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-24 kcal/mol
Surface area26590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.349, 69.349, 581.807
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEU(chain 'A' and (resid 45 through 66 or (resid 67...AA45 - 2985 - 258
12TRPTRPPROPRO(chain 'A' and (resid 45 through 66 or (resid 67...AA305 - 389265 - 349
23PROPROLEULEU(chain 'B' and (resid 45 through 48 or (resid 49...BB45 - 2985 - 258
24TRPTRPPROPRO(chain 'B' and (resid 45 through 48 or (resid 49...BB305 - 389265 - 349
35PROPROLEULEU(chain 'C' and (resid 45 through 48 or (resid 49...CC45 - 2985 - 258
36TRPTRPPROPRO(chain 'C' and (resid 45 through 48 or (resid 49...CC305 - 389265 - 349
47PROPROLEULEU(chain 'D' and (resid 45 through 48 or (resid 49...DD45 - 2985 - 258
48TRPTRPPROPRO(chain 'D' and (resid 45 through 48 or (resid 49...DD305 - 389265 - 349

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Components

#1: Protein
Synaptic vesicle membrane protein VAT-1 homolog / Vesicle Amine Transport-1


Mass: 38054.074 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VAT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99536
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium nitrate, PEG 3350, BisTris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 74674 / % possible obs: 99.9 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 13.32
Reflection shellResolution: 2.3→2.44 Å / Rmerge(I) obs: 0.575 / Num. unique obs: 11708

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A27

4a27


Resolution: 2.3→48.68 Å / Cross valid method: FREE R-VALUE / σ(F): 81.43 / Phase error: 19.9299
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2027 3735 5 %
Rwork0.1796 70939 -
obs0.1857 74674 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10320 0 0 225 10545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006310546
X-RAY DIFFRACTIONf_angle_d0.676714337
X-RAY DIFFRACTIONf_chiral_restr0.05211648
X-RAY DIFFRACTIONf_plane_restr0.00451849
X-RAY DIFFRACTIONf_dihedral_angle_d18.50123859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.28751790.27653391X-RAY DIFFRACTION93.34
2.34-2.380.26891860.24333525X-RAY DIFFRACTION94.99
2.38-2.430.27311800.24623435X-RAY DIFFRACTION95.02
2.43-2.480.26311870.24393541X-RAY DIFFRACTION94.98
2.48-2.530.25521790.23763406X-RAY DIFFRACTION95.01
2.53-2.590.24461850.23363511X-RAY DIFFRACTION94.97
2.59-2.650.24911850.22713527X-RAY DIFFRACTION95.02
2.65-2.730.24891830.22473466X-RAY DIFFRACTION94.98
2.73-2.810.23781840.21643492X-RAY DIFFRACTION94.99
2.81-2.90.25031860.20923534X-RAY DIFFRACTION95
2.9-30.25231860.21043537X-RAY DIFFRACTION95
3-3.120.23271840.19953498X-RAY DIFFRACTION95
3.12-3.260.19551850.19753514X-RAY DIFFRACTION95
3.26-3.430.22481870.18813555X-RAY DIFFRACTION95
3.43-3.650.20991890.17953595X-RAY DIFFRACTION94.98
3.65-3.930.19881850.16853522X-RAY DIFFRACTION95.01
3.93-4.330.18261920.15063642X-RAY DIFFRACTION94.97
4.33-4.950.15141910.13913635X-RAY DIFFRACTION95.01
4.95-6.240.1741940.16533671X-RAY DIFFRACTION94.96
6.24-48.680.18972070.17923931X-RAY DIFFRACTION95

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