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- PDB-6lhr: Crystal structure of the complex between Vesicle Amine Transport-... -

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Basic information

Entry
Database: PDB / ID: 6lhr
TitleCrystal structure of the complex between Vesicle Amine Transport-1 and NADP
ComponentsSynaptic vesicle membrane protein VAT-1 homolog
KeywordsOXIDOREDUCTASE / VAT1 / Complex / Quinone
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Synaptic vesicle membrane protein VAT-1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 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 9, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,1908
Polymers152,2164
Non-polymers2,9744
Water88349
1
A: Synaptic vesicle membrane protein VAT-1 homolog
B: Synaptic vesicle membrane protein VAT-1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5954
Polymers76,1082
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-29 kcal/mol
Surface area26090 Å2
MethodPISA
2
C: Synaptic vesicle membrane protein VAT-1 homolog
D: Synaptic vesicle membrane protein VAT-1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5954
Polymers76,1082
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-30 kcal/mol
Surface area26390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.258, 96.290, 112.350
Angle α, β, γ (deg.)90.000, 123.133, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-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
11PROPROTHRTHR(chain 'A' and (resid 46 through 293 or resid 300 through 388))AA46 - 2926 - 252
12ALAALAPROPRO(chain 'A' and (resid 46 through 293 or resid 300 through 388))AA300 - 387260 - 347
23PROPROTHRTHR(chain 'B' and resid 46 through 388)BB46 - 2926 - 252
24ALAALAPROPRO(chain 'B' and resid 46 through 388)BB300 - 387260 - 347
35PROPROTHRTHR(chain 'C' and (resid 46 through 293 or resid 300 through 388))CC46 - 2926 - 252
36ALAALAPROPRO(chain 'C' and (resid 46 through 293 or resid 300 through 388))CC300 - 387260 - 347
47PROPROTHRTHRchain 'D'DD46 - 2926 - 252
48ALAALAPROPROchain 'D'DD300 - 387260 - 347

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Components

#1: Protein
Synaptic vesicle membrane protein VAT-1 homolog


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: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3000, Sodium citrate

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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: Jul 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.62→50 Å / Num. obs: 46822 / % possible obs: 98.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 63.69 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.02
Reflection shellResolution: 2.62→2.77 Å / Rmerge(I) obs: 0.64 / Num. unique obs: 7533

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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: 2.62→48.15 Å / SU ML: 0.3611 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.6386
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2462 2340 5 %
Rwork0.2075 44435 -
obs0.2095 46775 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.16 Å2
Refinement stepCycle: LAST / Resolution: 2.62→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10300 0 192 49 10541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007910730
X-RAY DIFFRACTIONf_angle_d0.955314616
X-RAY DIFFRACTIONf_chiral_restr0.05671672
X-RAY DIFFRACTIONf_plane_restr0.00661852
X-RAY DIFFRACTIONf_dihedral_angle_d17.56863868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.680.35291360.31462578X-RAY DIFFRACTION97.17
2.68-2.730.39361380.28742629X-RAY DIFFRACTION99.46
2.73-2.80.32821370.27832598X-RAY DIFFRACTION99.38
2.8-2.870.32831390.27182623X-RAY DIFFRACTION99.32
2.87-2.950.32861370.26732613X-RAY DIFFRACTION99.24
2.95-3.030.3151380.27072607X-RAY DIFFRACTION99.49
3.03-3.130.37511370.29362604X-RAY DIFFRACTION98.85
3.13-3.240.35711350.29192591X-RAY DIFFRACTION98.77
3.24-3.370.30431380.28032604X-RAY DIFFRACTION98.85
3.37-3.520.28611380.24682634X-RAY DIFFRACTION99.18
3.52-3.710.28321380.21332611X-RAY DIFFRACTION99.53
3.71-3.940.23731370.19712607X-RAY DIFFRACTION99.31
3.94-4.250.22431380.18292615X-RAY DIFFRACTION98.64
4.25-4.670.20881370.16232603X-RAY DIFFRACTION98
4.67-5.350.19491370.16452607X-RAY DIFFRACTION97.93
5.35-6.740.21781400.19762653X-RAY DIFFRACTION98.87
6.74-48.150.16011400.15682658X-RAY DIFFRACTION97.76

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