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- PDB-4a27: Crystal structure of human synaptic vesicle membrane protein VAT-... -

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Basic information

Entry
Database: PDB / ID: 4a27
TitleCrystal structure of human synaptic vesicle membrane protein VAT-1 homolog-like protein
ComponentsSYNAPTIC VESICLE MEMBRANE PROTEIN VAT-1 HOMOLOG-LIKE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity / zinc ion binding
Similarity search - Function
Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Zinc-binding dehydrogenase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily ...Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Zinc-binding dehydrogenase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Synaptic vesicle membrane protein VAT-1 homolog-like
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.1 Å
AuthorsVollmar, M. / Shafqat, N. / Muniz, J.R.C. / Krojer, T. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. ...Vollmar, M. / Shafqat, N. / Muniz, J.R.C. / Krojer, T. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Yue, W.W. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Synaptic Vesicle Membrane Protein Vat-1 Homolog-Like Protein
Authors: Vollmar, M. / Shafqat, N. / Muniz, J.R.C. / Krojer, T. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Yue, W.W. / Oppermann, U.
History
DepositionSep 22, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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-LIKE
B: SYNAPTIC VESICLE MEMBRANE PROTEIN VAT-1 HOMOLOG-LIKE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,35011
Polymers76,7912
Non-polymers5599
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint10.9 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.509, 62.104, 83.795
Angle α, β, γ (deg.)90.00, 106.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SYNAPTIC VESICLE MEMBRANE PROTEIN VAT-1 HOMOLOG-LIKE / HUMAN SYNAPTIC VESICLE MEMBRANE PROTEIN VAT-1 HOMOLOG-LIKE PROTEIN


Mass: 38395.465 Da / Num. of mol.: 2 / Fragment: RESIDUES 41-389
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9HCJ6, Oxidoreductases
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSTARTING RESIDUES ARE DUE TO CONSTRUCT DESIGN.

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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: 2.26 Å3/Da / Density % sol: 45.6 % / Description: NONE
Crystal growDetails: 0.20 M NABR, 0.1 M BISTRISPROPANE PH 6.5, 20.0% PEG 3350, 10.0% ETHYLENE GLYCOL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→19.76 Å / Num. obs: 40044 / % possible obs: 99.8 % / Observed criterion σ(I): 2.3 / Redundancy: 4.7 % / Biso Wilson estimate: 39.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: PDB ENTRY 1YB5

1yb5


Resolution: 2.1→19.59 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 10.067 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.22956 2009 5 %RANDOM
Rwork0.1848 ---
obs0.18702 38011 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.655 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å2-3.25 Å2
2---0.12 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4681 0 36 137 4854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224801
X-RAY DIFFRACTIONr_bond_other_d0.0040.023226
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.986485
X-RAY DIFFRACTIONr_angle_other_deg1.15237895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3075618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22124.324185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36115796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2611523
X-RAY DIFFRACTIONr_chiral_restr0.0910.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215309
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02934
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 127 -
Rwork0.265 2700 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8951-0.24350.40871.72160.33850.3245-0.26030.08150.2746-0.07140.05830.1589-0.14760.11960.2020.2082-0.066-0.12790.37370.04840.1739-3.614714.71734.4085
21.15870.05330.98750.01690.05370.9221-0.0612-0.06020.0597-0.02470.01760.0576-0.00820.00020.04350.2206-0.0079-0.02840.2189-0.02590.3138-21.15794.2365-0.493
31.2469-0.36570.77880.8084-1.15171.70530.31190.3739-0.0965-0.2381-0.22820.03070.37360.3892-0.08370.28560.11-0.05270.2816-0.05910.2548-22.6271-4.3656-20.8309
41.9035-0.04911.55390.43580.14161.4821-0.0584-0.01040.08960.0910.00490.07150.00770.17930.05350.17960.01460.00660.2621-0.01650.2258-15.30325.05730.2081
50.2341-0.0540.3060.4984-0.14890.4312-0.04090.0875-0.02520.09070.0647-0.0449-0.010.0548-0.02390.2552-0.01210.03610.2926-0.02240.2279-45.43257.0974-39.2694
615.6199-32.8413-28.8908108.363630.208377.15391.48930.1024-0.8949-3.6347-3.67811.5308-1.47372.7022.18880.14050.14690.00680.4580.20540.3546-37.930131.7597-37.0866
71.334-0.17241.16560.3943-0.35871.158-0.03480.23010.24050.0757-0.1652-0.0522-0.0640.20960.20.24610.02-0.00990.27350.05950.2865-29.982315.488-25.9289
80.2860.3055-0.490.69590.11072.0452-0.0301-0.01590.04-0.06920.10880.0229-0.11510.1013-0.07870.29390.02290.0110.264-0.02320.2048-48.94616.9873-41.0672
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 117
2X-RAY DIFFRACTION2A118 - 226
3X-RAY DIFFRACTION3A227 - 312
4X-RAY DIFFRACTION4A313 - 386
5X-RAY DIFFRACTION5B40 - 212
6X-RAY DIFFRACTION6B213 - 220
7X-RAY DIFFRACTION7B221 - 337
8X-RAY DIFFRACTION8B338 - 386

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