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- PDB-1i7l: CRYSTAL STRUCTURE ANALYSIS OF THE COMPLEX OF THE C DOMAIN OF SYNA... -

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Basic information

Entry
Database: PDB / ID: 1i7l
TitleCRYSTAL STRUCTURE ANALYSIS OF THE COMPLEX OF THE C DOMAIN OF SYNAPSIN II FROM RAT WITH ATP
ComponentsSYNAPSIN II
KeywordsNEUROPEPTIDE / SYNAPSE / PHOSPHORYLATION / SYNAPSIN IIA C-DOMAIN / ATP BINDING
Function / homology
Function and homology information


synaptic vesicle cycle / Serotonin Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / synaptic vesicle clustering / extrinsic component of synaptic vesicle membrane / regulation of neurotransmitter secretion / SNARE complex / calcium-ion regulated exocytosis / neurotransmitter secretion / cytoskeletal protein binding ...synaptic vesicle cycle / Serotonin Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / synaptic vesicle clustering / extrinsic component of synaptic vesicle membrane / regulation of neurotransmitter secretion / SNARE complex / calcium-ion regulated exocytosis / neurotransmitter secretion / cytoskeletal protein binding / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle membrane / calcium-dependent protein binding / synaptic vesicle / presynapse / postsynaptic density / glutamatergic synapse / synapse / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Synapsin / Synapsin, conserved site / Synapsin, phosphorylation site / Synapsin, pre-ATP-grasp domain / Synapsin, ATP-binding domain / Synapsin, N-terminal domain / Synapsin, ATP binding domain / Synapsin N-terminal / Synapsins signature 1. / Synapsins signature 2. ...Synapsin / Synapsin, conserved site / Synapsin, phosphorylation site / Synapsin, pre-ATP-grasp domain / Synapsin, ATP-binding domain / Synapsin, N-terminal domain / Synapsin, ATP binding domain / Synapsin N-terminal / Synapsins signature 1. / Synapsins signature 2. / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Synapsin-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsEsser, L. / Palnitkar, M. / Deisenhofer, J.
CitationJournal: To be Published
Title: ATP Binding Independent of Metal Cations in Synapsin II
Authors: Esser, L. / Palnitkar, M. / Deisenhofer, J.
History
DepositionMar 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: SYNAPSIN II
B: SYNAPSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1754
Polymers70,1612
Non-polymers1,0142
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-18 kcal/mol
Surface area26580 Å2
MethodPISA
2
A: SYNAPSIN II
B: SYNAPSIN II
hetero molecules

A: SYNAPSIN II
B: SYNAPSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,3508
Polymers140,3214
Non-polymers2,0294
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area15210 Å2
ΔGint-60 kcal/mol
Surface area48730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.275, 121.275, 165.891
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsThe biological assembly is a dimer in the asymmetric unit.

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Components

#1: Protein SYNAPSIN II


Mass: 35080.328 Da / Num. of mol.: 2 / Fragment: C DOMAIN (RESIDUES 113-421)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: Q63537
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: PEG 4000, sodium chloride, TRIS, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.943 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2000
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.943 Å / Relative weight: 1
ReflectionResolution: 2.26→20 Å / Num. all: 32684 / Num. obs: 31094 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 31.6
Reflection shellResolution: 2.31→2.37 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 4.67 / Num. unique all: 2099 / % possible all: 96.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SYNCII model based on PDB ENTRY 1AUV

1auv


Resolution: 2.35→12 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 456569.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2260 8 %RANDOM
Rwork0.22 ---
all-28241 --
obs-28241 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.34 Å2 / ksol: 0.288 e/Å3
Displacement parametersBiso mean: 40.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å22.47 Å20 Å2
2--2.22 Å20 Å2
3----4.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.35→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4924 0 62 195 5181
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.4
X-RAY DIFFRACTIONc_mcbond_it1.751.5
X-RAY DIFFRACTIONc_mcangle_it2.792
X-RAY DIFFRACTIONc_scbond_it2.532
X-RAY DIFFRACTIONc_scangle_it3.522.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.37 381 8.3 %
Rwork0.289 4214 -
obs--92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CIS_PEPTIDE.PARAMATP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ATP.PARAM
X-RAY DIFFRACTION5ATP_A.PARAM

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