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- PDB-1px2: Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.ATP ... -

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Basic information

Entry
Database: PDB / ID: 1px2
TitleCrystal Structure of Rat Synapsin I C Domain Complexed to Ca.ATP (Form 1)
ComponentsSynapsin I
KeywordsMEMBRANE PROTEIN / ATP binding / ATP grasp / calcium (II) ion
Function / homology
Function and homology information


synaptic vesicle cycle / Serotonin Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / extrinsic component of synaptic vesicle membrane / synaptic vesicle clustering / regulation of synaptic vesicle cycle / synaptonemal complex / neurotransmitter secretion / regulation of synaptic vesicle exocytosis / presynaptic active zone ...synaptic vesicle cycle / Serotonin Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / extrinsic component of synaptic vesicle membrane / synaptic vesicle clustering / regulation of synaptic vesicle cycle / synaptonemal complex / neurotransmitter secretion / regulation of synaptic vesicle exocytosis / presynaptic active zone / neuron development / synapse organization / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle membrane / calcium-dependent protein binding / synaptic vesicle / presynapse / cell body / actin binding / postsynaptic density / cytoskeleton / axon / dendrite / synapse / protein kinase binding / Golgi apparatus / ATP binding / identical protein binding
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-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsBrautigam, C.A. / Chelliah, Y. / Deisenhofer, J.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Tetramerization and ATP binding by a protein comprising the A, B, and C domains of rat synapsin I.
Authors: Brautigam, C.A. / Chelliah, Y. / Deisenhofer, J.
#1: Journal: Embo J. / Year: 1998
Title: Synapsin I is structurally similar to ATP-utilizing enzymes
Authors: Esser, L. / Wang, C.R. / Hosaka, M. / Smagula, C.S. / Sudhof, T.C. / Deisenhofer, J.
History
DepositionJul 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synapsin I
B: Synapsin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1736
Polymers91,0792
Non-polymers1,0954
Water5,873326
1
A: Synapsin I
B: Synapsin I
hetero molecules

A: Synapsin I
B: Synapsin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,34712
Polymers182,1584
Non-polymers2,1898
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area14980 Å2
ΔGint-108 kcal/mol
Surface area48320 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.000, 96.000, 305.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe second half of the (presumably) biological tetramer is generated by the twofold axis: -y + 1, -x + 1, -z + 1/6

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Components

#1: Protein Synapsin I /


Mass: 45539.398 Da / Num. of mol.: 2 / Fragment: A, B, & C domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: SYN1 / Plasmid: pSYNABC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09951
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Details: Sigma Chemical Corp
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


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


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEGMME 5K, Tris, NaCl, Ca.ATP, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 299K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17.5 mg/mlprotein1drop
210 mMcalcium ATP1drop
3150 mMTris1reservoirpH7.5
415-20 %(w/v)PEG5000 MME1reservoir
5300 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.942 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2000
RadiationMonochromator: Horizontally bent Si(111), with monochromatic mirrors of Rh-coated Si
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.942 Å / Relative weight: 1
ReflectionResolution: 2.23→40 Å / Num. all: 41721 / Num. obs: 41721 / % possible obs: 99.8 % / Redundancy: 11.2 % / Biso Wilson estimate: 28.5 Å2 / Rsym value: 0.082 / Net I/σ(I): 29.9
Reflection shellResolution: 2.23→2.31 Å / Redundancy: 9 % / Mean I/σ(I) obs: 6.1 / Num. unique all: 4060 / Rsym value: 0.391 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 40542 / Num. measured all: 467389 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.391

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AUX, Ca and ATP-gamma-S removed

1aux


Resolution: 2.23→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: modified Engh & Huber
Details: Although the A, B, and C domains of rat synapsin I were included in crystallization, only the C domain was observed. Some residues have side chains that are set to occupancies of 0.00 due to disorder.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2033 5 %random
Rwork0.203 ---
all0.205 40481 --
obs0.205 40481 97.1 %-
Solvent computationSolvent model: flat model / Bsol: 40.9992 Å2 / ksol: 0.326988 e/Å3
Displacement parametersBiso mean: 39.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å22.73 Å20 Å2
2--1.11 Å20 Å2
3----2.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.23→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4678 0 64 326 5068
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.49
LS refinement shellResolution: 2.23→2.37 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.287 297 4.7 %
Rwork0.233 5971 -
obs-5971 92.8 %
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.49

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