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- PDB-1auv: STRUCTURE OF THE C DOMAIN OF SYNAPSIN IA FROM BOVINE BRAIN -

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Basic information

Entry
Database: PDB / ID: 1auv
TitleSTRUCTURE OF THE C DOMAIN OF SYNAPSIN IA FROM BOVINE BRAIN
ComponentsSYNAPSIN IA
KeywordsTRANSFERASE / SYNAPSE / PHOSPHORYLATION / SYNAPSIN IA C-DOMAIN
Function / homology
Function and homology information


synaptic vesicle clustering / neurotransmitter secretion / cell projection / synapse organization / synaptic vesicle / synaptic vesicle membrane / actin binding / Golgi apparatus / ATP binding
Similarity search - Function
Synapsin / Synapsin, conserved site / Synapsin, phosphorylation site / Synapsin, pre-ATP-grasp domain / Synapsin, ATP-binding domain / Synapsin pre-ATP-grasp domain / Synapsin, ATP binding domain / Synapsin N-terminal domain / Synapsins signature 1. / Synapsins signature 2. ...Synapsin / Synapsin, conserved site / Synapsin, phosphorylation site / Synapsin, pre-ATP-grasp domain / Synapsin, ATP-binding domain / Synapsin pre-ATP-grasp domain / Synapsin, ATP binding domain / Synapsin N-terminal domain / Synapsins signature 1. / Synapsins signature 2. / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, subdomain 1 / ATP-grasp fold, B domain / 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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.15 Å
AuthorsEsser, L. / Wang, C. / Deisenhofer, J.
Citation
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.
#1: Journal: Protein Sci. / Year: 1997
Title: Identification, Expression, and Crystallization of the Protease-Resistant Conserved Domain of Synapsin I
Authors: Wang, C.R. / Esser, L. / Smagula, C.S. / Sudhof, T.C. / Deisenhofer, J.
#2: Journal: Science / Year: 1989
Title: Synapsins: Mosaics of Shared and Individual Domains in a Family of Synaptic Vesicle Phosphoproteins
Authors: Sudhof, T.C. / Czernik, A.J. / Kao, H.T. / Takei, K. / Johnston, P.A. / Horiuchi, A. / Kanazir, S.D. / Wagner, M.A. / Perin, M.S. / De Camilli, P. / Greengard, P.
History
DepositionSep 2, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 15, 2012Group: Structure summary
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SYNAPSIN IA
B: SYNAPSIN IA


Theoretical massNumber of molelcules
Total (without water)70,8362
Polymers70,8362
Non-polymers00
Water2,900161
1
A: SYNAPSIN IA
B: SYNAPSIN IA

A: SYNAPSIN IA
B: SYNAPSIN IA


Theoretical massNumber of molelcules
Total (without water)141,6714
Polymers141,6714
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)76.400, 76.400, 180.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.414908, -0.346441, 0.841326), (-0.332841, -0.80279, -0.494717), (0.846799, -0.48529, 0.217774)
Vector: 61.62489, 107.25087, 0.29079)

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Components

#1: Protein SYNAPSIN IA


Mass: 35417.820 Da / Num. of mol.: 2 / Fragment: RESIDUES 110 - 420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Cell line: B834 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P17599
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.83 %
Description: DATA WERE COLLECTED USING THE INVERSE BEAM METHOD
Crystal growTemperature: 299 K / pH: 7.25
Details: PROTEIN WAS CRYSTALLIZED FROM 5 % PEG 4000, 50 MM HEPES, PH 7.25 AT 26 DEG. CELSIUS., temperature 299K
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop / Details: Wang, C.R., (1997) Protein Sci., 6, 2264.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 %PEG40001drop
2100 mMTris-HCl1drop
30.3 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Oct 1, 1995 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 55873 / % possible obs: 74.3 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 14.6
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 1.58 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.113 / % possible all: 48
Reflection
*PLUS
Num. measured all: 105390

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.15→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.255 5178 9.9 %RANDOM
Rwork0.199 ---
obs0.199 52329 81.4 %-
Displacement parametersBiso mean: 37.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4636 0 0 161 4797
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.38
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.41.5
X-RAY DIFFRACTIONx_mcangle_it5.422
X-RAY DIFFRACTIONx_scbond_it3.492
X-RAY DIFFRACTIONx_scangle_it5.132.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 600 10.3 %
Rwork0.287 5202 -
obs--54.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX_ACE_LE.PROTOPHCSDX_ACE_LE.PRO
X-RAY DIFFRACTION2HT_OT.INP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.38

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