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- PDB-1aux: STRUCTURE OF THE C DOMAIN OF SYNAPSIN IA FROM BOVINE BRAIN WITH C... -

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Basic information

Entry
Database: PDB / ID: 1aux
TitleSTRUCTURE OF THE C DOMAIN OF SYNAPSIN IA FROM BOVINE BRAIN WITH CALCIUM ATP-GAMMA-S BOUND
ComponentsSYNAPSIN IA
KeywordsTRANSFERASE / SYNAPSE / PHOSPHORYLATION / SYNAPSIN IA C-DOMAIN / ATP-BINDING
Function / homology
Function and homology information


neurotransmitter secretion / cell projection / synaptic vesicle membrane / synaptic vesicle / 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, 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Synapsin-1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 6, 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: Non-polymer description
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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_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 IA
B: SYNAPSIN IA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9316
Polymers69,8042
Non-polymers1,1274
Water97354
1
A: SYNAPSIN IA
B: SYNAPSIN IA
hetero molecules

A: SYNAPSIN IA
B: SYNAPSIN IA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,86112
Polymers139,6084
Non-polymers2,2538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)76.160, 76.160, 182.330
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: (-0.445, -0.317, 0.8375), (-0.3213, -0.8165, -0.4798), (0.8359, -0.4826, 0.2615)
Vector: 61.4888, 106.8471, -0.1025)

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Components

#1: Protein SYNAPSIN IA


Mass: 34901.980 Da / Num. of mol.: 2 / Fragment: C DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PSYB21 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-ALPHA / References: UniProt: P17599
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsONE CALCIUM ION AND ONE MOLECULE OF ADENOSINE DIPHOSPHATE MONOTHIOPHOSPHATE (ATP-GAMMA-S) ARE BOUND ...ONE CALCIUM ION AND ONE MOLECULE OF ADENOSINE DIPHOSPHATE MONOTHIOPHOSPHATE (ATP-GAMMA-S) ARE BOUND PER MONOMER.

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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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growpH: 7.25
Details: PROTEIN WAS CRYSTALLIZED FROM 5 % PEG 4000, 100 MM HEPES, PH 7.25, THEN DIRECTLY TRANSFERRED TO 30 % PEG 4000, 50 MM HEPES, PH 7.5, 50 MM NACL. AFTER 12 H, CRYSTALS WERE TRANSFERRED TO 30 % ...Details: PROTEIN WAS CRYSTALLIZED FROM 5 % PEG 4000, 100 MM HEPES, PH 7.25, THEN DIRECTLY TRANSFERRED TO 30 % PEG 4000, 50 MM HEPES, PH 7.5, 50 MM NACL. AFTER 12 H, CRYSTALS WERE TRANSFERRED TO 30 % PEG, 75 MM HEPES, PH 7.5, 75 MM NACL, 2.5 MM CACL2, 2.5 MM ATP-GAMMA-S FOR 23 H.
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: 140 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 28177 / % possible obs: 88 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 15.5
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 1.44 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.21 / % possible all: 71.7
Reflection
*PLUS
Num. measured all: 88952

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AUV

1auv


Resolution: 2.3→20 Å / Rfactor Rfree error: 0.006 / 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
Rfree0.269 2226 8.6 %RANDOM
Rwork0.206 ---
obs0.206 25761 92.1 %-
Displacement parametersBiso mean: 53.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4634 0 64 54 4752
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.5
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_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.11.5
X-RAY DIFFRACTIONx_mcangle_it4.992
X-RAY DIFFRACTIONx_scbond_it3.172
X-RAY DIFFRACTIONx_scangle_it4.842.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 245 8 %
Rwork0.339 2830 -
obs--67.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX_ACE_LE.PROTOPHCSDX_ACE_LE.PRO
X-RAY DIFFRACTION2HT_OT.INPAPS_1.TOP
X-RAY DIFFRACTION3APS_1.PAR
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_deg1.4

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