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- PDB-5h4z: Crystal structure of S202G mutant of human SYT-5 C2A domain -

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Basic information

Entry
Database: PDB / ID: 5h4z
TitleCrystal structure of S202G mutant of human SYT-5 C2A domain
ComponentsSynaptotagmin-5
KeywordsMETAL BINDING PROTEIN / mutant
Function / homology
Function and homology information


proximal neuron projection / neuronal dense core vesicle membrane / dense core granule / calcium ion-regulated exocytosis of neurotransmitter / regulation of calcium ion-dependent exocytosis / calcium-dependent phospholipid binding / syntaxin binding / clathrin binding / phosphatidylserine binding / regulation of dopamine secretion ...proximal neuron projection / neuronal dense core vesicle membrane / dense core granule / calcium ion-regulated exocytosis of neurotransmitter / regulation of calcium ion-dependent exocytosis / calcium-dependent phospholipid binding / syntaxin binding / clathrin binding / phosphatidylserine binding / regulation of dopamine secretion / synaptic vesicle endocytosis / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / Regulation of insulin secretion / synaptic vesicle membrane / recycling endosome membrane / chemical synaptic transmission / protein heterodimerization activity / axon / neuronal cell body / calcium ion binding / perinuclear region of cytoplasm
Similarity search - Function
Synaptotagmin / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsQiu, X. / Ge, J. / Yan, X. / Gao, Y. / Teng, M. / Niu, L.
Funding support China, 2items
OrganizationGrant numberCountry
Natural Science Foundation of Zhejiang ProvinceLQ14C050001 China
National Natural Science Foundation of China31400683 China
CitationJournal: Int. J. Biol. Macromol. / Year: 2017
Title: Structural analysis of Ca(2+)-binding pocket of synaptotagmin 5 C2A domain
Authors: Qiu, X. / Ge, J. / Gao, Y. / Teng, M. / Niu, L.
History
DepositionNov 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Aug 16, 2017Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Nov 8, 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
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_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_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.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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptotagmin-5
B: Synaptotagmin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5799
Polymers34,3032
Non-polymers2767
Water84747
1
A: Synaptotagmin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2724
Polymers17,1511
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-21 kcal/mol
Surface area7340 Å2
MethodPISA
2
B: Synaptotagmin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3075
Polymers17,1511
Non-polymers1564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-24 kcal/mol
Surface area7110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.005, 118.656, 109.464
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Synaptotagmin-5 / / Synaptotagmin V / SytV


Mass: 17151.418 Da / Num. of mol.: 2 / Fragment: UNP residues 102-242 / Mutation: S202G, R111Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYT5 / Plasmid: p28 / Production host: Escherichia coli (E. coli) / References: UniProt: O00445
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.6 Å3/Da / Density % sol: 71.18 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1M calcium acetate, 0.1M sodium acetate pH 4.0, 10%(w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 9990 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.167 / Net I/σ(I): 15.6
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H4Y

5h4y


Resolution: 3.01→50 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.869 / SU B: 13.452 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.772 / ESU R Free: 0.368
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25745 474 4.8 %RANDOM
Rwork0.19997 ---
obs0.20254 9496 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 22.754 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å20 Å20 Å2
2--3.78 Å20 Å2
3----2.16 Å2
Refinement stepCycle: 1 / Resolution: 3.01→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 7 47 2046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222044
X-RAY DIFFRACTIONr_bond_other_d0.0010.021375
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.9682774
X-RAY DIFFRACTIONr_angle_other_deg0.83433343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0075257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76323.91392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.25915324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7631513
X-RAY DIFFRACTIONr_chiral_restr0.0740.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212301
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02424
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_it0.6731.51275
X-RAY DIFFRACTIONr_mcbond_other0.0581.5523
X-RAY DIFFRACTIONr_mcangle_it1.26422041
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1263769
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0444.5732
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: 3.014→3.092 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.472 36 -
Rwork0.326 570 -
obs--83.82 %

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