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- PDB-5g58: Crystal structure of A190T mutant of human hippocalcin AT 2.5 A r... -

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Basic information

Entry
Database: PDB / ID: 5g58
TitleCrystal structure of A190T mutant of human hippocalcin AT 2.5 A resolution
ComponentsNeuron-specific calcium-binding protein hippocalcin
KeywordsCALCIUM BINDING PROTEIN / CA BINDING PROTEIN / CALCIUM- BINDING PROTEIN
Function / homology
Function and homology information


response to ketamine / response to Aroclor 1254 / regulation of voltage-gated calcium channel activity / cellular response to electrical stimulus / cellular response to L-glutamate / neuronal cell body membrane / dendritic spine head / regulation of postsynaptic neurotransmitter receptor internalization / inner ear development / positive regulation of protein targeting to membrane ...response to ketamine / response to Aroclor 1254 / regulation of voltage-gated calcium channel activity / cellular response to electrical stimulus / cellular response to L-glutamate / neuronal cell body membrane / dendritic spine head / regulation of postsynaptic neurotransmitter receptor internalization / inner ear development / positive regulation of protein targeting to membrane / regulation of signal transduction / dendrite membrane / dendrite cytoplasm / cellular response to calcium ion / calcium-mediated signaling / kinase binding / actin binding / retina development in camera-type eye / perikaryon / axon / calcium ion binding / glutamatergic synapse / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Recoverin family / EF hand domain / EF-hand domain pair / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Neuron-specific calcium-binding protein hippocalcin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.54 Å
AuthorsAntonyuk, S.V. / Helassa, N. / Lian, L.Y. / Haynes, L.P. / Burgoyne, R.D.
CitationJournal: Hum. Mol. Genet. / Year: 2017
Title: Biophysical and functional characterization of hippocalcin mutants responsible for human dystonia.
Authors: Helassa, N. / Antonyuk, S.V. / Lian, L.Y. / Haynes, L.P. / Burgoyne, R.D.
History
DepositionMay 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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: Neuron-specific calcium-binding protein hippocalcin
E: Neuron-specific calcium-binding protein hippocalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2078
Polymers44,9672
Non-polymers2406
Water61334
1
A: Neuron-specific calcium-binding protein hippocalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6044
Polymers22,4831
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Neuron-specific calcium-binding protein hippocalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6044
Polymers22,4831
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.660, 50.660, 283.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Neuron-specific calcium-binding protein hippocalcin / Calcium-binding protein BDR-2


Mass: 22483.428 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPCA, BDR2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P84074
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATION A190T

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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: 2.38 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 5.5
Details: 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.5, 18% V/V 2-PROPANOL, 16% W/V PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2016 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.54→43.87 Å / Num. obs: 13592 / % possible obs: 99.7 % / Redundancy: 4.6 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.7
Reflection shellResolution: 2.54→2.6 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.9 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.54→43.87 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.941 / SU B: 31.237 / SU ML: 0.311 / Cross valid method: THROUGHOUT / ESU R: 1.18 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24642 676 5 %RANDOM
Rwork0.21544 ---
obs0.21708 12828 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.581 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0.19 Å20 Å2
2---0.37 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.54→43.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2998 0 6 34 3038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023058
X-RAY DIFFRACTIONr_bond_other_d0.0060.022855
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9684112
X-RAY DIFFRACTIONr_angle_other_deg1.35336603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3225366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04824.395157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36415571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.091522
X-RAY DIFFRACTIONr_chiral_restr0.0830.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023432
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02702
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_it2.1175.0061470
X-RAY DIFFRACTIONr_mcbond_other2.1155.0051469
X-RAY DIFFRACTIONr_mcangle_it3.487.5021834
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1075.2581588
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.537→2.603 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 47 -
Rwork0.375 899 -
obs--98.54 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9965-0.20890.60892.0598-0.14483.1099-0.124-0.2510.3341-0.0071-0.07560.0662-0.461-0.33040.19960.07450.0641-0.03720.076-0.04880.04341.22411.9621.284
21.2173-0.52030.09161.2157-0.78964.0532-0.07480.159-0.1674-0.0964-0.2202-0.13930.4998-0.03430.29490.0759-0.02680.04850.10950.01890.08046.539-6.13225.674
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 190
2X-RAY DIFFRACTION2E6 - 190

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