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- PDB-5m6c: CRYSTAL STRUCTURE OF T71N MUTANT OF HUMAN HIPPOCALCIN -

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Basic information

Entry
Database: PDB / ID: 5m6c
TitleCRYSTAL STRUCTURE OF T71N MUTANT OF HUMAN HIPPOCALCIN
Components(Neuron-specific calcium-binding protein hippocalcin) x 2
KeywordsCALCIUM BINDING PROTEIN
Function / homology
Function and homology information


response to ketamine / regulation of voltage-gated calcium channel activity / response to Aroclor 1254 / 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 / regulation of voltage-gated calcium channel activity / response to Aroclor 1254 / 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 / retina development in camera-type eye / actin binding / perikaryon / axon / calcium ion binding / glutamatergic synapse / identical protein binding / membrane / cytoplasm / cytosol
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 / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHelassa, N. / Antonyuk, S.V. / Lian, L.Y. / Haynes, L.P. / Burgoyne, R.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme Trust United Kingdom
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
DepositionOct 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.4Jan 17, 2024Group: 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 / struct_conn / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)45,2038
Polymers44,9632
Non-polymers2406
Water23413
1
A: Neuron-specific calcium-binding protein hippocalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5874
Polymers22,4661
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
E: Neuron-specific calcium-binding protein hippocalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6174
Polymers22,4961
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.160, 51.160, 284.061
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 7 - 187 / Label seq-ID: 7 - 187

Dom-IDAuth asym-IDLabel asym-ID
1AA
2EB

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Components

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


Mass: 22466.402 Da / Num. of mol.: 1 / Mutation: T71N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPCA, BDR2 / Plasmid: PE-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P84074
#2: Protein Neuron-specific calcium-binding protein hippocalcin / Calcium-binding protein BDR-2


Mass: 22496.428 Da / Num. of mol.: 1 / Mutation: T71N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPCA, BDR2 / Plasmid: PE-SUMO / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P84074
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.38 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 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: I04-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→47.3 Å / Num. obs: 8283 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 62 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.122 / Net I/σ(I): 4.9
Reflection shellResolution: 3→3.18 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.31 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5g4p

5g4p


Resolution: 3→47.3 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.861 / SU B: 31.597 / SU ML: 0.551 / Cross valid method: THROUGHOUT / ESU R Free: 0.538 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28268 426 5.1 %RANDOM
Rwork0.21859 ---
obs0.22195 7856 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 78.297 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.18 Å20 Å2
2---0.35 Å20 Å2
3---1.14 Å2
Refinement stepCycle: 1 / Resolution: 3→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 6 13 3013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193063
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.9674119
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5165367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41224.375160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.18915573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7511523
X-RAY DIFFRACTIONr_chiral_restr0.0770.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212337
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.8137.8521468
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.19611.7691832
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6847.8471595
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.28863.9014503
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 532 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2E
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 19 -
Rwork0.348 592 -
obs--99.19 %

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