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- PDB-5g4p: Crystal structure of human hippocalcin at 2.4 A resolution -

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Basic information

Entry
Database: PDB / ID: 5g4p
TitleCrystal structure of human hippocalcin at 2.4 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 Aroclor 1254 / response to ketamine / regulation of voltage-gated calcium channel activity / cellular response to electrical stimulus / cellular response to L-glutamate / regulation of postsynaptic neurotransmitter receptor internalization / neuronal cell body membrane / dendritic spine head / inner ear development / positive regulation of protein targeting to membrane ...response to Aroclor 1254 / response to ketamine / regulation of voltage-gated calcium channel activity / cellular response to electrical stimulus / cellular response to L-glutamate / regulation of postsynaptic neurotransmitter receptor internalization / neuronal cell body membrane / dendritic spine head / inner ear development / positive regulation of protein targeting to membrane / dendrite membrane / cellular response to calcium ion / dendrite cytoplasm / calcium-mediated signaling / kinase binding / retina development in camera-type eye / actin binding / perikaryon / axon / glutamatergic synapse / calcium ion binding / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Recoverin family / EF hand / 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: 2.42 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 15, 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 1.2Jan 10, 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
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_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

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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)45,1478
Polymers44,9072
Non-polymers2406
Water61334
1
A: Neuron-specific calcium-binding protein hippocalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5744
Polymers22,4531
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)22,5744
Polymers22,4531
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.970, 50.970, 284.582
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A6 - 188
2114E6 - 188

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.866381, 0.488524, -0.10358), (-0.489584, -0.871797, -0.016675), (-0.098447, 0.036265, 0.994481)-1.75082, 4.80396, 23.27215

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Components

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


Mass: 22453.402 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

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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: I02 / 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: 2.42→43.56 Å / Num. obs: 15734 / % possible obs: 98.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 63.7 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.07
Reflection shellResolution: 2.42→2.59 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.8 / % 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: PDB ENTRY 5AEQ

5aeq


Resolution: 2.42→47.43 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 36.292 / SU ML: 0.37 / Cross valid method: THROUGHOUT / ESU R: 0.573 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27685 770 4.9 %RANDOM
Rwork0.22519 ---
obs0.22766 14886 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.609 Å2
Baniso -1Baniso -2Baniso -3
1--2.56 Å2-1.28 Å20 Å2
2---2.56 Å20 Å2
3---8.29 Å2
Refinement stepCycle: 1 / Resolution: 2.42→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 0 6 34 3012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023068
X-RAY DIFFRACTIONr_bond_other_d0.0020.022808
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.9674082
X-RAY DIFFRACTIONr_angle_other_deg1.04436490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4515366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43124.675154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.34915555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.271519
X-RAY DIFFRACTIONr_chiral_restr0.0920.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023417
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02690
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_it2.483.2271477
X-RAY DIFFRACTIONr_mcbond_other2.4813.2231476
X-RAY DIFFRACTIONr_mcangle_it3.1814.8081834
X-RAY DIFFRACTIONr_mcangle_other3.184.8131835
X-RAY DIFFRACTIONr_scbond_it3.3243.3441591
X-RAY DIFFRACTIONr_scbond_other3.3233.3481592
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6684.8982249
X-RAY DIFFRACTIONr_long_range_B_refined8.80330.33913091
X-RAY DIFFRACTIONr_long_range_B_other8.80330.34413092
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2815 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.670.5
medium thermal4.922
LS refinement shellResolution: 2.42→2.483 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 62 -
Rwork0.362 1057 -
obs--99.29 %
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)
11.0505-0.91560.71122.8293-0.71311.88280.22860.21040.1639-0.1517-0.5329-0.1593-0.02960.46950.30440.58430.13740.06150.73860.12130.0599.7257.0430.046
20.990.04330.69910.2840.35513.5787-0.454-0.25470.05160.1099-0.15960.13910.0899-0.5940.61360.73130.06880.05750.6503-0.10920.1356-8.8773.014-24.63
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 188
2X-RAY DIFFRACTION2E5 - 189

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