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- PDB-6xu4: Crystal structure of the genetically-encoded FGCaMP calcium indic... -

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Basic information

Entry
Database: PDB / ID: 6xu4
TitleCrystal structure of the genetically-encoded FGCaMP calcium indicator in its calcium-bound state
ComponentsFGCamp
KeywordsFLUORESCENT PROTEIN / FGCamp / calcium sensor / calcium indicator / genetically encoded / troponin / florescent protein
Function / homology
Function and homology information


spindle pole body organization / spore germination / central plaque of spindle pole body / hyphal tip / cell tip / enzyme regulator activity / regulation of cell cycle / calcium ion binding
Similarity search - Function
Ca2+ insensitive EF hand / EF hand / : / 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
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.18 Å
AuthorsBoyko, K.M. / Nikolaeva, A.Y. / Korzhenevskiy, D.A. / Barykina, N.V. / Subach, O.M. / Subach, F.V.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
Russian Science Foundation16-15-10323 Russian Federation
Russian Foundation for Basic Research19-04-00395 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2020
Title: FGCaMP7, an Improved Version of Fungi-Based Ratiometric Calcium Indicator for In Vivo Visualization of Neuronal Activity.
Authors: Barykina, N.V. / Sotskov, V.P. / Gruzdeva, A.M. / Wu, Y.K. / Portugues, R. / Subach, O.M. / Chefanova, E.S. / Plusnin, V.V. / Ivashkina, O.I. / Anokhin, K.V. / Vlaskina, A.V. / ...Authors: Barykina, N.V. / Sotskov, V.P. / Gruzdeva, A.M. / Wu, Y.K. / Portugues, R. / Subach, O.M. / Chefanova, E.S. / Plusnin, V.V. / Ivashkina, O.I. / Anokhin, K.V. / Vlaskina, A.V. / Korzhenevskiy, D.A. / Nikolaeva, A.Y. / Boyko, K.M. / Rakitina, T.V. / Varizhuk, A.M. / Pozmogova, G.E. / Subach, F.V.
History
DepositionJan 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: FGCamp
B: FGCamp
E: FGCamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,87113
Polymers140,4703
Non-polymers40110
Water543
1
A: FGCamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9845
Polymers46,8231
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FGCamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9845
Polymers46,8231
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: FGCamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9043
Polymers46,8231
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.561, 163.561, 143.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23E
14B
24E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLEULEUAA1 - 1831 - 183
21ARGARGLEULEUBB1 - 1831 - 183
12VALVALMETMETAA187 - 412185 - 410
22VALVALMETMETBB187 - 412185 - 410
13PHEPHETHRTHRAA283 - 337281 - 335
23PHEPHETHRTHREC283 - 337281 - 335
14PHEPHETHRTHRBB283 - 337281 - 335
24PHEPHETHRTHREC283 - 337281 - 335

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein FGCamp


Mass: 46823.461 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Aspergillus fumigatus, Aequorea victoria / Source: (gene. exp.) Aspergillus niger (mold) / Production host: Escherichia coli (E. coli) / References: UniProt: P60204*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.4 Å3/Da / Density % sol: 63.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.5 M Ammonium sulfate; 10%DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.18→89.94 Å / Num. obs: 33268 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.985 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.04 / Rrim(I) all: 0.106 / Net I/σ(I): 13.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.18-3.3470.8763051843530.7260.3530.9472.4100
10.55-89.9460.039625010480.9760.020.04434.999.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
HKL-2000data reduction
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EK7

3ek7


Resolution: 3.18→89.94 Å / Cor.coef. Fo:Fc: 0.852 / Cor.coef. Fo:Fc free: 0.755 / SU B: 23.011 / SU ML: 0.405 / SU R Cruickshank DPI: 0.9505 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.95 / ESU R Free: 0.509
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3483 1653 5 %RANDOM
Rwork0.2791 ---
obs0.2825 31561 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 172.16 Å2 / Biso mean: 79.989 Å2 / Biso min: 40.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 3.18→89.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6410 0 2440 3 8853
Biso mean--85.47 45.19 -
Num. residues----504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136604
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175827
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.6558837
X-RAY DIFFRACTIONr_angle_other_deg1.221.59113515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6685819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6424.006352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.162151093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3821531
X-RAY DIFFRACTIONr_chiral_restr0.0710.2869
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027415
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021318
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A40210.13
12B40210.13
21A62570.12
22B62570.12
31A17030.11
32E17030.11
41B15970.13
42E15970.13
LS refinement shellResolution: 3.18→3.263 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 123 -
Rwork0.292 2300 -
all-2423 -
obs--100 %

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