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- PDB-5mwc: Crystal structure of the genetically-encoded green calcium indica... -

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Basic information

Entry
Database: PDB / ID: 5mwc
TitleCrystal structure of the genetically-encoded green calcium indicator NTnC in its calcium bound state
Componentsgenetically-encoded green calcium indicator NTnC
KeywordsFLUORESCENT PROTEIN / Green fluorescent protein / calcium indicator / calcium bound / genetically-encoded
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsBoyko, K.M. / Nikolaeva, A.Y. / Korzhenevskiy, D.A. / Rakitina, T.V. / Popov, V.O. / Subach, O.M. / Barykina, N.V. / Subach, F.V.
Funding support Russian Federation, 3items
OrganizationGrant numberCountry
Russian Science Foundation14-24-00172 Russian Federation
Russian Science Foundation16-15-10323 Russian Federation
Russian Foundation for Basic Research15-04-03383 Russian Federation
CitationJournal: To Be Published
Title: Enchanced variant of genetically-encoded green calcium indicator NTnC
Authors: Subach, O.M. / Barykina, N.V. / Piatkevich, K.D. / Sotskov, V.P. / Roshchina, M.A. / Kunitsyna, T.A. / Malyshev, A.Y. / Varizhuk, A.M. / Pozmogova, G.E. / Anokhin, K.V. / Enikolopov, G.N. / ...Authors: Subach, O.M. / Barykina, N.V. / Piatkevich, K.D. / Sotskov, V.P. / Roshchina, M.A. / Kunitsyna, T.A. / Malyshev, A.Y. / Varizhuk, A.M. / Pozmogova, G.E. / Anokhin, K.V. / Enikolopov, G.N. / Boyko, K.M. / Nikolaeva, A.Y. / Korzhenevskiy, D.A. / Rakitina, T.V. / Popov, V.O. / Subach, F.V.
History
DepositionJan 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 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.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 / _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
D: genetically-encoded green calcium indicator NTnC
A: genetically-encoded green calcium indicator NTnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2245
Polymers70,1042
Non-polymers1203
Water82946
1
D: genetically-encoded green calcium indicator NTnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1323
Polymers35,0521
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: genetically-encoded green calcium indicator NTnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0922
Polymers35,0521
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.100, 82.100, 157.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 13 - 303 / Label seq-ID: 13 - 301

Dom-IDAuth asym-IDLabel asym-ID
1DA
2AB

NCS ensembles :
ID
1
2

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Components

#1: Protein genetically-encoded green calcium indicator NTnC


Mass: 35052.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Three residues GYG form chromophore ligand named CR2.
Source: (gene. exp.) synthetic construct (others) / Plasmid: pBAD/His / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 46 / 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: 1.89 Å3/Da / Density % sol: 35.01 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M Sodium acetate, 22.5% PEG3350, 10% PEG400, 5% DMSO.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Sep 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.45→72.8 Å / Num. obs: 20432 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 8.933 % / Biso Wilson estimate: 63.624 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.066 / Χ2: 0.978 / Net I/σ(I): 23.84
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.45-2.59.3870.9732.311870.7341.026100
2.5-2.69.3970.7373.0220870.8070.778100
2.6-2.79.3010.566417950.8740.59899.9
2.7-2.89.2890.4025.6615510.9350.425100
2.8-39.2450.2528.8525130.9720.26699.7
3-48.560.07425.0464260.9980.07999.7
4-108.7880.03156.24456010.03399.7
10-507.4790.02171.653130.9990.02385.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HVF

4hvf


Resolution: 2.45→72.8 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.899 / SU B: 17.423 / SU ML: 0.366 / Cross valid method: THROUGHOUT / ESU R: 0.732 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.30971 1063 5.2 %RANDOM
Rwork0.23885 ---
obs0.24259 19409 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.224 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å2-0 Å2-0 Å2
2--0.22 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: 1 / Resolution: 2.45→72.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4112 0 3 46 4161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194234
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.861.9475712
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9455518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01224.184196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1815632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2571518
X-RAY DIFFRACTIONr_chiral_restr0.1250.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213282
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_it4.5856.3022105
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.0149.4342610
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.96.2682128
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.74917251
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: 14588 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1D
2A
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 64 -
Rwork0.373 1419 -
obs--99.87 %

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