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- PDB-4l12: Crystal structure of EGFP-based Calcium Sensor CatchER complexed ... -

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Basic information

Entry
Database: PDB / ID: 4l12
TitleCrystal structure of EGFP-based Calcium Sensor CatchER complexed with Gd
ComponentsEGFP-based Calcium Sensor CatchER
KeywordsCALCIUM BINDING PROTEIN / chromophore / luminescence / fluorescent protein / calcium sensor / metal ions / gadolinium
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
GADOLINIUM ATOM / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsZhang, Y. / Weber, I.T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural basis for a hand-like site in the calcium sensor CatchER with fast kinetics.
Authors: Zhang, Y. / Reddish, F. / Tang, S. / Zhuo, Y. / Wang, Y.F. / Yang, J.J. / Weber, I.T.
History
DepositionJun 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EGFP-based Calcium Sensor CatchER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4563
Polymers26,1411
Non-polymers3152
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.062, 88.334, 118.167
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-636-

HOH

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Components

#1: Protein EGFP-based Calcium Sensor CatchER / Green fluorescent protein


Mass: 26141.316 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Mutation: F64L, S65T, S147E, M153T, V163A, S202D, Q204E, F223E, T225E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42212
#2: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Gd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUE SER 65 UNDERWENT MUTATION TO THR 65. THR 65, TYR 66, AND GLY 67 CIRCULARIZED INTO ONE CHROMOPHORE.

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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: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 51 mM HEPES, pH 7.0, 1 mM beta-mercaptoethanol, 50 mM sodium acetate, 17% PEG4000, 2 mM gadolinium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 23, 2011
RadiationMonochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 30260 / Num. obs: 30260 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.2
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 8.7 / % possible all: 93.8

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OKW

2okw


Resolution: 1.78→27.13 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.199 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21965 1526 5 %RANDOM
Rwork0.19604 ---
all0.1972 30260 --
obs0.1972 28732 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 1.78→27.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 2 138 1982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221973
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.9762682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9465249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64325.842101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27415354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.549156
X-RAY DIFFRACTIONr_chiral_restr0.1010.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021519
X-RAY DIFFRACTIONr_nbd_refined0.2490.2832
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21288
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2141
X-RAY DIFFRACTIONr_metal_ion_refined0.1720.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.214
X-RAY DIFFRACTIONr_mcbond_it0.9591.51217
X-RAY DIFFRACTIONr_mcangle_it1.53721924
X-RAY DIFFRACTIONr_scbond_it2.373893
X-RAY DIFFRACTIONr_scangle_it3.7054.5750
LS refinement shellResolution: 1.78→1.829 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 92 -
Rwork0.253 1917 -
obs--90.54 %

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