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- PDB-8dj8: Crystal Structure of Calgreen 1 protein -

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Basic information

Entry
Database: PDB / ID: 8dj8
TitleCrystal Structure of Calgreen 1 protein
ComponentsCalgreen One
KeywordsFLUORESCENT PROTEIN / Florescent Protein
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciesCorynactis californica (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHung, L.-W. / Nguyen, H.B. / Waldo, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structure and Function of Engineered Variants of GFP-type Green Fluorescent protein from Corynactis californica (tentative)
Authors: Nguyen, H.B. / Hung, L.-W. / Waldo, G.S.
History
DepositionJun 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 10, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 13, 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: Calgreen One


Theoretical massNumber of molelcules
Total (without water)25,1031
Polymers25,1031
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.156, 81.156, 84.977
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-447-

HOH

21A-451-

HOH

31A-452-

HOH

41A-461-

HOH

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Components

#1: Protein Calgreen One


Mass: 25103.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynactis californica (sea anemone) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium citrate, pH 5.6 20% (v/v) 2-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97941 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 1, 2011
Diffraction measurementDetails: 0.50 degrees, 1.4 sec, detector distance 260.00 mm
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionAv R equivalents: 0.09 / Number: 246296
ReflectionResolution: 2→50 Å / Num. obs: 19593 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.57 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/av σ(I): 26.442 / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 3 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 1.403 / Num. unique obs: 839 / Rsym value: 0.668 / % possible all: 77
Cell measurementReflection used: 246296

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX1.20.4487refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A46

2a46


Resolution: 2→36.62 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 19.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1978 1865 10.13 %
Rwork0.1686 16548 -
obs0.1716 18413 93.24 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.3 Å2 / Biso mean: 35.4953 Å2 / Biso min: 19.55 Å2
Refinement stepCycle: final / Resolution: 2→36.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1699 0 0 164 1863
Biso mean---41.84 -
Num. residues----211
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.060.27951120.2451930104270
2.06-2.120.22141170.2231113123084
2.12-2.180.23981410.20331203134489
2.18-2.260.22961310.19221235136692
2.26-2.350.22641460.18471234138092
2.35-2.460.24431340.16591279141394
2.46-2.590.1981470.16661287143496
2.59-2.750.20751510.17011321147297
2.75-2.960.20751430.17621338148198
2.96-3.260.21291540.17071370152499
3.26-3.730.14861550.155713601515100
3.73-4.70.18371630.140314011564100
4.7-36.620.19551710.17421477164899
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)
15.12770.49411.78661.9230.39893.2490.1217-0.4889-0.35950.2850.01240.00960.4510.0021-0.12790.34540.04360.0580.28910.03390.252412.739-8.9378.962
22.64970.40350.40622.0780.27762.7398-0.0587-0.0615-0.03680.04830.0391-0.0680.105-0.01760.00680.20490.02940.02090.18680.00220.218914.533-2.8761.58
33.14931.1270.88564.18891.55433.8183-0.19890.1734-0.1138-0.49180.1838-0.246-0.11870.21450.0040.1909-0.00630.02120.2031-0.0110.229120.692-1.818-6.438
42.72131.66520.55085.78380.72882.6428-0.1735-0.085-0.2660.02660.1636-0.20890.40020.2620.06420.24490.06820.03170.3163-0.04190.307524.407-4.6282.655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 7:50 )A7 - 50
2X-RAY DIFFRACTION2( CHAIN A AND RESID 51:139 )A51 - 139
3X-RAY DIFFRACTION3( CHAIN A AND RESID 140:183 )A140 - 183
4X-RAY DIFFRACTION4( CHAIN A AND RESID 184:219 )A184 - 219

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