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- PDB-4gob: Low pH Crystal Structure of a reconstructed Kaede-type Red Fluore... -

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Basic information

Entry
Database: PDB / ID: 4gob
TitleLow pH Crystal Structure of a reconstructed Kaede-type Red Fluorescent Protein, Least Evolved Ancestor (LEA)
ComponentsKaede-type Fluorescent Protein
KeywordsFLUORESCENT PROTEIN / Beta-Barrel / Luminescent Protein
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 / Resolution: 1.53 Å
AuthorsKim, H. / Grunkemeyer, T.J. / Chen, L. / Fromme, R. / Wachter, R.M.
CitationJournal: Biochemistry / Year: 2013
Title: Acid-base catalysis and crystal structures of a least evolved ancestral GFP-like protein undergoing green-to-red photoconversion.
Authors: Kim, H. / Grunkemeyer, T.J. / Modi, C. / Chen, L. / Fromme, R. / Matz, M.V. / Wachter, R.M.
History
DepositionAug 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_rmsd_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kaede-type Fluorescent Protein
B: Kaede-type Fluorescent Protein
C: Kaede-type Fluorescent Protein
D: Kaede-type Fluorescent Protein


Theoretical massNumber of molelcules
Total (without water)105,7364
Polymers105,7364
Non-polymers00
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8890 Å2
ΔGint-4 kcal/mol
Surface area33000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.439, 100.789, 120.113
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Kaede-type Fluorescent Protein


Mass: 26434.064 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pGEM-T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 20% PEG 4000, 0.12M mM Glycine-phosphate, 100 mM magnesium chloride, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 14, 2012
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si 111
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. all: 264165 / Num. obs: 165103 / % possible obs: 94.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 22.5
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.2 / % possible all: 98.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→33.98 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.59 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.093 / ESU R Free: 0.087
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23105 7050 5 %RANDOM
Rwork0.17531 ---
obs0.17808 134936 94.06 %-
all-197089 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.595 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2--0.34 Å2-0 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.53→33.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7051 0 0 294 7345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.027421
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9710038
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025897
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.98324.261352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.547151276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4891533
X-RAY DIFFRACTIONr_chiral_restr0.1020.21016
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215757
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr3.31637421
X-RAY DIFFRACTIONr_sphericity_free24.675582
X-RAY DIFFRACTIONr_sphericity_bonded26.89257421
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 488 -
Rwork0.161 9945 -
obs--98.42 %

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