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- PDB-4ges: crystal structure of GFP-TYR151PYZ with an unnatural amino acid i... -

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Basic information

Entry
Database: PDB / ID: 4ges
Titlecrystal structure of GFP-TYR151PYZ with an unnatural amino acid incorporation
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / fluorescence / electron transduction
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
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsDong, J. / Liu, X. / Li, J. / Wang, J. / Gong, W.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: Genetic incorporation of a metal-chelating amino Acid as a probe for protein electron transfer.
Authors: Liu, X. / Li, J. / Dong, J. / Hu, C. / Gong, W. / Wang, J.
History
DepositionAug 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 13, 2023Group: 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
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 / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,8831
Polymers27,8831
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.717, 50.809, 62.364
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 Green fluorescent protein


Mass: 27883.260 Da / Num. of mol.: 1 / Mutation: P99S, M153T, V163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.9
Details: 60~100mg/ml protein sample in 50 mM Hepes, pH 7.5, reservior solution:16~19% PEG 3000, 100mM Tris pH 8.9,0.2M calcium acetate, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.23→50 Å / Num. all: 63375 / Num. obs: 62551 / % possible obs: 98.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.09 / Rsym value: 0.077 / Net I/σ(I): 23.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
CNSrefinement
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GFL

1gfl


Resolution: 1.23→45.87 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.149 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18773 3167 5.1 %RANDOM
Rwork0.16293 ---
all0.17 59944 --
obs0.16414 59267 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.004 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å20 Å2
2---0.84 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.23→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 0 206 2019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221916
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9612606
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.5625248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4225.16193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2215330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.929157
X-RAY DIFFRACTIONr_chiral_restr0.1010.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211474
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_it1.1231.51166
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76621893
X-RAY DIFFRACTIONr_scbond_it2.3393750
X-RAY DIFFRACTIONr_scangle_it3.4914.5703
X-RAY DIFFRACTIONr_rigid_bond_restr1.20831916
X-RAY DIFFRACTIONr_sphericity_free5.1373206
X-RAY DIFFRACTIONr_sphericity_bonded2.79531864
LS refinement shellResolution: 1.23→1.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 234 -
Rwork0.205 4036 -
obs-4036 92.89 %
Refinement TLS params.Method: refined / Origin x: -3.5351 Å / Origin y: -0.9052 Å / Origin z: 2.6935 Å
111213212223313233
T0.0012 Å2-0.0012 Å20.0005 Å2-0.0078 Å2-0.0002 Å2--0.0039 Å2
L0.0706 °20.0223 °20.0145 °2-0.4066 °20.1608 °2--0.3833 °2
S0.001 Å °-0.0009 Å °0.0075 Å °0.0188 Å °-0.0251 Å °0.0096 Å °0.014 Å °-0.0109 Å °0.0241 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B2 - 231
2X-RAY DIFFRACTION1B301 - 506

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