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- PDB-4p1q: GREEN FLUORESCENT PROTEIN E222H VARIANT -

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Basic information

Entry
Database: PDB / ID: 4p1q
TitleGREEN FLUORESCENT PROTEIN E222H VARIANT
ComponentsGreen fluorescent protein
KeywordsLUMINESCENT PROTEIN / CHROMOPHORE / BETA-BARREL / LUMINESCENCE / PHOTOPROTEIN / BIOLUMINESCENCE / FLUORESCENT PROTEIN
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 / Resolution: 1.5 Å
AuthorsKlein, M. / Carius, Y. / Auerbach, D. / Franz, S. / Jung, G. / Lancaster, C.R.D.
CitationJournal: Chembiochem / Year: 2014
Title: Replacement of Highly Conserved E222 by the Photostable Non-photoconvertible Histidine in GFP.
Authors: Auerbach, D. / Klein, M. / Franz, S. / Carius, Y. / Lancaster, C.R. / Jung, G.
History
DepositionFeb 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Structure summary
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / entity_src_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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_conn.ptnr2_symmetry
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8462
Polymers25,8231
Non-polymers231
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-6 kcal/mol
Surface area10440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.600, 62.200, 67.570
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: 25822.963 Da / Num. of mol.: 1 / Mutation: E222H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42212
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Na-acetate, PEG 3350 / PH range: 7.5 - 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.5→33.81 Å / Num. obs: 34827 / % possible obs: 99.95 % / Redundancy: 9.6 % / Biso Wilson estimate: 6.4 Å2 / Rsym value: 0.083 / Net I/σ(I): 6.3

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementResolution: 1.5→45.76 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.015 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17228 1751 5 %RANDOM
Rwork0.1362 ---
obs0.13802 33076 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.324 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.75 Å20 Å2
3---0.96 Å2
Refinement stepCycle: final / Resolution: 1.5→45.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 1 283 2105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0191955
X-RAY DIFFRACTIONr_bond_other_d0.0020.021829
X-RAY DIFFRACTIONr_angle_refined_deg2.3621.9582664
X-RAY DIFFRACTIONr_angle_other_deg1.11834241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8095253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49524.9100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55615337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.855159
X-RAY DIFFRACTIONr_chiral_restr0.2230.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212264
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02463
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_it1.3780.962937
X-RAY DIFFRACTIONr_mcbond_other1.3210.957936
X-RAY DIFFRACTIONr_mcangle_it2.0721.4381176
X-RAY DIFFRACTIONr_mcangle_other2.0861.4441177
X-RAY DIFFRACTIONr_scbond_it2.4051.2231018
X-RAY DIFFRACTIONr_scbond_other2.4041.231019
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.661.7391476
X-RAY DIFFRACTIONr_long_range_B_refined6.3819.5672336
X-RAY DIFFRACTIONr_long_range_B_other6.1658.882211
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 124 -
Rwork0.157 2437 -
obs--100 %

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