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- PDB-2awm: GFP R96A chromophore maturation recovery mutant R96A Q183R -

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Basic information

Entry
Database: PDB / ID: 2awm
TitleGFP R96A chromophore maturation recovery mutant R96A Q183R
Componentsgreen fluorescent protein
KeywordsLUMINESCENT PROTEIN / GFP chromophore recovery mutant R96A Q183R / barrel
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: 1.7 Å
AuthorsWood, T.I. / Barondeau, D.P. / Hitomi, C. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D.
CitationJournal: Biochemistry / Year: 2005
Title: Defining the role of arginine 96 in green fluorescent protein fluorophore biosynthesis.
Authors: Wood, T.I. / Barondeau, D.P. / Hitomi, C. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D.
History
DepositionSep 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_label_seq_id / _struct_conn_type.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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE RESIDUE SER A 65 IS MUTATED TO THR A 65. THR A 65, TYR A 66 AND GLY A 67 ARE MODIFIED TO ...SEQUENCE RESIDUE SER A 65 IS MUTATED TO THR A 65. THR A 65, TYR A 66 AND GLY A 67 ARE MODIFIED TO MAKE CHROMOPHORE (CRO A 66).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7493
Polymers25,7011
Non-polymers492
Water5,549308
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.510, 62.340, 71.260
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: 25700.873 Da / Num. of mol.: 1 / Mutation: F64L, S65T, R96A, F99S, M153T, V163A, Q183R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/DE3 pRIL / References: UniProt: P42212
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4000, Magnesium chloride, HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.984 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2003
RadiationMonochromator: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 24741 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.4 / Redundancy: 2.7 % / Biso Wilson estimate: 10.9 Å2 / Rsym value: 0.057 / Net I/σ(I): 18.4
Reflection shellResolution: 1.7→1.81 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 2318 / Rsym value: 0.356 / % possible all: 91.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EMA

1ema


Resolution: 1.7→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3.4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1145 -RANDOM
Rwork0.164 ---
all0.223 ---
obs0.223 24741 91.1 %-
Displacement parametersBiso mean: 10.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.9 Å20 Å20 Å2
2---2.74 Å20 Å2
3---5.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 14 296 2102
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.023
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.259 175 -
Rwork0.24 --
obs-3464 82 %

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