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- PDB-2awk: GFP R96M mature chromophore -

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Basic information

Entry
Database: PDB / ID: 2awk
TitleGFP R96M mature chromophore
Componentsgreen fluorescent protein
KeywordsLUMINESCENT PROTEIN / GFP chromophore formation barrel / slow maturation mutant
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: 1.15 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / 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 / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
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

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Assembly

Deposited unit
A: green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7562
Polymers25,7321
Non-polymers241
Water8,323462
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.235, 62.350, 71.067
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: 25731.926 Da / Num. of mol.: 1 / Fragment: residues 1-229 / Mutation: F64L, S65T, R96M, F99S, M153T, V163A
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.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4000, Magnesium chloride, HEPES, pH 8.00, 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: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.15→20 Å / Num. obs: 74907 / % possible obs: 91.9 % / Observed criterion σ(I): 2.39 / Redundancy: 2.91 % / Biso Wilson estimate: 8.9 Å2 / Rsym value: 0.037 / Net I/σ(I): 26.06
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 2.95 % / Mean I/σ(I) obs: 2.39 / Rsym value: 0.359 / % possible all: 67.1

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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: 1.15→19.95 Å / Num. parameters: 19767 / Num. restraintsaints: 23412 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.188 3607 -RANDOM
all0.188 ---
obs0.141 -86.2 %-
Displacement parametersBiso mean: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å20 Å2
2---2.64 Å20 Å2
3---4.08 Å2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 1746.93 / Occupancy sum non hydrogen: 2184.97
FreeObs
Luzzati coordinate error0.14 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.15→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 1 462 4031
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
LS refinement shellResolution: 1.15→1.22 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.307 418 -
Rwork0.33 --
obs--60.6 %

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