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- PDB-4ogs: Crystal structure of GFP S205A/T203V at 2.2 A resolution -

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Basic information

Entry
Database: PDB / ID: 4ogs
TitleCrystal structure of GFP S205A/T203V at 2.2 A resolution
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / beta-can
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 / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsRemington, S.J. / Saif, M.
CitationJournal: Phys Chem Chem Phys / Year: 2014
Title: Insight into the structure and the mechanism of the slow proton transfer in the GFP double mutant T203V/S205A.
Authors: Wineman-Fisher, V. / Simkovitch, R. / Shomer, S. / Gepshtein, R. / Huppert, D. / Saif, M. / Kallio, K. / Remington, S.J. / Miller, Y.
History
DepositionJan 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8903
Polymers53,8552
Non-polymers351
Water2,792155
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,9271
Polymers26,9271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9632
Polymers26,9271
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.609, 86.609, 119.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Green fluorescent protein


Mass: 26927.410 Da / Num. of mol.: 2 / Mutation: S205A, T203V
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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Crystals were produced using 1 uL protein (26 mg/ml in 0.1 M imidazole, pH 7.8) mixed with 1 uL well solution, Crystallization screens varied from 22% to 32% (w:v) polyethylene glycol ...Details: Crystals were produced using 1 uL protein (26 mg/ml in 0.1 M imidazole, pH 7.8) mixed with 1 uL well solution, Crystallization screens varied from 22% to 32% (w:v) polyethylene glycol monomethyl ether (PEG) 2000 and 0.05M to 0.2M KBr at room temperature, for a range of pH values near neutrality, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 26, 2012
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. all: 27559 / Num. obs: 27588 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 31

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Processing

Software
NameVersionClassification
HKL-2000data collection
EPMRphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→15 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.891 / SU B: 12.381 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3063 778 5.1 %RANDOM
Rwork0.18119 ---
obs0.18738 14492 65.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.205 Å2
Baniso -1Baniso -2Baniso -3
1-3.02 Å20 Å20 Å2
2--3.02 Å20 Å2
3----6.03 Å2
Refinement stepCycle: LAST / Resolution: 2.21→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3519 0 1 155 3675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193611
X-RAY DIFFRACTIONr_bond_other_d0.0010.023275
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.9554906
X-RAY DIFFRACTIONr_angle_other_deg0.837521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7375448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25224.706170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.97215557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8411513
X-RAY DIFFRACTIONr_chiral_restr0.0840.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214182
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02859
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.213→2.269 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.693 1 -
Rwork0.469 42 -
obs--2.62 %

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