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- PDB-5hzo: GFP mutant S205G -

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Basic information

Entry
Database: PDB / ID: 5hzo
TitleGFP mutant S205G
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / mutant / excited state proton transfer
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
D-MALATE / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsRemington, S.J. / Trujillo, K.
Funding support United States, Israel, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1021374 United States
Binational Science FoundationBSF-2010082 Israel
CitationJournal: To Be Published
Title: Ultrafast Dynamics and Mechanisms of Proton Transfer in the GFP S205G Mutant
Authors: Wineman-Fisher, V. / Simkovitch, R. / Huppert, D. / Trujillo, K. / Remington, S.J. / Miller, Y.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_torsion / struct_conn
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_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,7565
Polymers52,9922
Non-polymers7653
Water2,000111
1
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6302
Polymers26,4961
Non-polymers1341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1263
Polymers26,4961
Non-polymers6312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.031, 96.284, 151.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Green fluorescent protein /


Mass: 26495.816 Da / Num. of mol.: 2 / Fragment: UNP residues 1-235
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-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C4H6O5
#3: Chemical ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 1.0 M malate, pH 8.0, Tris, 0.3 M NaCl, 1% n-nonyl-beta-D maltoside

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 24, 2010
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.49→75 Å / Num. obs: 13474 / % possible obs: 96.9 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.8
Reflection shellResolution: 2.49→2.54 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.3 / % possible all: 12.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EMB

1emb


Resolution: 2.49→10 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.858 / SU B: 14.872 / SU ML: 0.317 / Cross valid method: THROUGHOUT / ESU R Free: 0.42 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27598 644 4.9 %RANDOM
Rwork0.175 ---
obs0.17993 12468 75.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.05 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å20 Å2-0 Å2
2--3.29 Å20 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 2.49→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3586 0 50 111 3747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193726
X-RAY DIFFRACTIONr_bond_other_d0.0040.023369
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.9655054
X-RAY DIFFRACTIONr_angle_other_deg1.0033.0057746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6515454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27124.689177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.49815569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8131514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214268
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02878
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_it2.3813.8471827
X-RAY DIFFRACTIONr_mcbond_other2.3783.8481826
X-RAY DIFFRACTIONr_mcangle_it3.7735.7612276
X-RAY DIFFRACTIONr_mcangle_other3.7725.7622277
X-RAY DIFFRACTIONr_scbond_it2.5473.9831899
X-RAY DIFFRACTIONr_scbond_other2.5463.9811896
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0275.8952777
X-RAY DIFFRACTIONr_long_range_B_refined6.69630.5524059
X-RAY DIFFRACTIONr_long_range_B_other6.69730.5534045
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.49→2.551 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 14 -
Rwork0.309 171 -
obs--15.42 %

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