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- PDB-2whu: Fluorescent Protein mKeima at pH 8.0 -

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Basic information

Entry
Database: PDB / ID: 2whu
TitleFluorescent Protein mKeima at pH 8.0
ComponentsLARGE STOKES SHIFT FLUORESCENT PROTEIN
KeywordsFLUORESCENT PROTEIN / MKEIMA / STOKES SHIFT
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Large stokes shift fluorescent protein
Function and homology information
Biological speciesMontipora sp. 20 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsViolot, S. / Carpentier, P. / Blanchoin, L. / Bourgeois, D.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Reverse Ph-Dependence of Chromophore Protonation Explains the Large Stokes Shift of the Red Fluorescent Protein Mkeima
Authors: Violot, S. / Carpentier, P. / Blanchoin, L. / Bourgeois, D.
History
DepositionMay 6, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 23, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / 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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA", "BA", "CA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA", "BA", "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LARGE STOKES SHIFT FLUORESCENT PROTEIN
B: LARGE STOKES SHIFT FLUORESCENT PROTEIN
C: LARGE STOKES SHIFT FLUORESCENT PROTEIN
D: LARGE STOKES SHIFT FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)108,9274
Polymers108,9274
Non-polymers00
Water2,648147
1
A: LARGE STOKES SHIFT FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)27,2321
Polymers27,2321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LARGE STOKES SHIFT FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)27,2321
Polymers27,2321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LARGE STOKES SHIFT FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)27,2321
Polymers27,2321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: LARGE STOKES SHIFT FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)27,2321
Polymers27,2321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)225.110, 57.750, 93.070
Angle α, β, γ (deg.)90.00, 108.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
LARGE STOKES SHIFT FLUORESCENT PROTEIN / MKEIMA


Mass: 27231.686 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Montipora sp. 20 (invertebrata) / Plasmid: PET15-B / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q1JV70
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE NUMBERING STARTS AT MET 0 AS VAL 1 HAS BEEN INSERTED RESULTING FROM THE WT TO KOZAK ...RESIDUE NUMBERING STARTS AT MET 0 AS VAL 1 HAS BEEN INSERTED RESULTING FROM THE WT TO KOZAK CONSENSUS SEQUENCE MODIFICATION.

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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: 2.62 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 21% PEG 6000, 0.4M NACL, 0.15M PHOSPHATE PH5.6, VAPOR DIFFUSION, TEMPERATURE 293K, pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 6, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.65→44.81 Å / Num. obs: 33282 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 50.036 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.6
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WHT

2wht


Resolution: 2.65→44.81 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.86 / SU B: 16.544 / SU ML: 0.344 / Cross valid method: THROUGHOUT / ESU R: 0.945 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDE CHAIN FOR B ARG 202 ARE MISSING. CRYSTAL HAS BEEN SOAKED IN MOTHER LIQUOR BUFFERED AT PH8 BEFORE DATA COLLECTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.30694 1720 5.2 %RANDOM
Rwork0.2351 ---
obs0.23892 31480 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.222 Å2
Baniso -1Baniso -2Baniso -3
1--6 Å20 Å2-4.49 Å2
2--6.4 Å20 Å2
3----3.33 Å2
Refinement stepCycle: LAST / Resolution: 2.65→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6926 0 0 147 7073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227118
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1741.9719605
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4045852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12224.434327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.326151197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4341531
X-RAY DIFFRACTIONr_chiral_restr0.1280.2972
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025487
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.270.23459
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.24657
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2353
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1111.54436
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57126915
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.46833153
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5744.52690
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: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 97 -
Rwork0.334 2290 -
obs--99.83 %

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