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- PDB-2whs: Fluorescent Protein mKeima at pH 3.8 -

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Basic information

Entry
Database: PDB / ID: 2whs
TitleFluorescent Protein mKeima at pH 3.8
ComponentsLARGE STOKES SHIFT FLUORESCENT PROTEIN
KeywordsFLUORESCENT PROTEIN / STOKES SHIFT / MKEIMA
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: 2.1 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 / Refinement description / 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: Atomic model / Data collection ...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_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn / struct_site
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 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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 SHEETS PRESENTED AS "BA" 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 SHEETS PRESENTED AS "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 SHEETS PRESENTED AS "DA" 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.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,98315
Polymers108,9274
Non-polymers1,05711
Water13,709761
1
A: LARGE STOKES SHIFT FLUORESCENT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5204
Polymers27,2321
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LARGE STOKES SHIFT FLUORESCENT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5204
Polymers27,2321
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LARGE STOKES SHIFT FLUORESCENT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4243
Polymers27,2321
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: LARGE STOKES SHIFT FLUORESCENT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5204
Polymers27,2321
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.570, 98.100, 123.270
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
LARGE STOKES SHIFT FLUORESCENT PROTEIN


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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 761 / 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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 3.8
Details: 0.2M LITHIUM SULPHATE, 20% PEG 3350, 0.1M PHOSPHATE CITRATE PH 3.8, VAPOR DIFFUSION, TEMPERATURE 293K

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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: 2.1→76.7 Å / Num. obs: 65627 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 27.337 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.3
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.2 / % possible all: 98.7

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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: 2.1→76.7 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.128 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: RESIDUE NUMEROTATION START AT MET 0 AS VAL 1 HAS BEEN INSERTED RESULTING FROM THE WT TO KOZAK CONSENSUS SEQUENCE MODIFICATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.24788 3332 5.1 %RANDOM
Rwork0.19011 ---
obs0.19302 62294 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.326 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å20 Å2
2--3.72 Å20 Å2
3----1.8 Å2
Refinement stepCycle: LAST / Resolution: 2.1→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7100 0 55 761 7916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227345
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8661.989920
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.145877
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66524.277332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.219151231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1181534
X-RAY DIFFRACTIONr_chiral_restr0.120.21001
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025618
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.23111
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.24835
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2577
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.283
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4931.54558
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70227106
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.62233488
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5764.52813
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: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 220 -
Rwork0.23 4508 -
obs--98.42 %

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