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- PDB-4dxq: Crystal Structure of a reconstructed Kaede-type Red Fluorescent P... -

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Basic information

Entry
Database: PDB / ID: 4dxq
TitleCrystal Structure of a reconstructed Kaede-type Red Fluorescent Protein, LEA Q38A
ComponentsLEA Q38A GFP-LIKE PROTEINS
KeywordsLUMINESCENT PROTEIN / BETA BARREL
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciesSynthetic Construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKim, H. / Wachter, R.M.
CitationJournal: Biochemistry / Year: 2013
Title: Acid-Base Catalysis and Crystal Structures of a Least Evolved Ancestral GFP-like Protein Undergoing Green-to-Red Photoconversion.
Authors: Kim, H. / Grunkemeyer, T.J. / Modi, C. / Chen, L. / Fromme, R. / Matz, M.V. / Wachter, R.M.
History
DepositionFeb 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Dec 4, 2013Group: Database references
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_polymer_linkage.auth_atom_id_1 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LEA Q38A GFP-LIKE PROTEINS


Theoretical massNumber of molelcules
Total (without water)26,4341
Polymers26,4341
Non-polymers00
Water2,882160
1
A: LEA Q38A GFP-LIKE PROTEINS

A: LEA Q38A GFP-LIKE PROTEINS

A: LEA Q38A GFP-LIKE PROTEINS

A: LEA Q38A GFP-LIKE PROTEINS


Theoretical massNumber of molelcules
Total (without water)105,7364
Polymers105,7364
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area8290 Å2
ΔGint-11 kcal/mol
Surface area31730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.990, 81.140, 117.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein LEA Q38A GFP-LIKE PROTEINS / KAEDE-TYPE RED FLUORESCENT PROTEIN


Mass: 26434.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synthetic Construct (others) / Plasmid: pGEM-T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.085M tris, 0.085M sodium acetate, 16% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 13, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→34.5 Å / Num. all: 101622 / Num. obs: 17887 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.6
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→30.88 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.207 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R Free: 0.157
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23617 898 5 %RANDOM
Rwork0.18538 ---
obs0.18795 16950 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.473 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 0 160 1901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221786
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.972407
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0875212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64724.21783
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29915304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.77157
X-RAY DIFFRACTIONr_chiral_restr0.130.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211365
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.7881.51062
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.54221710
X-RAY DIFFRACTIONr_scbond_it3.7683724
X-RAY DIFFRACTIONr_scangle_it4.9424.5697
X-RAY DIFFRACTIONr_rigid_bond_restr2.6231786
X-RAY DIFFRACTIONr_sphericity_free6.0713160
X-RAY DIFFRACTIONr_sphericity_bonded5.53831740
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 65 -
Rwork0.266 1245 -
obs--99.92 %

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