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- PDB-6qsm: mTFP* open conformation: I197C-Y200H-Y204H mutant for enhanced me... -

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Basic information

Entry
Database: PDB / ID: 6qsm
TitlemTFP* open conformation: I197C-Y200H-Y204H mutant for enhanced metal binding
ComponentsGFP-like fluorescent chromoprotein cFP484
KeywordsFLUORESCENT PROTEIN / BETA BARREL / ARTIFICIAL METALLOENZYME / BIOCONJUGATION / PROTEIN DESIGN / THERMOSTABLE
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / GFP-like fluorescent chromoprotein cFP484
Function and homology information
Biological speciesClavularia sp. (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsFischer, J. / Renn, D. / Arold, T.A. / Groll, M.
CitationJournal: Acs Catalysis / Year: 2019
Title: A Robust and Versatile Host Protein for the Design and Evaluation of Artificial Metal Centers
Authors: Fischer, J. / Renn, D. / Quitterer, F. / Radhakrishnan, A. / Liu, M. / Makki, A. / Rajjaka, A. / Ghoprade, S. / Rueping, M. / Arold, T.A. / Groll, M. / Eppinger, J.
History
DepositionFeb 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GFP-like fluorescent chromoprotein cFP484


Theoretical massNumber of molelcules
Total (without water)25,1281
Polymers25,1281
Non-polymers00
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-0 kcal/mol
Surface area10240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.958, 70.549, 74.926
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 GFP-like fluorescent chromoprotein cFP484


Mass: 25128.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clavularia sp. (invertebrata) / Plasmid: PET303 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q9U6Y3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 1.94 Å3/Da / Density % sol: 36.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100 mM MES, 22% PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: May 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 24258 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.1
Reflection shellResolution: 1.65→1.75 Å / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DENZOdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HQK

2hqk


Resolution: 1.65→15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.656 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.097 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19612 1209 5 %RANDOM
Rwork0.15211 ---
obs0.15274 23005 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.131 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0 Å20 Å2
2--0.47 Å2-0 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 0 188 1945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131836
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171679
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.6742485
X-RAY DIFFRACTIONr_angle_other_deg1.3171.5993920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5975223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21823.19194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68215323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.242158
X-RAY DIFFRACTIONr_chiral_restr0.0720.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022047
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02389
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_it1.0951.269877
X-RAY DIFFRACTIONr_mcbond_other1.0781.267876
X-RAY DIFFRACTIONr_mcangle_it1.5031.9051099
X-RAY DIFFRACTIONr_mcangle_other1.5091.9071100
X-RAY DIFFRACTIONr_scbond_it1.4541.526959
X-RAY DIFFRACTIONr_scbond_other1.4491.525959
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8342.1811385
X-RAY DIFFRACTIONr_long_range_B_refined2.90115.3231996
X-RAY DIFFRACTIONr_long_range_B_other2.75714.8251957
X-RAY DIFFRACTIONr_rigid_bond_restr0.87533514
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 83 -
Rwork0.27 1651 -
obs--98.69 %

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