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- PDB-4q9x: mTFP* PdCl2 soak -

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Basic information

Entry
Database: PDB / ID: 4q9x
TitlemTFP* PdCl2 soak
ComponentsGFP-like fluorescent chromoprotein cFP484
KeywordsFLUORESCENT PROTEIN / artificial metalloenzyme / metalloenzyme / bioconjugation / protein design / thermostable / temperature stable / solvent stable / robust
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
CARBONATE ION / PALLADIUM ION / GFP-like fluorescent chromoprotein cFP484
Similarity search - Component
Biological speciesClavularia sp. (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFischer, J. / Quitterer, F. / Groll, M. / Eppinger, J.
CitationJournal: To be Published
Title: mTFP*: An imperishable and versatile protein host for anchoring diverse ligands and organocatalysts
Authors: Fischer, J. / Quitterer, F. / Groll, M. / Eppinger, J.
History
DepositionMay 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GFP-like fluorescent chromoprotein cFP484
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,27715
Polymers25,1881
Non-polymers1,08914
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.470, 83.630, 37.820
Angle α, β, γ (deg.)90.00, 112.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GFP-like fluorescent chromoprotein cFP484


Mass: 25188.408 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 (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q9U6Y3
#2: Chemical
ChemComp-PD / PALLADIUM ION


Mass: 106.420 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Pd
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.01 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25.9% PEG3000 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2013
RadiationMonochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 15738 / Num. obs: 15454 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 16.5
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 1.9 / % possible all: 98.3

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HQK

2hqk


Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 9.238 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21653 773 5 %RANDOM
Rwork0.17641 ---
obs0.17849 14681 98.51 %-
all-15454 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.467 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20.77 Å2
2---0.03 Å2-0 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 17 64 1832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.021801
X-RAY DIFFRACTIONr_bond_other_d0.0010.021683
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9812427
X-RAY DIFFRACTIONr_angle_other_deg0.67733893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5915211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01824.41986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16715314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.221158
X-RAY DIFFRACTIONr_chiral_restr0.0670.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212009
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02409
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_it1.9372.698850
X-RAY DIFFRACTIONr_mcbond_other1.9332.696849
X-RAY DIFFRACTIONr_mcangle_it2.5284.0471059
X-RAY DIFFRACTIONr_mcangle_other2.5274.0491060
X-RAY DIFFRACTIONr_scbond_it2.2613.024951
X-RAY DIFFRACTIONr_scbond_other2.2423.023948
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8214.4221365
X-RAY DIFFRACTIONr_long_range_B_refined3.53922.731993
X-RAY DIFFRACTIONr_long_range_B_other3.44122.5961982
X-RAY DIFFRACTIONr_rigid_bond_restr1.36433483
X-RAY DIFFRACTIONr_sphericity_free26.728530
X-RAY DIFFRACTIONr_sphericity_bonded8.55953485
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 56 -
Rwork0.279 1059 -
obs--98.32 %
Refinement TLS params.Method: refined / Origin x: 30.8909 Å / Origin y: -11.486 Å / Origin z: 45.8575 Å
111213212223313233
T0.0478 Å2-0.0186 Å2-0.0061 Å2-0.0659 Å20.0079 Å2--0.0459 Å2
L1.6263 °2-0.0294 °2-0.0858 °2-1.616 °2-0.655 °2--2.2539 °2
S0.0223 Å °-0.0141 Å °0.0798 Å °-0.1644 Å °-0.0697 Å °-0.1512 Å °0.1938 Å °-0.1634 Å °0.0474 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 217
2X-RAY DIFFRACTION1A901 - 912

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