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- PDB-4r6d: Modified mTFP* for enhanced metal binding: co-crystallization wit... -

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Basic information

Entry
Database: PDB / ID: 4r6d
TitleModified mTFP* for enhanced metal binding: co-crystallization with CuCl2
ComponentsGFP-like fluorescent chromoprotein cFP484
KeywordsFLUORESCENT PROTEIN / beta barrel topology / engineered metalloenzyme / Diels-Alderase
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
COPPER (II) ION / GFP-like fluorescent chromoprotein cFP484
Similarity search - Component
Biological speciesClavularia sp. (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsFischer, J. / Quitterer, F. / Groll, M. / Eppinger, J.
CitationJournal: TO BE PUBLISHED
Title: Modified mTFP* for enhanced metal binding: co-crystallization with CuCl2
Authors: Fischer, J. / Quitterer, F. / Groll, M. / Eppinger, J.
History
DepositionAug 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 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_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.conn_type_id / _struct_conn.id / _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_label_seq_id / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,9523
Polymers24,8251
Non-polymers1272
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.198, 67.656, 84.271
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: 24825.068 Da / Num. of mol.: 1 / Fragment: unp residues 44-258
Mutation: H63Y, H80N, L82I, S100T, N101T, Q104A, L110F, A118P, D119N, M151L, R161Y, F162L, D163K, M165E, L179T, K180G, E182D, P183A, I187R, V196K, I199V, S200K, S202K, H210Y, C213V, S217T, K220R, ...Mutation: H63Y, H80N, L82I, S100T, N101T, Q104A, L110F, A118P, D119N, M151L, R161Y, F162L, D163K, M165E, L179T, K180G, E182D, P183A, I187R, V196K, I199V, S200K, S202K, H210Y, C213V, S217T, K220R, V224A, I239C, Y246H, L251V, N254S, Y259N, L261T, L262F
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(DE3)gold / References: UniProt: Q9U6Y3
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jun 6, 2014
RadiationMonochromator: BRUKER MICROSTAR MICRO-FOCUS (MONTEL OPTICS) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→70 Å / Num. all: 32546 / Num. obs: 32526 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17
Reflection shellResolution: 1.55→1.65 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.7.0032refinement
PROTEUM PLUSPLUSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4Q9W

4q9w


Resolution: 1.55→10 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.44 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19397 1642 5.1 %RANDOM
Rwork0.15066 ---
obs0.1529 30761 99.75 %-
all-32403 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.456 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å2-0 Å2
2--0.46 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.55→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 2 310 2058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191816
X-RAY DIFFRACTIONr_bond_other_d0.0010.021699
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9752457
X-RAY DIFFRACTIONr_angle_other_deg0.75633937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2925219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08524.41986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18515319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.615158
X-RAY DIFFRACTIONr_chiral_restr0.0940.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212043
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02415
X-RAY DIFFRACTIONr_mcbond_it1.2551.011864
X-RAY DIFFRACTIONr_mcbond_other1.2551.01863
X-RAY DIFFRACTIONr_mcangle_it1.4941.521081
X-RAY DIFFRACTIONr_mcangle_other1.4941.5211082
X-RAY DIFFRACTIONr_scbond_it1.8811.315952
X-RAY DIFFRACTIONr_scbond_other1.8811.315952
X-RAY DIFFRACTIONr_scangle_other2.0761.8421374
X-RAY DIFFRACTIONr_long_range_B_refined3.50710.7552270
X-RAY DIFFRACTIONr_long_range_B_other2.6469.4942106
X-RAY DIFFRACTIONr_rigid_bond_restr2.34533514
X-RAY DIFFRACTIONr_sphericity_free32.773571
X-RAY DIFFRACTIONr_sphericity_bonded9.34253707
LS refinement shellResolution: 1.55→1.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 107 -
Rwork0.294 2209 -
obs--99.31 %
Refinement TLS params.Method: refined / Origin x: 15.9045 Å / Origin y: -2.5472 Å / Origin z: -3.564 Å
111213212223313233
T0.0014 Å20.0008 Å2-0.0005 Å2-0.0128 Å2-0 Å2--0.0084 Å2
L0.035 °2-0.0088 °2-0.0084 °2-0.0128 °2-0.0074 °2--0.0657 °2
S0.0022 Å °-0.001 Å °0.001 Å °-0.0036 Å °-0.0013 Å °0.0019 Å °0.0069 Å °0.0007 Å °-0.0009 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 217
2X-RAY DIFFRACTION1A901 - 902
3X-RAY DIFFRACTION1A1001 - 1310

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