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- PDB-4q9w: mTFP*: a robust and versatile host protein at 1.00 A resolution -

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Basic information

Entry
Database: PDB / ID: 4q9w
TitlemTFP*: a robust and versatile host protein at 1.00 A resolution
ComponentsGFP-like fluorescent chromoprotein cFP484
KeywordsFLUORESCENT PROTEIN / beta barrel / 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
GFP-like fluorescent chromoprotein cFP484
Similarity search - Component
Biological speciesClavularia sp. (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
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
B: GFP-like fluorescent chromoprotein cFP484


Theoretical massNumber of molelcules
Total (without water)50,3772
Polymers50,3772
Non-polymers00
Water13,709761
1
A: GFP-like fluorescent chromoprotein cFP484


Theoretical massNumber of molelcules
Total (without water)25,1881
Polymers25,1881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GFP-like fluorescent chromoprotein cFP484


Theoretical massNumber of molelcules
Total (without water)25,1881
Polymers25,1881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.520, 85.170, 63.140
Angle α, β, γ (deg.)90.00, 100.32, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999887, 0.002002, 0.014914), (2.2E-5, 0.990917, -0.134473), (-0.015048, 0.134459, 0.990805)14.17932, 1.44306, 32.47114

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Components

#1: Protein GFP-like fluorescent chromoprotein cFP484


Mass: 25188.408 Da / Num. of mol.: 2
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, 220R, ...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, 220R, V224A, H242Y, 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-Gold(DE3) / References: UniProt: Q9U6Y3
#2: 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: 2.02 Å3/Da / Density % sol: 39.19 %
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: Jun 8, 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→10 Å / Num. all: 215374 / Num. obs: 204329 / % possible obs: 94.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 15.6
Reflection shellResolution: 1→1.1 Å / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.8 / % possible all: 88.1

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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: pdb entry 2HQK

2hqk


Resolution: 1→10 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.568 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.023 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14995 10217 5 %RANDOM
Rwork0.1308 ---
obs0.13175 194111 94.89 %-
all-204328 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.239 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å2-0.13 Å2
2---0.29 Å2-0 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 0 761 4317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023863
X-RAY DIFFRACTIONr_bond_other_d0.0010.023590
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.9765255
X-RAY DIFFRACTIONr_angle_other_deg0.78138337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9875480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43524.457184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37315680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7581518
X-RAY DIFFRACTIONr_chiral_restr0.0980.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214434
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02888
X-RAY DIFFRACTIONr_mcbond_it0.9860.8751842
X-RAY DIFFRACTIONr_mcbond_other0.9850.8731841
X-RAY DIFFRACTIONr_mcangle_it1.2091.3182333
X-RAY DIFFRACTIONr_mcangle_other1.2091.3212334
X-RAY DIFFRACTIONr_scbond_it1.3911.0972021
X-RAY DIFFRACTIONr_scbond_other1.381.0912019
X-RAY DIFFRACTIONr_scangle_other1.6481.5542917
X-RAY DIFFRACTIONr_long_range_B_refined3.1129.9635099
X-RAY DIFFRACTIONr_long_range_B_other2.3768.4164599
X-RAY DIFFRACTIONr_rigid_bond_restr2.37537451
X-RAY DIFFRACTIONr_sphericity_free25.8125125
X-RAY DIFFRACTIONr_sphericity_bonded7.16457972
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 683 -
Rwork0.225 12973 -
obs--86.6 %
Refinement TLS params.

S32: 0.0013 Å ° / T23: -0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0343-0.00970.00160.02510.00880.02120.00090.00090.0027-0.0024-0.0008-0.0002-0.0028-0.00010.0055-0.00010.00270.00610.00160.9475-14.843928.3701
20.0256-0.00110.00020.00640.00410.01060.00080.00030.0012-0.0007-0.001-0.0008-0.00150.00020.005-0.00020.00260.00580.0024-13.1273-16.6998-2.1051
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 220
2X-RAY DIFFRACTION2B1 - 220

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