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- PDB-5h89: Crystal structure of mRojoA mutant - T16V - P63Y - W143G - L163V -

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Basic information

Entry
Database: PDB / ID: 5h89
TitleCrystal structure of mRojoA mutant - T16V - P63Y - W143G - L163V
ComponentsmRojoA fluorescent protein
KeywordsFLUORESCENT PROTEIN / quantum yield / protein engineering
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
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.76 Å
AuthorsPandelieva, A.T. / Tremblay, V. / Sarvan, S. / Chica, R.A. / Couture, J.-F.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Brighter Red Fluorescent Proteins by Rational Design of Triple-Decker Motif.
Authors: Pandelieva, A.T. / Baran, M.J. / Calderini, G.F. / McCann, J.L. / Tremblay, V. / Sarvan, S. / Davey, J.A. / Couture, J.F. / Chica, R.A.
History
DepositionDec 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / pdbx_validate_polymer_linkage / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mRojoA fluorescent protein
B: mRojoA fluorescent protein
C: mRojoA fluorescent protein
D: mRojoA fluorescent protein


Theoretical massNumber of molelcules
Total (without water)110,5044
Polymers110,5044
Non-polymers00
Water9,944552
1
A: mRojoA fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,6261
Polymers27,6261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: mRojoA fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,6261
Polymers27,6261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: mRojoA fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,6261
Polymers27,6261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: mRojoA fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,6261
Polymers27,6261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.031, 108.149, 74.000
Angle α, β, γ (deg.)90.00, 105.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
mRojoA fluorescent protein


Mass: 27626.049 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Gene: PAmCherry / Production host: Escherichia coli (E. coli) / References: UniProt: D1MPT3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Source detailsTHIS SEQUENCE WAS BASED ON THE PAMCHERRY1 PROTEIN (UNP REFERENCE D1MPT3). RESIDUES MET 64, TYR 65, ...THIS SEQUENCE WAS BASED ON THE PAMCHERRY1 PROTEIN (UNP REFERENCE D1MPT3). RESIDUES MET 64, TYR 65, AND GLY 68 form a CHROMOPHORE residue CH6. This is a new engineered protein for which the starting point is also an engineered protein. Namely, it was generated using the sequence corresponding to the structure 3NEZ. The mutations listed in the title refer to the mutations compared to 3NEZ.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 125mM Bis-Tris, 200mM MgCl2 and 25% Peg3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→71.39 Å / Biso Wilson estimate: 19.11 Å2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.76→71.39 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.123 / SU Rfree Blow DPI: 0.115 / SU Rfree Cruickshank DPI: 0.116
RfactorNum. reflection% reflectionSelection details
Rfree0.218 4277 5.02 %RANDOM
Rwork0.184 ---
obs0.186 85121 96.1 %-
Displacement parametersBiso mean: 23.37 Å2
Baniso -1Baniso -2Baniso -3
1-4.5166 Å20 Å22.1054 Å2
2---3.7841 Å20 Å2
3----0.7326 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.76→71.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6849 0 92 552 7493
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017207HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.149696HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2544SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes184HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1105HARMONIC5
X-RAY DIFFRACTIONt_it7207HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.95
X-RAY DIFFRACTIONt_other_torsion16.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion866SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8499SEMIHARMONIC4

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