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- PDB-2pxs: Crystal Structure of N66D Mutant of Green Fluorescent Protein fro... -

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Basic information

Entry
Database: PDB / ID: 2pxs
TitleCrystal Structure of N66D Mutant of Green Fluorescent Protein from Zoanthus sp. at 2.2 A Resolution (Mature State)
ComponentsGFP-like fluorescent chromoprotein FP506
KeywordsFLUORESCENT PROTEIN / Zoanthus family / red fluorescent protein / green fluorescent protein / chromophore structure
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / GFP-like fluorescent chromoprotein FP506
Function and homology information
Biological speciesZoanthus sp. (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPletnev, S.V. / Pletneva, N.V. / Tikhonova, T.V. / Pletnev, V.Z.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Refined crystal structures of red and green fluorescent proteins from the button polyp Zoanthus.
Authors: Pletneva, N. / Pletnev, V. / Tikhonova, T. / Pakhomov, A.A. / Popov, V. / Martynov, V.I. / Wlodawer, A. / Dauter, Z. / Pletnev, S.
History
DepositionMay 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GFP-like fluorescent chromoprotein FP506
B: GFP-like fluorescent chromoprotein FP506


Theoretical massNumber of molelcules
Total (without water)51,5012
Polymers51,5012
Non-polymers00
Water4,288238
1
A: GFP-like fluorescent chromoprotein FP506

A: GFP-like fluorescent chromoprotein FP506

A: GFP-like fluorescent chromoprotein FP506

A: GFP-like fluorescent chromoprotein FP506


Theoretical massNumber of molelcules
Total (without water)103,0024
Polymers103,0024
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_455-x+y-1,y,-z1
2
B: GFP-like fluorescent chromoprotein FP506

B: GFP-like fluorescent chromoprotein FP506

B: GFP-like fluorescent chromoprotein FP506

B: GFP-like fluorescent chromoprotein FP506


Theoretical massNumber of molelcules
Total (without water)103,0024
Polymers103,0024
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
crystal symmetry operation7_554y,x,-z-1/31
crystal symmetry operation10_444-y-1,-x-1,-z-1/31
Unit cell
Length a, b, c (Å)101.510, 101.510, 271.217
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein GFP-like fluorescent chromoprotein FP506 / zFP506


Mass: 25750.500 Da / Num. of mol.: 2 / Mutation: N66D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zoanthus sp. (invertebrata) / Plasmid: pQE30-zGFP506_N66D / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U6Y5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 3.91 Å3/Da / Density % sol: 68.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M bis-tris propane, 1.8 M tri-ammonium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 42936 / % possible obs: 99.8 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.066 / Χ2: 0.94 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.2814.70.66341840.785100
2.28-2.3714.70.47142050.804100
2.37-2.4814.70.3542270.826100
2.48-2.6114.70.24942270.902100
2.61-2.7714.70.16442171.028100
2.77-2.9914.60.11142811.013100
2.99-3.2914.60.06942761.018100
3.29-3.7614.30.0643181.003100
3.76-4.7314.10.0543620.95699.6
4.73-3013.30.04846391.06798.8

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Phasing

Phasing MRRfactor: 0.401 / Cor.coef. Fo:Fc: 0.599
Highest resolutionLowest resolution
Rotation3.5 Å47.95 Å
Translation3.5 Å47.95 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: zGFP506

Resolution: 2.2→29.3 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.249 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2160 5.2 %RANDOM
Rwork0.176 ---
obs0.178 41863 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.077 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3670 0 0 238 3908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223778
X-RAY DIFFRACTIONr_angle_refined_deg1.7931.9755116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1325450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47424.217166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58215638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.771516
X-RAY DIFFRACTIONr_chiral_restr0.1190.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022932
X-RAY DIFFRACTIONr_nbd_refined0.2130.21641
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22499
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.222
X-RAY DIFFRACTIONr_mcbond_it1.1181.52336
X-RAY DIFFRACTIONr_mcangle_it1.94423670
X-RAY DIFFRACTIONr_scbond_it2.95431706
X-RAY DIFFRACTIONr_scangle_it4.5124.51446
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 149 -
Rwork0.253 2951 -
obs-3100 100 %

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