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- PDB-6ylp: EGFP_in_Acidic_env Directionality of Optical Properties of Fluore... -

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Basic information

Entry
Database: PDB / ID: 6ylp
TitleEGFP_in_Acidic_env Directionality of Optical Properties of Fluorescent Proteins
ComponentseGFP_in_Acidic_env
KeywordsFLUORESCENT PROTEIN / eGFP
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsMyskova, J. / Rybakova, O. / Brynda, J. / Lazar, J.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicCZ.02.1.01/0.0/0.0/16_019/0000729 Czech Republic
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Directionality of light absorption and emission in representative fluorescent proteins.
Authors: Myskova, J. / Rybakova, O. / Brynda, J. / Khoroshyy, P. / Bondar, A. / Lazar, J.
History
DepositionApr 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
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_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: eGFP_in_Acidic_env
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6502
Polymers28,5551
Non-polymers951
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-4 kcal/mol
Surface area10200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.970, 62.150, 68.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein eGFP_in_Acidic_env


Mass: 28555.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 41.91 %
Description: A - long axis of crystal B, C - diagonal to the crystal faces
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.8 / Details: PEG 8000, potassium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Aug 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.55→46.12 Å / Num. obs: 61255 / % possible obs: 99.9 % / Redundancy: 5.771 % / Biso Wilson estimate: 26.127 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.06 / Χ2: 1.041 / Net I/σ(I): 16.94 / Num. measured all: 353489 / Scaling rejects: 272
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.592.490.8941.0311353456345600.3731.15799.9
1.59-1.632.630.7211.3411580440344030.490.92100
1.63-1.682.9540.5881.7612838434643460.6280.725100
1.68-1.733.6660.4882.4215174414241390.7580.57499.9
1.73-1.794.290.4263.0617315403640360.8350.487100
1.79-1.854.6010.3044.3718013391539150.9250.344100
1.85-1.924.8040.2346.2418161379337800.9580.26399.7
1.92-26.0290.16110.0221758361736090.9860.17799.8
2-2.096.8840.12913.9624046349634930.9930.1499.9
2.09-2.198.2540.10817.7827412332133210.9960.115100
2.19-2.318.020.09820.0625424317231700.9960.10599.9
2.31-2.457.9620.07923.423853299629960.9980.084100
2.45-2.627.2880.06626.4120326278927890.9980.071100
2.62-2.838.1660.06231.0621526263626360.9980.066100
2.83-3.18.8170.04639.1221116239523950.9990.048100
3.1-3.478.4580.03749.9418456218221820.9990.039100
3.47-48.2030.03156.0115823192919290.9990.033100
4-4.98.5270.02762.88138231622162110.02999.9
4.9-6.937.50.03352.769412125512550.9990.035100
6.93-46.128.9410.02965.52608068568010.03199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.342
Highest resolutionLowest resolution
Rotation46.12 Å3.5 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y0G

2y0g


Resolution: 1.55→46.12 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.1897 / WRfactor Rwork: 0.1627 / FOM work R set: 0.8281 / SU B: 1.747 / SU ML: 0.064 / SU R Cruickshank DPI: 0.0821 / SU Rfree: 0.0829 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 1620 5 %RANDOM
Rwork0.1761 ---
obs0.1776 30780 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 101.51 Å2 / Biso mean: 23.201 Å2 / Biso min: 13.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0 Å2
2---0.6 Å20 Å2
3---0.57 Å2
Refinement stepCycle: final / Resolution: 1.55→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 468 152 2418
Biso mean--21.25 30.22 -
Num. residues----164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191888
X-RAY DIFFRACTIONr_bond_other_d0.0020.021746
X-RAY DIFFRACTIONr_angle_refined_deg1.721.9662560
X-RAY DIFFRACTIONr_angle_other_deg0.91834031
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9275234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16425.05493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15115316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.15157
X-RAY DIFFRACTIONr_chiral_restr0.090.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212150
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02439
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 118 -
Rwork0.261 2250 -
all-2368 -
obs--100 %

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