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- PDB-6sm0: Venus 66 p-Azido-L-Phenylalanin (azF) variant, dark grown -

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Basic information

Entry
Database: PDB / ID: 6sm0
TitleVenus 66 p-Azido-L-Phenylalanin (azF) variant, dark grown
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / Venus 66 Fluorescent protein / azF variant / Aequoria victoria / GFP / Non-canonical Amino Acid / 3D X-ray Structure Determination
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / OXYGEN MOLECULE / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.91 Å
AuthorsRizkallah, P.J. / Al Maslookhi, H.S. / Jones, D.D.
CitationJournal: Chem Sci / Year: 2021
Title: Stalling chromophore synthesis of the fluorescent protein Venus reveals the molecular basis of the final oxidation step.
Authors: Auhim, H.S. / Grigorenko, B.L. / Harris, T.K. / Aksakal, O.E. / Polyakov, I.V. / Berry, C. / Gomes, G.D.P. / Alabugin, I.V. / Rizkallah, P.J. / Nemukhin, A.V. / Jones, D.D.
History
DepositionAug 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_refine_tls / pdbx_refine_tls_group
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_seq_id
Revision 1.2Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8874
Polymers25,6941
Non-polymers1933
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-32 kcal/mol
Surface area10450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.947, 63.251, 69.915
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 Green fluorescent protein


Mass: 25693.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 10mM Zn Cl2, 100 mM Na acetate, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.91→63.25 Å / Num. obs: 18146 / % possible obs: 99.9 % / Redundancy: 5.7 % / CC1/2: 0.989 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.075 / Rrim(I) all: 0.181 / Net I/σ(I): 7.4 / Num. measured all: 103864 / Scaling rejects: 624
Reflection shell

Diffraction-ID: 1 / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.91-1.963.71.145492013170.3550.7011.3531.8
8.54-63.255.50.06613812500.9970.030.07313.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.99 Å46.9 Å
Translation4.99 Å46.9 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.2data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J8A

4j8a


Resolution: 1.91→46.95 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.2459 / WRfactor Rwork: 0.1892 / FOM work R set: 0.8002 / SU B: 8.883 / SU ML: 0.133 / SU R Cruickshank DPI: 0.1826 / SU Rfree: 0.1639 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.243 922 5.1 %RANDOM
Rwork0.1951 ---
obs0.1976 17175 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.64 Å2 / Biso mean: 19.64 Å2 / Biso min: 9.49 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å2-0 Å20 Å2
2--0.85 Å2-0 Å2
3---0.38 Å2
Refinement stepCycle: final / Resolution: 1.91→46.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 8 213 2034
Biso mean--52.25 29.57 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131895
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171711
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.6612568
X-RAY DIFFRACTIONr_angle_other_deg1.3671.5953995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6495232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65324.38898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16815322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.547156
X-RAY DIFFRACTIONr_chiral_restr0.0840.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022142
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02378
LS refinement shellResolution: 1.91→1.959 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.317 65 -
Rwork0.276 1238 -
obs--98.56 %
Refinement TLS params.Method: refined / Origin x: 25.314 Å / Origin y: 2.844 Å / Origin z: 3.583 Å
111213212223313233
T0.062 Å20.0053 Å20.0022 Å2-0.0085 Å2-0.0011 Å2--0.0025 Å2
L1.1785 °2-0.1634 °20.0566 °2-2.0445 °20.2696 °2--1.412 °2
S-0.0378 Å °-0.0421 Å °0.0514 Å °0.0308 Å °0.0439 Å °-0.0029 Å °-0.038 Å °-0.0894 Å °-0.0061 Å °

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