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- PDB-6mas: X-ray Structure of Branchiostoma floridae fluorescent protein lanFP10G -

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Basic information

Entry
Database: PDB / ID: 6mas
TitleX-ray Structure of Branchiostoma floridae fluorescent protein lanFP10G
ComponentsUncharacterized protein
KeywordsFLUORESCENT PROTEIN / Gly-Tyr-Gly chromophore
Function / homologyGreen fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Uncharacterized protein
Function and homology information
Biological speciesBranchiostoma floridae (Florida lancelet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMuslinkina, L. / Pletneva, N. / Pletnev, V. / Pletnev, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001E United States
Department of Energy (DOE, United States)W-31-109-Eng-38 United States
CitationJournal: J. Mol. Biol. / Year: 2019
Title: Structural Factors Enabling Successful GFP-Like Proteins with Alanine as the Third Chromophore-Forming Residue.
Authors: Muslinkina, L. / Roldan-Salgado, A. / Gaytan, P. / Juarez-Gonzalez, V.R. / Rudino, E. / Pletneva, N. / Pletnev, V. / Dauter, Z. / Pletnev, S.
History
DepositionAug 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,15115
Polymers207,5068
Non-polymers6457
Water44,3352461
1
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0297
Polymers103,7534
Non-polymers2763
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9450 Å2
ΔGint-31 kcal/mol
Surface area32260 Å2
MethodPISA
2
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1218
Polymers103,7534
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-36 kcal/mol
Surface area32680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.875, 104.309, 116.142
Angle α, β, γ (deg.)90.000, 95.320, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized protein


Mass: 25938.270 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Branchiostoma floridae (Florida lancelet)
Gene: BRAFLDRAFT_75522 / Production host: Escherichia coli (E. coli) / References: UniProt: C3YRA2
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2461 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Imidazole pH 7.0, 20% PEG 6,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2018 / Details: m
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 451144 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.035 / Rrim(I) all: 0.069 / Χ2: 0.879 / Net I/σ(I): 8.5 / Num. measured all: 1703469
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.3-1.353.70.556449780.7640.3380.6530.796
1.35-1.43.70.449449720.8290.2720.5260.806
1.4-1.463.70.341450210.8930.2060.40.813
1.46-1.543.70.232449860.9490.1390.2710.826
1.54-1.643.80.169450380.9720.1010.1970.856
1.64-1.763.80.124451080.9850.0740.1450.855
1.76-1.943.80.091450950.990.0540.1060.945
1.94-2.223.80.081451300.9890.0480.0940.969
2.22-2.83.90.055452080.9950.0320.0631.03
2.8-303.90.027456080.9980.0160.0320.874

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HVF

4hvf


Resolution: 1.3→29.82 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / WRfactor Rfree: 0.1474 / WRfactor Rwork: 0.1197 / FOM work R set: 0.9017 / SU B: 1.446 / SU ML: 0.027 / SU R Cruickshank DPI: 0.0383 / SU Rfree: 0.0378 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1467 4625 1 %RANDOM
Rwork0.1195 ---
obs0.1198 446480 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.23 Å2 / Biso mean: 15.252 Å2 / Biso min: 2.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.1 Å2
2--0.17 Å20 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 1.3→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10408 0 3745 2472 16625
Biso mean--16.51 28.25 -
Num. residues----1280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01415428
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713427
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.68820974
X-RAY DIFFRACTIONr_angle_other_deg1.0351.64931671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62751910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.69522.987760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.782152612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.321560
X-RAY DIFFRACTIONr_chiral_restr0.0830.21922
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217651
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023125
X-RAY DIFFRACTIONr_rigid_bond_restr2.482328855
X-RAY DIFFRACTIONr_sphericity_free17.00951381
X-RAY DIFFRACTIONr_sphericity_bonded9.268529470
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 361 -
Rwork0.197 32382 -
all-32743 -
obs--98.13 %

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