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- PDB-6m9x: X-ray Structure of Branchiostoma floridae fluorescent protein lanFP10A -

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Basic information

Entry
Database: PDB / ID: 6m9x
TitleX-ray Structure of Branchiostoma floridae fluorescent protein lanFP10A
ComponentsFluorescent protein lanFP10AFluorescence
KeywordsFLUORESCENT PROTEIN / Gly-Tyr-Ala chromophore
Function / homologyGreen fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Green fluorescent protein
Function and homology information
Biological speciesBranchiostoma floridae (Florida lancelet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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 24, 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fluorescent protein lanFP10A
B: Fluorescent protein lanFP10A
C: Fluorescent protein lanFP10A
D: Fluorescent protein lanFP10A


Theoretical massNumber of molelcules
Total (without water)103,8094
Polymers103,8094
Non-polymers00
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8620 Å2
ΔGint-34 kcal/mol
Surface area32170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.011, 115.836, 128.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Fluorescent protein lanFP10A / Fluorescence


Mass: 25952.297 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Bicine 8.5, 20% PEG 10,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 1990
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 78944 / % possible obs: 99.6 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.026 / Rrim(I) all: 0.072 / Χ2: 0.907 / Net I/σ(I): 10 / Num. measured all: 579342
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.866.70.84377330.8050.3490.9150.86998.8
1.86-1.947.10.46477700.9230.1850.5010.89599.2
1.94-2.037.40.34977490.9580.1370.3750.90599.4
2.03-2.137.50.23978330.9760.0930.2560.95899.2
2.13-2.277.50.17377850.9870.0670.1850.9999.6
2.27-2.447.50.12578800.9930.0480.1340.94299.6
2.44-2.697.50.08678950.9960.0330.0920.93399.8
2.69-3.087.50.06379460.9980.0240.0670.90999.9
3.08-3.887.50.05380280.9980.0210.0570.911100
3.88-307.20.03883250.9990.0150.0410.74999.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HVF

4hvf


Resolution: 1.81→29.65 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.923 / SU ML: 0.118 / SU R Cruickshank DPI: 0.1454 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.144
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1571 2 %RANDOM
Rwork0.2008 ---
obs0.2019 77281 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.36 Å2 / Biso mean: 32.27 Å2 / Biso min: 16.46 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å20 Å20 Å2
2---0.6 Å2-0 Å2
3----1.17 Å2
Refinement stepCycle: final / Resolution: 1.81→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5208 0 1785 415 7408
Biso mean--39.12 33.86 -
Num. residues----640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0147254
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176304
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.6879831
X-RAY DIFFRACTIONr_angle_other_deg0.9421.64614823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3845870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.84123.184358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.881151193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.5891525
X-RAY DIFFRACTIONr_chiral_restr0.0750.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028137
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021463
LS refinement shellResolution: 1.81→1.857 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 99 -
Rwork0.263 5160 -
all-5259 -
obs--90.8 %

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