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- PDB-6m9y: X-ray Structure of Branchiostoma floridae fluorescent protein lanFP6A -

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Basic information

Entry
Database: PDB / ID: 6m9y
TitleX-ray Structure of Branchiostoma floridae fluorescent protein lanFP6A
Components(Fluorescent protein lanFP6A) x 2
KeywordsFLUORESCENT PROTEIN / Fluorescent Protein Branchiostoma floridae Gly-Tyr-Ala tripeptide hydrolysis
Function / homologyPantoate--beta-alanine Ligase; Chain: A,domain 2 - #40 / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesBranchiostoma floridae (Florida lancelet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fluorescent protein lanFP6A
B: Fluorescent protein lanFP6A
C: Fluorescent protein lanFP6A
D: Fluorescent protein lanFP6A


Theoretical massNumber of molelcules
Total (without water)52,1414
Polymers52,1414
Non-polymers00
Water10,863603
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.726, 98.169, 55.145
Angle α, β, γ (deg.)90.000, 108.070, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-493-

HOH

21B-519-

HOH

31D-493-

HOH

41D-516-

HOH

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Components

#1: Protein Fluorescent protein lanFP6A


Mass: 6316.218 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Branchiostoma floridae (Florida lancelet)
Gene: BRAFLDRAFT_75521 / Production host: Escherichia coli (E. coli) / References: UniProt: C3YRA1
#2: Protein Fluorescent protein lanFP6A


Mass: 19754.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Branchiostoma floridae (Florida lancelet)
Gene: BRAFLDRAFT_75521 / Production host: Escherichia coli (E. coli) / References: UniProt: C3YRA1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2M Ammonium Citrate pH 7.0, 20% PEG 3350

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 116582 / % possible obs: 93.7 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.029 / Rrim(I) all: 0.053 / Χ2: 0.544 / Net I/σ(I): 10.2 / Num. measured all: 284216
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.35-1.42.40.537112200.7310.4180.6840.54990.5
1.4-1.452.40.404112350.810.3080.510.53890.2
1.45-1.522.40.275112930.8920.2050.3450.53191.1
1.52-1.62.40.179114720.9380.1290.2220.50792.6
1.6-1.72.30.122117590.9650.0830.1480.48494.7
1.7-1.832.30.077119740.9760.0520.0940.51496.4
1.83-2.022.30.059119920.9670.040.0720.66796.4
2.02-2.312.30.048117200.9540.0330.0590.70694.3
2.31-2.912.60.036118450.9680.0240.0430.47994.9
2.91-302.80.034120720.9810.0210.040.595.9

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Processing

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

4hvf


Resolution: 1.35→28.03 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.172 / WRfactor Rwork: 0.1317 / FOM work R set: 0.8763 / SU B: 1.872 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0475 / SU Rfree: 0.0482 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1688 1079 1 %RANDOM
Rwork0.133 ---
obs0.1333 106408 86.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.1 Å2 / Biso mean: 19.371 Å2 / Biso min: 7.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.07 Å2
2---0.46 Å20 Å2
3---0.33 Å2
Refinement stepCycle: final / Resolution: 1.35→28.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3512 0 0 609 4121
Biso mean---34.07 -
Num. residues----440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0143766
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173280
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.6685114
X-RAY DIFFRACTIONr_angle_other_deg1.031.6427729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2545466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.01324.286189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56915623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.396158
X-RAY DIFFRACTIONr_chiral_restr0.0930.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024278
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02758
X-RAY DIFFRACTIONr_rigid_bond_restr3.4537046
X-RAY DIFFRACTIONr_sphericity_free25.6465364
X-RAY DIFFRACTIONr_sphericity_bonded12.55657189
LS refinement shellResolution: 1.351→1.386 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.173 47 -
Rwork0.171 3461 -
all-3508 -
obs--37.93 %

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