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- PDB-1xae: Crystal structure of wild type yellow fluorescent protein zFP538 ... -

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Basic information

Entry
Database: PDB / ID: 1xae
TitleCrystal structure of wild type yellow fluorescent protein zFP538 from Zoanthus
Componentsfluorescent protein FP538
KeywordsLUMINESCENT PROTEIN / fluorescent protein / beta-can / beta-barrel
Function / homology
Function and homology information


Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / GFP-like fluorescent chromoprotein FP538
Similarity search - Component
Biological speciesZoanthus sp. (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRemington, S.J. / Wachter, R.M. / Yarbrough, D.K. / Branchaud, B. / Anderson, D.C. / Kallio, K. / Lukyanov, K.A.
CitationJournal: Biochemistry / Year: 2005
Title: zFP538, a yellow-fluorescent protein from Zoanthus, contains a novel three-ring chromophore.
Authors: Remington, S.J. / Wachter, R.M. / Yarbrough, D.K. / Branchaud, B. / Anderson, D.C. / Kallio, K. / Lukyanov, K.A.
History
DepositionAug 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 999SEQUENCE RESIDUE LYS 66, TYR 67 AND GLY 68 ARE MODIFIED TO MAKE CHROMOPHORE (CH7 66).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: fluorescent protein FP538
B: fluorescent protein FP538
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5534
Polymers52,3962
Non-polymers1562
Water1,49583
1
A: fluorescent protein FP538
B: fluorescent protein FP538
hetero molecules

A: fluorescent protein FP538
B: fluorescent protein FP538
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1058
Polymers104,7934
Non-polymers3134
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Unit cell
Length a, b, c (Å)121.160, 121.160, 111.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological tetramer is assembled from the asymmetric unit and an adjacent crystallographic twofold.

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Components

#1: Protein fluorescent protein FP538


Mass: 26198.199 Da / Num. of mol.: 2 / Mutation: KYG66(CH7)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zoanthus sp. (invertebrata) / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM-109(DE3) / References: UniProt: Q9U6Y4
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 4.2 Å3/Da / Density % sol: 72.75 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 9
Details: ammonium sulfate, beta-mercaptoethanol, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 20, 2002 / Details: mirrors
RadiationMonochromator: Ni Mirror + Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. all: 29648 / Num. obs: 29648 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 10.8
Reflection shellResolution: 2.6→2.7 Å / Mean I/σ(I) obs: 1.7 / % possible all: 99.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
TNT5Erefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1XA9

1xa9


Resolution: 2.7→6 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: a posteriori / σ(F): 0 / Stereochemistry target values: TNT
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2893 -RANDOM
Rwork0.205 ---
all0.206 23882 --
obs0.206 23882 99.9 %-
Displacement parametersBiso mean: 55 Å2
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3525 0 8 83 3616
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.006
X-RAY DIFFRACTIONt_angle_deg1.6
LS refinement shellHighest resolution: 2.7 Å
RfactorNum. reflection% reflection
Rfree0.255 2893 -
Rwork0.205 --
obs-23882 99.9 %

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