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- PDB-3ai4: Crystal structure of yeast enhanced green fluorescent protein - m... -

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Basic information

Entry
Database: PDB / ID: 3ai4
TitleCrystal structure of yeast enhanced green fluorescent protein - mouse polymerase iota ubiquitin binding motif fusion protein
Componentsyeast enhanced green fluorescent protein,DNA polymerase iota
KeywordsFluorescent Protein / replication / UBM / Ubiquitin-binding motif / GFP / Fusion
Function / homology
Function and homology information


Translesion synthesis by POLI / Termination of translesion DNA synthesis / cellular response to UV-C / translesion synthesis / bioluminescence / generation of precursor metabolites and energy / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity ...Translesion synthesis by POLI / Termination of translesion DNA synthesis / cellular response to UV-C / translesion synthesis / bioluminescence / generation of precursor metabolites and energy / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / metal ion binding / nucleus
Similarity search - Function
DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Green Fluorescent Protein / Green fluorescent protein ...DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein / DNA polymerase iota
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSuzuki, N. / Wakatsuki, S. / Kawasaki, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Crystallization of small proteins assisted by green fluorescent protein
Authors: Suzuki, N. / Hiraki, M. / Yamada, Y. / Matsugaki, N. / Igarashi, N. / Kato, R. / Dikic, I. / Drew, D. / Iwata, S. / Wakatsuki, S. / Kawasaki, M.
History
DepositionMay 10, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 14, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_entry_details / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _pdbx_entry_details.sequence_details / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg
Revision 1.3Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: yeast enhanced green fluorescent protein,DNA polymerase iota
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1872
Polymers32,0911
Non-polymers961
Water5,332296
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.457, 87.457, 83.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-297-

HOH

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Components

#1: Protein yeast enhanced green fluorescent protein,DNA polymerase iota


Mass: 32090.928 Da / Num. of mol.: 1
Fragment: recidues 1-230 for yeast enhanced green fluorescent protein,UBIQUITIN BINDING MOTIF FUSION PROTEIN for DNA polymerase iota
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Mus musculus (house mouse)
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6R3M4, UniProt: P42212*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Compound detailsYEAST ENHANCED GREEN FLUORESCENT PROTEIN - MOUSE POLYMERASE IOTA UBIQUITIN BINDING MOTIF FUSION PROTEIN
Sequence detailsTHE SEQUENCE OF YEAST ENHANCED GREEN FLUORESCENT PROTEIN HAS BEEN DEPOSITED IN GENBANK WITH ...THE SEQUENCE OF YEAST ENHANCED GREEN FLUORESCENT PROTEIN HAS BEEN DEPOSITED IN GENBANK WITH ACCESSION CODE, ABI82055. residues -2,-1,0 are expression tags, and residue 68 CR2 is CHROMOPHORE (GLY-TYR-GLY).

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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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 2.0M Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 19, 2009 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. obs: 39422 / % possible obs: 90.7 % / Redundancy: 8.7 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 29
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 6.3 / Num. unique all: 2136 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREP10.2.35phasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GFL

1gfl


Resolution: 1.6→29 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.932 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22114 1971 5 %RANDOM
Rwork0.18942 ---
obs0.19101 37118 89.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2---0.42 Å20 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 5 296 2372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222126
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.861.9712876
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4165253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48425.429105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16715363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.68156
X-RAY DIFFRACTIONr_chiral_restr0.1260.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213534
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2121.51272
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.24422061
X-RAY DIFFRACTIONr_scbond_it3.3693854
X-RAY DIFFRACTIONr_scangle_it5.6114.5815
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.599→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 140 -
Rwork0.226 2963 -
obs--98.41 %
Refinement TLS params.Method: refined / Origin x: 5.3408 Å / Origin y: 28.5551 Å / Origin z: 23.8434 Å
111213212223313233
T0.012 Å20.01 Å2-0.007 Å2-0.0277 Å20.0003 Å2--0.022 Å2
L0.6491 °2-0.1249 °2-0.091 °2-0.5065 °2-0.0348 °2--0.3314 °2
S0.0109 Å °-0.0205 Å °-0.0289 Å °-0.015 Å °0.0104 Å °-0.0047 Å °0.0514 Å °0.0158 Å °-0.0213 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 230
2X-RAY DIFFRACTION1A243 - 271

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