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- PDB-3ako: Crystal Structure of the Reassembled Venus -

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Basic information

Entry
Database: PDB / ID: 3ako
TitleCrystal Structure of the Reassembled Venus
Components(Venus) x 2
KeywordsFLUORESCENT PROTEIN / Venus / GFP
Function / homologyHSP40/DNAj peptide-binding domain - #10 / HSP40/DNAj peptide-binding domain / Other non-globular / Green Fluorescent Protein / Green fluorescent protein / Special / Beta Barrel / Mainly Beta / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
Function and homology information
Biological speciesPlant transformation vector pSITEII-4C1 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsIsogai, M. / Tada, T.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Structure and characteristics of reassembled fluorescent protein, a new insight into the reassembly mechanisms
Authors: Isogai, M. / Kawamoto, Y. / Inahata, K. / Fukada, H. / Sugimoto, K. / Tada, T.
History
DepositionJul 15, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Nov 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: Venus
B: Venus
C: Venus
D: Venus
E: Venus
F: Venus
G: Venus
H: Venus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,65610
Polymers122,1898
Non-polymers4662
Water11,728651
1
A: Venus
B: Venus


Theoretical massNumber of molelcules
Total (without water)30,5472
Polymers30,5472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-32 kcal/mol
Surface area11110 Å2
MethodPISA
2
C: Venus
D: Venus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6433
Polymers30,5472
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-41 kcal/mol
Surface area10630 Å2
MethodPISA
3
E: Venus
F: Venus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9183
Polymers30,5472
Non-polymers3701
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-30 kcal/mol
Surface area10190 Å2
MethodPISA
4
G: Venus
H: Venus


Theoretical massNumber of molelcules
Total (without water)30,5472
Polymers30,5472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-30 kcal/mol
Surface area10120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.054, 116.046, 156.852
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Venus / YELLOW FLUORESCENT PROTEIN


Mass: 19895.383 Da / Num. of mol.: 4 / Fragment: N-terminal fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plant transformation vector pSITEII-4C1 (others)
Production host: Escherichia coli (E. coli)
#2: Protein
Venus / YELLOW FLUORESCENT PROTEIN


Mass: 10651.938 Da / Num. of mol.: 4 / Fragment: C-terminal fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plant transformation vector pSITEII-4C1 (others)
Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 651 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE DATABASES OF THE ENTITIES ARE NOT AVAILABLE IN UNIPROT AT PRESENT. SEQUENCE OF ENTITY 1 IS ...SEQUENCE DATABASES OF THE ENTITIES ARE NOT AVAILABLE IN UNIPROT AT PRESENT. SEQUENCE OF ENTITY 1 IS THE SAME AS RESIDUES 1-155 OF GB ADE48838, WITH N-TERMINAL EXPRESSION TAG 'MGHHHHHHHHHHSSGHIERH'; RESIDUES 66 CR2 IS A CHOROMOPHORE, AND THE ORIGINAL SEQUENCE IS GLY-TYR-GLY. SEQUENCE OF ENTITY 2 IS THE SAME AS RESIDUES 156-239 OF GB ADE48838, WITH A MET AT N-TERMINAL AND C-TERMINAL EXPRESSION TAG 'LEHHHHHH'.

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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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 0.1M HEPES, 0.2M lithium sulfate , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2010
RadiationMonochromator: Numerical link type Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 63893 / Num. obs: 60532 / % possible obs: 94.7 % / Redundancy: 11 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 23.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 5.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MYW

1myw


Resolution: 2.1→49.9 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.276 / SU ML: 0.115 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22919 3231 5.1 %RANDOM
Rwork0.16693 ---
obs0.17007 60532 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.411 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7185 0 30 651 7866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227554
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.781.97910231
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1245933
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42125.054370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.044151305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6331529
X-RAY DIFFRACTIONr_chiral_restr0.110.21095
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215793
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_it0.91.54513
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.68527296
X-RAY DIFFRACTIONr_scbond_it2.66933041
X-RAY DIFFRACTIONr_scangle_it4.2774.52911
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 214 -
Rwork0.189 4391 -
obs--99.85 %

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