[English] 日本語
Yorodumi
- PDB-3ako: Crystal Structure of the Reassembled Venus -

+
Open data


ID or keywords:

Loading...

-
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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY
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'.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more