[English] 日本語
Yorodumi
- PDB-3mgf: Crystal Structure of Monomeric Kusabira-Orange (MKO), Orange-Emit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mgf
TitleCrystal Structure of Monomeric Kusabira-Orange (MKO), Orange-Emitting GFP-like Protein, at pH 7.5
ComponentsFluorescent protein
KeywordsFLUORESCENT PROTEIN
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesVerrillofungia concinna (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsEbisawa, T. / Yamamura, A. / Ohtsuka, J. / Kameda, Y. / Hayakawa, K. / Nagata, K. / Tanokura, M.
CitationJournal: To be Published
Title: Crystal Structure of Monomeric Kusabira-Orange (MKO), Orange-Emitting GFP-like Protein, at pH 7.5
Authors: Ebisawa, T. / Yamamura, A. / Ohtsuka, J. / Kameda, Y. / Hayakawa, K. / Nagata, K. / Tanokura, M.
History
DepositionApr 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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_ref_seq_dif
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_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_chiral / pdbx_validate_main_chain_plane / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_polymer_linkage.auth_atom_id_1 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,9324
Polymers98,9324
Non-polymers00
Water15,331851
1
A: Fluorescent protein


Theoretical massNumber of molelcules
Total (without water)24,7331
Polymers24,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fluorescent protein


Theoretical massNumber of molelcules
Total (without water)24,7331
Polymers24,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fluorescent protein


Theoretical massNumber of molelcules
Total (without water)24,7331
Polymers24,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fluorescent protein


Theoretical massNumber of molelcules
Total (without water)24,7331
Polymers24,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.520, 83.760, 82.180
Angle α, β, γ (deg.)90.00, 110.75, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Fluorescent protein / Orange-Emitting GFP-like Protein


Mass: 24732.990 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Verrillofungia concinna (invertebrata) / Gene: mKO / Plasmid: MODIFIED PET-28(+) / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: Q6I7B2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 851 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M L-Proline, 0.1M HEPES, 10%(w/v) Polyethylene glycol 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 79034 / % possible obs: 99.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.79

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ZMW

2zmw


Resolution: 1.8→19.78 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.162 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.213 3963 5 %RANDOM
Rwork0.166 ---
obs0.169 79012 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 53.06 Å2 / Biso mean: 17.364 Å2 / Biso min: 5.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.04 Å2
2--0.04 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6787 0 0 851 7638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0216974
X-RAY DIFFRACTIONr_angle_refined_deg2.1151.9699404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9865836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72623.846312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.741151176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8661532
X-RAY DIFFRACTIONr_chiral_restr0.170.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215352
X-RAY DIFFRACTIONr_mcbond_it1.2811.54192
X-RAY DIFFRACTIONr_mcangle_it2.13826740
X-RAY DIFFRACTIONr_scbond_it3.57932782
X-RAY DIFFRACTIONr_scangle_it5.5384.52664
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 264 -
Rwork0.18 5493 -
all-5757 -
obs--99.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2054-0.1140.0550.8761-0.16440.06210.0387-0.0521-0.0035-0.141-0.1113-0.02980.0290.02490.07270.06840.02710.02240.0440.01380.032120.477-10.61224.374
20.1860.03090.12040.7291-0.00490.33150.0001-0.04820.0006-0.0713-0.03710.0722-0.0324-0.00570.0370.04580.0085-0.00390.0534-0.0060.02840.14811.47424.07
30.2654-0.188-0.12250.56680.16970.1784-0.0397-0.0082-0.0511-0.04840.0138-0.0422-0.01910.00580.02590.0692-0.00670.02630.0433-0.00830.024433.571-10.611-14.188
40.30680.12120.01230.8715-0.10970.09970.0252-0.08550.0752-0.1014-0.05410.130.04780.04140.02880.0443-0.0031-0.00610.0455-0.01440.043813.41311.472-11.962
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 218
2X-RAY DIFFRACTION2B3 - 218
3X-RAY DIFFRACTION3C3 - 218
4X-RAY DIFFRACTION4D3 - 218

+
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://pdbjlvh1.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