[English] 日本語
Yorodumi
- PDB-1mov: Crystal structure of Coral protein mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mov
TitleCrystal structure of Coral protein mutant
ComponentsGFP-like non-fluorescent chromoprotein
KeywordsLUMINESCENT PROTEIN / coral pigment / fluorescent conversion mutant / chromophore / rtms5
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
IODIDE ION / GFP-like non-fluorescent chromoprotein
Similarity search - Component
Biological speciesMontipora efflorescens (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPrescott, M. / Ling, M. / Beddoe, T. / Oakley, A.J. / Dove, S. / Hoegh-Guldberg, O. / Devenish, R.J. / Rossjohn, J.
CitationJournal: Structure / Year: 2003
Title: The 2.2 a crystal structure of a pocilloporin pigment reveals a nonplanar chromophore conformation.
Authors: Prescott, M. / Ling, M. / Beddoe, T. / Oakley, A.J. / Dove, S. / Hoegh-Guldberg, O. / Devenish, R.J. / Rossjohn, J.
History
DepositionSep 10, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GFP-like non-fluorescent chromoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3996
Polymers24,7641
Non-polymers6355
Water3,297183
1
A: GFP-like non-fluorescent chromoprotein
hetero molecules

A: GFP-like non-fluorescent chromoprotein
hetero molecules

A: GFP-like non-fluorescent chromoprotein
hetero molecules

A: GFP-like non-fluorescent chromoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,59424
Polymers99,0564
Non-polymers2,53820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455y-1/2,x+1/2,-z+1/21
crystal symmetry operation10_565-x,-y+1,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area11490 Å2
ΔGint-41 kcal/mol
Surface area31760 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.391, 131.391, 150.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-379-

HOH

-
Components

#1: Protein GFP-like non-fluorescent chromoprotein / Rtms 5 / Non-fluorescent pocilloporin


Mass: 24764.055 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-225 / Mutation: H146S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Montipora efflorescens (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: P83690
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: peg, tris, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
117 mg/mlprotein1drop
210-15 %PEG33501reservoir
30.1 MTris-HCl1reservoirpH8.2
40.2 Mpotassium iodide1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 25988 / Num. obs: 25988 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.335 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 176177
Reflection shell
*PLUS
% possible obs: 99.7 %

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MOU

1mou


Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 837 -random
Rwork0.225 ---
all0.225 25988 --
obs0.225 25124 99.7 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.238 Å20 Å20 Å2
2--3.238 Å20 Å2
3----6.477 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 5 183 1930
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1061.5
X-RAY DIFFRACTIONc_mcangle_it2.0362
X-RAY DIFFRACTIONc_scbond_it1.7962
X-RAY DIFFRACTIONc_scangle_it2.8312.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2crq.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.335
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

+
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