[English] 日本語
Yorodumi
- PDB-4xvp: X-ray structure of bGFP-C / EGFP complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xvp
TitleX-ray structure of bGFP-C / EGFP complex
Components
  • BGFP-C
  • Green fluorescent protein
KeywordsPROTEIN BINDING / ALPHAREP SCAFFOLD / COMPLEX / EGFP / PROTEIN ENGINEERING / HEAT-LIKE REPEAT / FLUORESCENT 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
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsChevrel, A. / Urvoas, A. / Li de la Sierra-Gallay, I. / Van Tilbeurgh, H. / Minard, P. / Valerio-Lepiniec, M.
CitationJournal: Biosci.Rep. / Year: 2015
Title: Specific GFP-binding artificial proteins ( alpha Rep): a new tool for in vitro to live cell applications.
Authors: Chevrel, A. / Urvoas, A. / de la Sierra-Gallay, I.L. / Aumont-Nicaise, M. / Moutel, S. / Desmadril, M. / Perez, F. / Gautreau, A. / van Tilbeurgh, H. / Minard, P. / Valerio-Lepiniec, M.
History
DepositionJan 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein
C: Green fluorescent protein
D: BGFP-C
E: BGFP-C
F: BGFP-C


Theoretical massNumber of molelcules
Total (without water)148,4906
Polymers148,4906
Non-polymers00
Water00
1
A: Green fluorescent protein
D: BGFP-C


Theoretical massNumber of molelcules
Total (without water)49,4972
Polymers49,4972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-6 kcal/mol
Surface area16260 Å2
MethodPISA
2
B: Green fluorescent protein
E: BGFP-C


Theoretical massNumber of molelcules
Total (without water)49,4972
Polymers49,4972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-7 kcal/mol
Surface area16510 Å2
MethodPISA
3
C: Green fluorescent protein
F: BGFP-C


Theoretical massNumber of molelcules
Total (without water)49,4972
Polymers49,4972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-6 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.520, 71.550, 179.200
Angle α, β, γ (deg.)90.00, 100.72, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23B
14A
24C
15B
25C
16B
26C
17D
27E
18D
28F
19E
29F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEUAA2 - 6423 - 85
21SERSERLEULEUBB2 - 6423 - 85
12SERSERLEULEUAA2 - 6423 - 85
22SERSERLEULEUCC2 - 6423 - 85
13VALVALLEULEUAA68 - 23187 - 250
23VALVALLEULEUBB68 - 23187 - 250
14VALVALLEULEUAA68 - 23187 - 250
24VALVALLEULEUCC68 - 23187 - 250
15SERSERLEULEUBB2 - 6423 - 85
25SERSERLEULEUCC2 - 6423 - 85
16VALVALLEULEUBB68 - 23187 - 250
26VALVALLEULEUCC68 - 23187 - 250
17HISHISLYSLYSDD9 - 1669 - 166
27HISHISLYSLYSEE9 - 1669 - 166
18HISHISLYSLYSDD9 - 1669 - 166
28HISHISLYSLYSFF9 - 1669 - 166
19HISHISLYSLYSEE9 - 1669 - 166
29HISHISLYSLYSFF9 - 1669 - 166

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

-
Components

#1: Protein Green fluorescent protein


Mass: 30641.279 Da / Num. of mol.: 3 / Mutation: F64L, S65T, H231L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: PQE81L / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Protein BGFP-C


Mass: 18855.465 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: PLASMID / Details (production host): PQE81L / Production host: Escherichia coli (E. coli)
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 50 mM tricine pH 6.9, 25% PEG4K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.4→46.7 Å / Num. obs: 17746 / % possible obs: 96.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.85
Reflection shellResolution: 3.4→3.6 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.03 / % possible all: 80.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDS13-Jan-2015data reduction
XSCALE13-Jan-2015data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EGFP PDB entry 1JBZ, 6-helix motif from alphaRep4 PDB entry 3LTJ

1jbz

3ltj


Resolution: 3.4→46.7 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.867 / SU B: 43.77 / SU ML: 0.666 / Cross valid method: THROUGHOUT / ESU R Free: 0.752 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2919 888 5 %RANDOM
Rwork0.20918 ---
obs0.21327 16858 96.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 118.154 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å26.92 Å2
2---3.86 Å20 Å2
3---2.54 Å2
Refinement stepCycle: 1 / Resolution: 3.4→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9144 0 0 0 9144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199318
X-RAY DIFFRACTIONr_bond_other_d0.0050.028958
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.97612558
X-RAY DIFFRACTIONr_angle_other_deg0.982320670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.39951146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.92524.797444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.268151665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9881554
X-RAY DIFFRACTIONr_chiral_restr0.0680.21374
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210488
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022034
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_it9.36711.3414611
X-RAY DIFFRACTIONr_mcbond_other9.36711.344610
X-RAY DIFFRACTIONr_mcangle_it14.46116.9935748
X-RAY DIFFRACTIONr_mcangle_other14.45916.9935749
X-RAY DIFFRACTIONr_scbond_it9.26912.1564706
X-RAY DIFFRACTIONr_scbond_other9.26812.1574707
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.91117.9096810
X-RAY DIFFRACTIONr_long_range_B_refined19.69789.83710547
X-RAY DIFFRACTIONr_long_range_B_other19.69689.84210548
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A30920.1
12B30920.1
21A31390.09
22C31390.09
31A96770.07
32B96770.07
41A96750.07
42C96750.07
51B31780.08
52C31780.08
61B96120.08
62C96120.08
71D102420.06
72E102420.06
81D102230.06
82F102230.06
91E102200.05
92F102200.05
LS refinement shellResolution: 3.396→3.484 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 46 -
Rwork0.397 876 -
obs--70.92 %

+
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