[English] 日本語
Yorodumi
- PDB-5erq: Gephyrin E domain at 1.55 angstrom resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5erq
TitleGephyrin E domain at 1.55 angstrom resolution
ComponentsGephyrin
KeywordsTRANSFERASE / Molybdenum cofactor / tungsten cofactor / Moco biosynthesis
Function / homology
Function and homology information


Molybdenum cofactor biosynthesis / glycine receptor clustering / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / gamma-aminobutyric acid receptor clustering / molybdopterin molybdotransferase / nitrate reductase activity / molybdopterin molybdotransferase activity ...Molybdenum cofactor biosynthesis / glycine receptor clustering / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / gamma-aminobutyric acid receptor clustering / molybdopterin molybdotransferase / nitrate reductase activity / molybdopterin molybdotransferase activity / postsynaptic specialization / inhibitory synapse / Mo-molybdopterin cofactor biosynthetic process / glycinergic synapse / postsynaptic neurotransmitter receptor diffusion trapping / response to metal ion / molybdopterin cofactor binding / postsynaptic specialization membrane / postsynaptic specialization, intracellular component / neurotransmitter receptor localization to postsynaptic specialization membrane / protein targeting / synapse assembly / tubulin binding / GABA-ergic synapse / synaptic membrane / establishment of protein localization / cytoplasmic side of plasma membrane / protein-macromolecule adaptor activity / molecular adaptor activity / postsynaptic membrane / dendritic spine / cytoskeleton / postsynapse / postsynaptic density / signaling receptor binding / neuronal cell body / dendrite / ATP binding / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Molybdopterin biosynthesis moeA protein; domain 3 / Molybdopterin biosynthesis moea protein, domain 3. / Beta-clip / MoeA, C-terminal, domain IV / Molybdenum cofactor biosynthesis proteins signature 2. / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis proteins signature 1. / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily ...Molybdopterin biosynthesis moeA protein; domain 3 / Molybdopterin biosynthesis moea protein, domain 3. / Beta-clip / MoeA, C-terminal, domain IV / Molybdenum cofactor biosynthesis proteins signature 2. / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis proteins signature 1. / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily / Molybdopterin biosynthesis protein MoeA-like / MoeA N-terminal region (domain I and II) / MoeA C-terminal region (domain IV) / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis, conserved site / MoaB/Mog-like domain / Molybdenum Cofactor Biosythetic Enzyme; Chain A / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / Beta Complex / Alpha-Beta Complex / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Gephyrin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsKasaragod, V.B. / Schindelin, H.
CitationJournal: Structure / Year: 2016
Title: Structural Framework for Metal Incorporation during Molybdenum Cofactor Biosynthesis.
Authors: Kasaragod, V.B. / Schindelin, H.
History
DepositionNov 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gephyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,47913
Polymers45,6521
Non-polymers82712
Water9,350519
1
A: Gephyrin
hetero molecules

A: Gephyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,95826
Polymers91,3052
Non-polymers1,65424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_557-x,y,-z+21
Buried area10580 Å2
ΔGint-59 kcal/mol
Surface area35520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.669, 99.287, 113.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1069-

HOH

21A-1284-

HOH

31A-1306-

HOH

41A-1324-

HOH

51A-1334-

HOH

61A-1403-

HOH

71A-1413-

HOH

81A-1417-

HOH

-
Components

#1: Protein Gephyrin / Putative glycine receptor-tubulin linker protein


Mass: 45652.395 Da / Num. of mol.: 1 / Fragment: UNP residues 318-736
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gphn, Gph / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q03555, molybdopterin adenylyltransferase, molybdopterin molybdotransferase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M sodium acetate, 25% MPD / PH range: 4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.55→43 Å / Num. obs: 71703 / % possible obs: 98.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.1
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 1.5 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PD0

4pd0


Resolution: 1.55→40.383 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.187 3553 5 %
Rwork0.1541 --
obs0.1557 71069 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→40.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3181 0 56 519 3756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013437
X-RAY DIFFRACTIONf_angle_d1.3344697
X-RAY DIFFRACTIONf_dihedral_angle_d12.711326
X-RAY DIFFRACTIONf_chiral_restr0.056546
X-RAY DIFFRACTIONf_plane_restr0.008626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.57120.28681430.2772611X-RAY DIFFRACTION98
1.5712-1.59370.24741610.26072658X-RAY DIFFRACTION98
1.5937-1.61750.29931430.25172657X-RAY DIFFRACTION98
1.6175-1.64280.30021320.24852663X-RAY DIFFRACTION98
1.6428-1.66970.24291440.23722663X-RAY DIFFRACTION98
1.6697-1.69850.23591310.22892652X-RAY DIFFRACTION98
1.6985-1.72940.28281390.21622661X-RAY DIFFRACTION98
1.7294-1.76260.22571360.2042687X-RAY DIFFRACTION98
1.7626-1.79860.22911710.19022650X-RAY DIFFRACTION98
1.7986-1.83770.23431300.19242646X-RAY DIFFRACTION97
1.8377-1.88050.20571510.18142665X-RAY DIFFRACTION99
1.8805-1.92750.21951320.17312700X-RAY DIFFRACTION99
1.9275-1.97960.21731360.17012695X-RAY DIFFRACTION99
1.9796-2.03790.16341380.15952692X-RAY DIFFRACTION98
2.0379-2.10360.16561530.14442695X-RAY DIFFRACTION99
2.1036-2.17880.17081250.1492740X-RAY DIFFRACTION99
2.1788-2.2660.14731460.14252690X-RAY DIFFRACTION99
2.266-2.36920.19521470.13982710X-RAY DIFFRACTION98
2.3692-2.4940.17321690.13912701X-RAY DIFFRACTION100
2.494-2.65030.18771270.15152753X-RAY DIFFRACTION99
2.6503-2.85490.17821490.14592719X-RAY DIFFRACTION100
2.8549-3.14210.20091420.14452766X-RAY DIFFRACTION100
3.1421-3.59650.17911400.13092762X-RAY DIFFRACTION99
3.5965-4.53020.15611240.11592814X-RAY DIFFRACTION100
4.5302-40.39690.16671440.15672866X-RAY DIFFRACTION98
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)
11.8848-1.1328-1.78743.59094.30547.13650.03270.0402-0.1156-0.13480.1957-0.22030.05380.4491-0.22370.15440.0471-0.01270.14050.04650.158318.8504130.0945108.0056
21.07130.4523-1.35690.3198-0.49211.81630.0953-0.181-0.04810.0795-0.10070.0423-0.07740.1045-0.00510.1397-0.0198-0.00040.17760.020.1608-2.3492131.1712147.0035
30.8931-0.54671.69140.9866-0.8713.7739-0.06120.16120.0143-0.0838-0.0326-0.0939-0.13640.17540.09240.1379-0.00660.01050.17610.0060.15484.2585139.997893.4894
43.49090.24531.09744.3296-1.52441.7572-0.17570.88710.1628-0.78210.1017-0.13680.07340.33430.02560.2534-0.03030.01050.35080.03450.193817.4244140.655992.6298
53.3008-0.11120.26233.20550.3023.44780.02090.31380.0681-0.28540.0338-0.2785-0.02590.3745-0.02050.13350.02340.04530.22220.00610.161321.4246133.09394.9431
61.54131.39990.32222.2129-0.05940.8245-0.07020.0688-0.1284-0.22680.07150.06340.1973-0.0193-0.00870.21250.0265-0.0110.145-0.01740.21135.438118.6488104.1133
77.8075-5.0654-1.177.0233-0.130.66070.22680.96670.2141-0.6330.02610.90320.0916-0.4184-0.25020.3012-0.0267-0.06190.31590.06130.3474-5.5949117.6357100.4648
83.98492.00382.38672.755-1.07054.38060.03990.1861-0.6103-0.3883-0.0396-0.11470.56620.09790.07790.33670.01260.04550.1275-0.01680.30015.2337109.2908100.04
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 319 through 349 )
2X-RAY DIFFRACTION2chain 'A' and (resid 350 through 506 )
3X-RAY DIFFRACTION3chain 'A' and (resid 507 through 550 )
4X-RAY DIFFRACTION4chain 'A' and (resid 551 through 580 )
5X-RAY DIFFRACTION5chain 'A' and (resid 581 through 627 )
6X-RAY DIFFRACTION6chain 'A' and (resid 628 through 686 )
7X-RAY DIFFRACTION7chain 'A' and (resid 687 through 712 )
8X-RAY DIFFRACTION8chain 'A' and (resid 713 through 736 )

+
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