[English] 日本語
Yorodumi
- PDB-5g2s: Crystal structure of the Mo-insertase domain Cnx1E from Arabidops... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5g2s
TitleCrystal structure of the Mo-insertase domain Cnx1E from Arabidopsis thaliana in complex with molybdate
ComponentsMOLYBDOPTERIN BIOSYNTHESIS PROTEIN CNX1
KeywordsTRANSFERASE / CNX1 / CNX1E / GEPHYRIN / GEPHE / MOLYBDENUM METABOLISM / MOEA / MO-INSERTASE / MOCO / MOLYBDENUM COFACTOR
Function / homology
Function and homology information


glycine receptor clustering / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / establishment of synaptic specificity at neuromuscular junction / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / gamma-aminobutyric acid receptor clustering / nitrate reductase activity / auxin-activated signaling pathway / Mo-molybdopterin cofactor biosynthetic process ...glycine receptor clustering / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / establishment of synaptic specificity at neuromuscular junction / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / gamma-aminobutyric acid receptor clustering / nitrate reductase activity / auxin-activated signaling pathway / Mo-molybdopterin cofactor biosynthetic process / molybdenum ion binding / postsynaptic neurotransmitter receptor diffusion trapping / response to metal ion / dendrite / ATP binding / cytosol
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
MOLYBDATE ION / Molybdopterin biosynthesis protein CNX1
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.838 Å
AuthorsKrausze, J. / Probst, C. / Kruse, T. / Heinz, D.W. / Mendel, R.R.
CitationJournal: Biochem.J. / Year: 2017
Title: Dimerization of the Plant Molybdenum Insertase Cnx1E is Required for Synthesis of the Molybdenum Cofactor.
Authors: Krausze, J. / Probst, C. / Curth, U. / Reichelt, J. / Saha, S. / Schafflik, D. / Heinz, D.W. / Mendel, R.R. / Kruse, T.
History
DepositionApr 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MOLYBDOPTERIN BIOSYNTHESIS PROTEIN CNX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0394
Polymers49,7631
Non-polymers2763
Water18010
1
A: MOLYBDOPTERIN BIOSYNTHESIS PROTEIN CNX1
hetero molecules

A: MOLYBDOPTERIN BIOSYNTHESIS PROTEIN CNX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0798
Polymers99,5262
Non-polymers5536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_857-x+3,y,-z+21
Buried area8250 Å2
ΔGint-60.3 kcal/mol
Surface area32350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.900, 122.330, 131.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein MOLYBDOPTERIN BIOSYNTHESIS PROTEIN CNX1


Mass: 49763.094 Da / Num. of mol.: 1
Fragment: MOLYBDOPTERIN MOLYBDOTRANSFERASE DOMAIN CNX1E, RESIDUE 1-451
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Strain: LER-1 / Plasmid: PQE80 DERIVATIVE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RK5204
References: UniProt: Q39054, molybdopterin molybdotransferase
#2: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE


Mass: 159.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: MoO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Description: DATA WERE PROCESSED UNDER THE ASSUMPTION THAT FRIEDEL'S LAW BE FALSE TO IDENTIFY THE MOLYBDENUM SITE.
Crystal growpH: 7.3
Details: 5 MM SODIUM MOLYBDATE; 5 MM MAGNESIUM CHLORIDE; 0.2 M LITHIUM SULFATE; 50 %(V/V) PEG 300; 0.1 M HEPES, PH 7.3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.77
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 23, 2015 / Details: TOROIDAL FOCUSING MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 2.84→50 Å / Num. obs: 24173 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.88 % / Biso Wilson estimate: 83.33 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.72
Reflection shellResolution: 2.84→2.91 Å / Redundancy: 6.39 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.838→44.802 Å / SU ML: 0.44 / σ(F): 1.36 / Phase error: 29.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2426 1206 5 %
Rwork0.2246 --
obs0.2255 24165 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.26 Å2
Refinement stepCycle: LAST / Resolution: 2.838→44.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2945 0 12 10 2967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033009
X-RAY DIFFRACTIONf_angle_d0.9384118
X-RAY DIFFRACTIONf_dihedral_angle_d14.9861809
X-RAY DIFFRACTIONf_chiral_restr0.051514
X-RAY DIFFRACTIONf_plane_restr0.005535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.838-2.95160.41291350.38782512X-RAY DIFFRACTION98
2.9516-3.08590.3291330.31232576X-RAY DIFFRACTION99
3.0859-3.24860.31771340.2932481X-RAY DIFFRACTION99
3.2486-3.4520.33691300.29382573X-RAY DIFFRACTION99
3.452-3.71840.2841300.24612558X-RAY DIFFRACTION100
3.7184-4.09240.27991350.22542570X-RAY DIFFRACTION99
4.0924-4.68410.18961340.1892550X-RAY DIFFRACTION100
4.6841-5.89930.23031390.2012569X-RAY DIFFRACTION100
5.8993-44.8080.19741360.19752570X-RAY DIFFRACTION100
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)
11.74210.0490.93481.071-0.21023.33080.1801-0.8381-0.00380.27790.08240.1796-0.3588-0.7419-0.14940.59810.11040.09860.83850.02230.709787.041817.197142.1395
21.02550.29950.31720.787-0.5311.73640.1132-0.53470.16880.4344-0.132-0.006-0.1664-0.10420.07490.72320.0154-0.02580.8365-0.0630.649299.537816.4337155.1773
32.8149-0.1339-0.65392.70890.80212.85110.05690.213-0.0428-0.197-0.04560.5012-0.2288-0.4929-0.02720.55750.0675-0.10160.78970.04010.753884.672912.7594113.5545
42.2624-0.2828-0.58831.9242-0.90441.88640.368-0.03980.4868-0.2024-0.31870.1753-0.58790.0072-0.12871.0959-0.05110.11330.84170.00980.820197.492134.3109119.2283
52.9913-0.3566-1.8585.9908-0.60341.58530.4570.62820.9604-0.1740.1945-0.0888-1.5113-0.2106-0.27351.07730.09330.08910.64540.1510.720898.334833.4566118.0069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 15 THROUGH 71 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 72 THROUGH 218 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 219 THROUGH 344 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 345 THROUGH 402 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 403 THROUGH 439 )

+
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