[English] 日本語
Yorodumi
- PDB-6etd: The Structure of the Mo-insertase domain Cnx1E from Arabidopsis t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6etd
TitleThe Structure of the Mo-insertase domain Cnx1E from Arabidopsis thaliana in complex with AMP
ComponentsMolybdopterin biosynthesis protein CNX1
KeywordsPLANT PROTEIN / Arabidopsis / Arabidopsis Proteins / Coenzymes / Metalloproteins / Catalytic Domain / Nucleotide Binding / Entropic Enzyme / Adenosine Monophosphate
Function / homology
Function and homology information


molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / molybdopterin molybdotransferase / nitrate reductase activity / molybdopterin molybdotransferase activity / auxin-activated signaling pathway / molybdenum ion binding / Mo-molybdopterin cofactor biosynthetic process / response to metal ion / ATP binding
Similarity search - Function
Molybdopterin biosynthesis moeA protein; domain 3 / Molybdopterin biosynthesis moea protein, domain 3. / Beta-clip / MoeA, C-terminal, domain IV / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis proteins signature 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 / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis proteins signature 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
ACETYL GROUP / ADENOSINE MONOPHOSPHATE / Molybdopterin biosynthesis protein CNX1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.723 Å
AuthorsKrausze, J.
CitationJournal: Biochem. J. / Year: 2018
Title: The functional principle of eukaryotic molybdenum insertases.
Authors: Krausze, J. / Hercher, T.W. / Zwerschke, D. / Kirk, M.L. / Blankenfeldt, W. / Mendel, R.R. / Kruse, T.
History
DepositionOct 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
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)50,53110
Polymers49,7791
Non-polymers7529
Water6,593366
1
A: Molybdopterin biosynthesis protein CNX1
hetero molecules

A: Molybdopterin biosynthesis protein CNX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,06220
Polymers99,5582
Non-polymers1,50418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area12780 Å2
ΔGint-56 kcal/mol
Surface area31950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.130, 123.640, 132.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Molybdopterin biosynthesis protein CNX1 / Molybdenum cofactor biosynthesis enzyme CNX1


Mass: 49779.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Oxidation of Cys-161 due to radiation damge / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CNX1, At5g20990, F22D1.6, T10F18.20 / Plasmid: pGpus-Cnx1E / Details (production host): pQE80 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): RK5204
References: UniProt: Q39054, molybdopterin molybdotransferase, molybdopterin adenylyltransferase

-
Non-polymers , 5 types, 375 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20 % (v/v) 1,2-Ehanediol; 10 % (w/v) PEG 8000; 0.3 M MgCl2; 0.3 M CaCl2; 0.1 M Tris/BICINE, 0.015 M MgxAMP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2017 / Details: Mirrors
RadiationMonochromator: SI111 double crystal with sagital bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.723→45.135 Å / Num. obs: 38415 / % possible obs: 66.8 % / Observed criterion σ(I): -3 / Redundancy: 4.43 % / Biso Wilson estimate: 29.06 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.073 / Rrim(I) all: 0.117 / Net I/σ(I): 8.1
Reflection shellResolution: 1.723→1.958 Å / Redundancy: 4.28 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2744 / CC1/2: 0.674 / Rpim(I) all: 0.555 / Rrim(I) all: 0.865 / % possible all: 15.1

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
MxCuBEdata collection
XDSJun 1, 2017data reduction
STARANISO1.0.5data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G2R

5g2r


Resolution: 1.723→45.13 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.142 / SU Rfree Blow DPI: 0.129 / SU Rfree Cruickshank DPI: 0.125
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2029 5.28 %RANDOM
Rwork0.177 ---
obs0.179 38413 66.7 %-
Displacement parametersBiso mean: 31.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.459 Å20 Å20 Å2
2--1.809 Å20 Å2
3----1.35 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 1.723→45.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3093 0 56 366 3515
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016491HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0711821HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1428SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes976HARMONIC5
X-RAY DIFFRACTIONt_it6491HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.62
X-RAY DIFFRACTIONt_other_torsion13.83
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion443SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7029SEMIHARMONIC4
LS refinement shellResolution: 1.723→1.77 Å
RfactorNum. reflection% reflection
Rfree0.3921 -4.17 %
Rwork0.2658 115 -
obs--2.73 %
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)
10.67940.00850.57570.3599-0.00951.35310.0548-0.23110.16140.1715-0.10340.0214-0.1684-0.21630.0486-0.0498-0.02430.0293-0.0274-0.0426-0.073529.544918.044826.7476
20.52370.0907-0.0820.75440.21091.13870.06210.0850.1021-0.139-0.03780.0909-0.2356-0.0514-0.0243-0.05590.04580.0013-0.04510.0339-0.05125.6120.5445-16.7968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|16 - 192 }
2X-RAY DIFFRACTION2{ A|193 - 442 }

+
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