[English] 日本語
Yorodumi
- PDB-7w8j: Dimethylformamidase, 2x(A2B2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7w8j
TitleDimethylformamidase, 2x(A2B2)
Components
  • N,N-dimethylformamidase large subunit
  • N,N-dimethylformamidase small subunit
KeywordsHYDROLASE / Amidohydrolase / mononuclear iron / AB polypeptide / tetramer
Function / homologyN,N-dimethylformamidase / N,N-dimethylformamidase activity / N,N-dimethylformamidase beta subunit-like, C-terminal / N,N-dimethylformamidase beta subunit-like, C-terminal / Concanavalin A-like lectin/glucanase domain superfamily / metal ion binding / : / N,N-dimethylformamidase large subunit / N,N-dimethylformamidase small subunit
Function and homology information
Biological speciesParacoccus sp. SSG05 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsVinothkumar, K.R. / Subramanian, R. / Arya, C. / Ramanathan, G.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)DBT/PR12422/MED/31/287/2014 India
CitationJournal: To Be Published
Title: Dimethylformamidase with a Unique Iron Center
Authors: Arya, C. / Ramanathan, G. / Vinothkumar, K.R. / Subramanian, R.
History
DepositionDec 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N,N-dimethylformamidase large subunit
B: N,N-dimethylformamidase small subunit
C: N,N-dimethylformamidase large subunit
D: N,N-dimethylformamidase small subunit
E: N,N-dimethylformamidase large subunit
F: N,N-dimethylformamidase small subunit
G: N,N-dimethylformamidase large subunit
H: N,N-dimethylformamidase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)409,92612
Polymers409,7028
Non-polymers2234
Water5,224290
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14B
24D
15B
25F
16B
26H
17C
27E
18C
28G
19D
29F
110D
210H
111E
211G
112F
212H

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
11METMETVALVALAA1 - 7621 - 762
21METMETVALVALCC1 - 7621 - 762
12METMETVALVALAA1 - 7621 - 762
22METMETVALVALEE1 - 7621 - 762
13METMETVALVALAA1 - 7621 - 762
23METMETVALVALGG1 - 7621 - 762
14SERSERLEULEUBB7 - 1317 - 131
24SERSERLEULEUDD7 - 1317 - 131
15SERSERLEULEUBB7 - 1317 - 131
25SERSERLEULEUFF7 - 1317 - 131
16SERSERLEULEUBB7 - 1317 - 131
26SERSERLEULEUHH7 - 1317 - 131
17METMETVALVALCC1 - 7621 - 762
27METMETVALVALEE1 - 7621 - 762
18METMETVALVALCC1 - 7621 - 762
28METMETVALVALGG1 - 7621 - 762
19SERSERLEULEUDD7 - 1317 - 131
29SERSERLEULEUFF7 - 1317 - 131
110SERSERLEULEUDD7 - 1317 - 131
210SERSERLEULEUHH7 - 1317 - 131
111METMETVALVALEE1 - 7621 - 762
211METMETVALVALGG1 - 7621 - 762
112SERSERLEULEUFF7 - 1317 - 131
212SERSERLEULEUHH7 - 1317 - 131

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

-
Components

#1: Protein
N,N-dimethylformamidase large subunit


Mass: 86341.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus sp. SSG05 (bacteria) / Gene: dmfase2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6NT79, N,N-dimethylformamidase
#2: Protein
N,N-dimethylformamidase small subunit


Mass: 16083.823 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus sp. SSG05 (bacteria) / Gene: dmfase1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6NWZ0, N,N-dimethylformamidase
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: DMFase, an amidohydrolase / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.4 MDa / Experimental value: YES
Source (natural)Organism: Paracoccus sp. (bacteria) / Strain: SSG05
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 (DE3)
Buffer solutionpH: 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHepes1
2200 mMSodium ChlorideNaCl1
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Enzyme after gel filtration was used for cryoEM grid prep. Sample was held at 37 degrees before application on the grid.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K / Details: wait time - 10 seconds and 3.5 seconds blot

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 130841 X / Nominal defocus max: 3200 nm / Nominal defocus min: 850 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 79 K
Image recordingAverage exposure time: 60 sec. / Electron dose: 28.3 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 548
Details: One image was collected per hole. Total of 25 frames was saved and each frame has ~1.13 e/A2
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

-
Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement
EM software
IDNameVersionCategory
1Gautomatchparticle selection
2EPU1.1image acquisition
4Gctf1.06CTF correction
7Coot0.9.5model fitting
8UCSF Chimera1.15model fitting
10REFMAC5.8.0267model refinement
11RELION3.1initial Euler assignment
12RELION3.1final Euler assignment
13RELION3.1classification
14RELION3.13D reconstruction
Image processingDetails: From the 548 images, MotionCor2 was used for full frame alignment. After CTF estimation, 528 micrographs were selected and used for further extraction. Two rounds of 2D classification of ...Details: From the 548 images, MotionCor2 was used for full frame alignment. After CTF estimation, 528 micrographs were selected and used for further extraction. Two rounds of 2D classification of extracted particles resulted in 30689 particles and used for refinement.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 114182
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28964 / Algorithm: BACK PROJECTION
Details: The final reconstruction was from a single 3D class after B-factor weighting and aberration correction in Relion 3.1
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 73.98 / Protocol: OTHER / Space: RECIPROCAL
Details: Servalcat was used along with Refmac to calculate fofc maps and extensively used for modelling.
Atomic model building

3D fitting-ID: 1 / Accession code: 6LVB / Initial refinement model-ID: 1 / PDB-ID: 6LVB

6lvb

/ Source name: PDB / Type: experimental model

IDPdb chain-ID
1A
2B
RefinementResolution: 2.5→160.5 Å / Cor.coef. Fo:Fc: 0.933 / SU B: 9.317 / SU ML: 0.197 / ESU R: 0.287
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.30613 --
obs0.30613 318579 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 73.986 Å2
Refinement stepCycle: 1 / Total: 28678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0030.01329230
ELECTRON MICROSCOPYr_bond_other_d0.0310.01726052
ELECTRON MICROSCOPYr_angle_refined_deg1.2361.64439714
ELECTRON MICROSCOPYr_angle_other_deg1.1071.58159910
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.51553576
ELECTRON MICROSCOPYr_dihedral_angle_2_deg31.44121.3591796
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.68154490
ELECTRON MICROSCOPYr_dihedral_angle_4_deg11.90815254
ELECTRON MICROSCOPYr_chiral_restr0.0440.23578
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.0233940
ELECTRON MICROSCOPYr_gen_planes_other0.0010.027352
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it0.0127.9714220
ELECTRON MICROSCOPYr_mcbond_other0.0127.9714219
ELECTRON MICROSCOPYr_mcangle_it0.02311.95517770
ELECTRON MICROSCOPYr_mcangle_other0.02311.95517771
ELECTRON MICROSCOPYr_scbond_it0.0047.97115010
ELECTRON MICROSCOPYr_scbond_other0.0047.97115011
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other0.0111.95621927
ELECTRON MICROSCOPYr_long_range_B_refined0.279119278
ELECTRON MICROSCOPYr_long_range_B_other0.278119186
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: ELECTRON MICROSCOPY / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A499420.07
12C499420.07
21A499400.07
22E499400.07
31A512440.01
32G512440.01
41B79560.1
42D79560.1
51B79400.11
52F79400.11
61B83340.02
62H83340.02
71C512840.01
72E512840.01
81C499760.07
82G499760.07
91D82960.02
92F82960.02
101D79380.11
102H79380.11
111E499720.07
112G499720.07
121F79540.1
122H79540.1
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.663 23651 -
obs--100 %

+
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