[English] 日本語
Yorodumi
- PDB-4nwo: Computationally Designed Two-Component Self-Assembling Tetrahedra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nwo
TitleComputationally Designed Two-Component Self-Assembling Tetrahedral Cage T33-15
Components
  • Chorismate mutase AroH
  • Molybdenum cofactor biosynthesis protein MogA
KeywordsPROTEIN BINDING / two-component / self-assembling / tetrahedron / designed protein cage / computational design / protein engineering / multimerization / nanomaterial / nanostructure / molybdenum cofactor biosynthesis protein / mog / chorismate mutase / isomerase
Function / homology
Function and homology information


molybdopterin cofactor biosynthetic process / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / chorismate metabolic process / chorismate mutase / chorismate mutase activity / Mo-molybdopterin cofactor biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / ATP binding ...molybdopterin cofactor biosynthetic process / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / chorismate metabolic process / chorismate mutase / chorismate mutase activity / Mo-molybdopterin cofactor biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Chorismate mutase, AroH class / Chorismate mutase type I / Chorismate mutase domain profile. / : / Molybdenum cofactor biosynthesis proteins signature 1. / RutC-like / Molybdenum cofactor biosynthesis, conserved site / MoaB/Mog-like domain / Molybdenum Cofactor Biosythetic Enzyme; Chain A / RutC-like superfamily ...Chorismate mutase, AroH class / Chorismate mutase type I / Chorismate mutase domain profile. / : / Molybdenum cofactor biosynthesis proteins signature 1. / RutC-like / Molybdenum cofactor biosynthesis, conserved site / MoaB/Mog-like domain / Molybdenum Cofactor Biosythetic Enzyme; Chain A / RutC-like superfamily / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chorismate mutase AroH / Chorismate mutase AroH / Molybdopterin adenylyltransferase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
Thermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsMcNamara, D.E. / King, N.P. / Bale, J.B. / Sheffler, W. / Baker, D. / Yeates, T.O.
CitationJournal: Nature / Year: 2014
Title: Accurate design of co-assembling multi-component protein nanomaterials.
Authors: King, N.P. / Bale, J.B. / Sheffler, W. / McNamara, D.E. / Gonen, S. / Gonen, T. / Yeates, T.O. / Baker, D.
History
DepositionDec 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_ref_seq_dif / struct_site
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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Molybdenum cofactor biosynthesis protein MogA
B: Chorismate mutase AroH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6043
Polymers33,5642
Non-polymers401
Water362
1
A: Molybdenum cofactor biosynthesis protein MogA
B: Chorismate mutase AroH
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)403,24636
Polymers402,76524
Non-polymers48112
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_564z,x+1,y-11
crystal symmetry operation9_465y-1,z+1,x1
crystal symmetry operation28_597x,-y+9/2,-z+5/21
crystal symmetry operation30_588z,-x+7/2,-y+7/21
crystal symmetry operation35_487y-1,-z+7/2,-x+5/21
crystal symmetry operation51_757-x+5/2,y,-z+5/21
crystal symmetry operation56_768-z+5/2,x+1,-y+7/21
crystal symmetry operation58_867-y+7/2,z+1,-x+5/21
crystal symmetry operation74_795-x+5/2,-y+9/2,z1
crystal symmetry operation79_784-z+5/2,-x+7/2,y-11
crystal symmetry operation84_885-y+7/2,-z+7/2,x1
Buried area52360 Å2
ΔGint-532 kcal/mol
Surface area112540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.520, 213.520, 213.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432

-
Components

#1: Protein Molybdenum cofactor biosynthesis protein MogA


Mass: 19049.074 Da / Num. of mol.: 1
Mutation: Y20T, E21A, D30L, T31A, D34L, F110E, K135D, K137A, R140S, E141D, D144L, V168M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: mogA, SO_0065 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EKM7
#2: Protein Chorismate mutase AroH


Mass: 14514.650 Da / Num. of mol.: 1
Mutation: E12N, E13S, E17T, A18S, H20I, Q21I, R24I, E25L, L28E, R109S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: aroG, aroH / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q84FH6, UniProt: Q5SJY4*PLUS, chorismate mutase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.02 Å3/Da / Density % sol: 59.29 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 100 mM sodium cacodylate pH 6.5, 200 mM calcium acetate, 28% (v/v) PEG 300, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→75.491 Å / Num. obs: 10783 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.59 % / Biso Wilson estimate: 79.22 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 19.43
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 14.34 % / Rmerge(I) obs: 1.863 / Mean I/σ(I) obs: 2.25 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.81 Å75.49 Å
Translation6.81 Å75.49 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K6A AND 1UFY

3k6a

1ufy


Resolution: 2.8→75.49 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.252 1079 10.01 %
Rwork0.202 --
obs0.207 10782 99.9 %
all-10796 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.65 Å2
Refinement stepCycle: LAST / Resolution: 2.8→75.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 1 2 2011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032041
X-RAY DIFFRACTIONf_angle_d0.772805
X-RAY DIFFRACTIONf_dihedral_angle_d10.277705
X-RAY DIFFRACTIONf_chiral_restr0.028364
X-RAY DIFFRACTIONf_plane_restr0.005357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8008-2.92820.37471300.29671167X-RAY DIFFRACTION100
2.9282-3.08260.33931320.28161183X-RAY DIFFRACTION100
3.0826-3.27580.30361310.24721183X-RAY DIFFRACTION100
3.2758-3.52870.28391310.20771179X-RAY DIFFRACTION100
3.5287-3.88380.25071340.18211206X-RAY DIFFRACTION100
3.8838-4.44570.22551350.17851217X-RAY DIFFRACTION100
4.4457-5.60080.23811360.17611225X-RAY DIFFRACTION100
5.6008-75.51810.2281500.21141343X-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)
13.9602-1.756-1.39864.33820.41564.6552-0.0492-0.13420.01630.1836-0.13960.1034-0.1954-0.19350.17820.546-0.0721-0.03910.5929-0.03110.547229.3791451.4425254.2646
22.84611.9792-1.8934.8858-3.18138.49520.09480.0219-0.3252-0.08720.06540.21540.368-0.1152-0.16130.610.0139-0.08880.6411-0.08650.6688238.0269450.3726281.1316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 173 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 114 )

+
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