[English] 日本語
Yorodumi
- PDB-4zsv: Structure of a fusion protein with a helix linker, 2ARH-3-3KAW-1.0 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zsv
TitleStructure of a fusion protein with a helix linker, 2ARH-3-3KAW-1.0
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / protein design / bionanotechnology / protein assembly / symmetry / biomaterials
Function / homologyUncharacterised conserved protein UCP017998 / Protein of unknown function (DUF1122) / Protein of unknown function DUF326 / Domain of Unknown Function (DUF326) / Uncharacterized cysteine-rich protein YhjQ-like / Acyl-CoA N-acyltransferase / DUF1122 domain-containing protein / Four-helix bundle copper-binding protein
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
Pseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.2 Å
AuthorsLai, Y.-T. / Yeates, T.O.
CitationJournal: Protein Eng.Des.Sel. / Year: 2015
Title: On the predictability of the orientation of protein domains joined by a spanning alpha-helical linker.
Authors: Lai, Y.T. / Jiang, L. / Chen, W. / Yeates, T.O.
History
DepositionMay 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Mar 6, 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_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)70,5692
Polymers70,5692
Non-polymers00
Water0
1
A: Uncharacterized protein
B: Uncharacterized protein

A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)141,1384
Polymers141,1384
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_454-x+y-1,y,-z-1/21
Buried area7900 Å2
ΔGint-43 kcal/mol
Surface area56340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.610, 191.610, 114.690
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 3 - 296 / Label seq-ID: 12 - 305

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Uncharacterized protein


Mass: 35284.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria), (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: VF5, ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: aq_1966, PA2107 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O67778, UniProt: Q9I208

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.31 Å3/Da / Density % sol: 71.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.9M ammonium tartrate dibasic

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.2→95.81 Å / Num. obs: 9491 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 19.3 % / Biso Wilson estimate: 158.244 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.065 / Χ2: 0.943 / Net I/σ(I): 35.75 / Num. measured all: 183546
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
4.2-4.310.9660.517.55135096756690.52399.1
4.31-4.430.9820.3969.57137236716710.406100
4.43-4.560.9860.32211.94133656576570.33100
4.56-4.70.990.25414.21123656186180.261100
4.7-4.850.9930.22616.11121826156150.232100
4.85-5.020.9940.21216.67111935935930.218100
5.02-5.210.9960.18118.67105355785780.186100
5.21-5.420.9960.16521.29112865535530.169100
5.42-5.660.9970.16620.88107615325320.171100
5.66-5.940.9960.15821.97101105095080.16299.8
5.94-6.260.9980.12725.5896004924920.131100
6.26-6.640.9990.08935.1586704674670.091100
6.64-7.10.9990.06543.4980674364360.067100
7.1-7.670.9990.05356.5483904224220.054100
7.67-8.410.03873.2673213773760.03999.7
8.4-9.3910.02797.8865063503500.028100
9.39-10.8510.022109.4552913143140.023100
10.85-13.2810.021121.1650372732730.022100
13.28-18.7910.021121.7437112262260.022100
18.7910.017127.4919241421410.01899.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.2→95.81 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.3453 / WRfactor Rwork: 0.2938 / FOM work R set: 0.5353 / SU B: 138.785 / SU ML: 1.515 / SU Rfree: 1.2231 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3762 949 10 %RANDOM
Rwork0.333 ---
obs0.3374 8541 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50 Å2 / Biso mean: 49.581 Å2 / Biso min: 50 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20.45 Å20 Å2
2--0.91 Å20 Å2
3----2.94 Å2
Refinement stepCycle: final / Resolution: 4.2→95.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4764 0 0 0 4764
Num. residues----588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194866
X-RAY DIFFRACTIONr_bond_other_d0.0030.024642
X-RAY DIFFRACTIONr_angle_refined_deg1.0331.9766540
X-RAY DIFFRACTIONr_angle_other_deg0.822310696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7625586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23123.175252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.68915884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7461550
X-RAY DIFFRACTIONr_chiral_restr0.0560.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215496
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021162
Refine LS restraints NCS

Ens-ID: 1 / Number: 17956 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 4.2→4.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.489 66 -
Rwork0.529 598 -
all-664 -
obs--99.1 %

+
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