[English] 日本語
Yorodumi
- PDB-8jzc: Crystal structure of Geobacillus stearothermophilus NarJ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jzc
TitleCrystal structure of Geobacillus stearothermophilus NarJ
ComponentsNitrate reductase molybdenum cofactor assembly chaperone
KeywordsCHAPERONE / redox enzyme maturation protein / NarJ subfamily
Function / homology
Function and homology information


nitrate reductase / nitrate reductase activity / chaperone-mediated protein complex assembly / nitrate assimilation / unfolded protein binding
Similarity search - Function
Nitrate reductase chaperone, NarJ / DMSO/Nitrate reductase chaperone / TorD-like superfamily / Nitrate reductase delta subunit
Similarity search - Domain/homology
Nitrate reductase molybdenum cofactor assembly chaperone
Similarity search - Component
Biological speciesGeobacillus stearothermophilus ATCC 7953 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSong, W.S. / Kim, J.H. / Namgung, B. / Cho, H.Y. / Oh, H.B. / Yoon, S.I.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00208153 Korea, Republic Of
National Research Foundation (NRF, Korea)2022R1I1A1A01068105 Korea, Republic Of
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Complementary hydrophobic interaction of the redox enzyme maturation protein NarJ with the signal peptide of the respiratory nitrate reductase NarG.
Authors: Song, W.S. / Kim, J.H. / Namgung, B. / Cho, H.Y. / Shin, H. / Oh, H.B. / Ha, N.C. / Yoon, S.I.
History
DepositionJul 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitrate reductase molybdenum cofactor assembly chaperone


Theoretical massNumber of molelcules
Total (without water)21,9011
Polymers21,9011
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.514, 78.514, 88.055
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
Components

#1: Protein Nitrate reductase molybdenum cofactor assembly chaperone


Mass: 21901.465 Da / Num. of mol.: 1 / Mutation: V61I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus ATCC 7953 (bacteria)
Strain: ATCC 7953 / Gene: narJ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0K9HWM0

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.62 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate, glycerol, PEG 550, Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. obs: 10633 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 58.12 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 26.9
Reflection shellResolution: 2.55→2.59 Å / Rmerge(I) obs: 0.503 / Num. unique obs: 514

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model

Resolution: 2.55→29.35 Å / SU ML: 0.2735 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5068
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.257 538 5.12 %
Rwork0.2126 9970 -
obs0.2148 10508 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.46 Å2
Refinement stepCycle: LAST / Resolution: 2.55→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1339 0 0 0 1339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00391369
X-RAY DIFFRACTIONf_angle_d0.61091867
X-RAY DIFFRACTIONf_chiral_restr0.0396210
X-RAY DIFFRACTIONf_plane_restr0.0049244
X-RAY DIFFRACTIONf_dihedral_angle_d14.8791815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.810.33061490.29192441X-RAY DIFFRACTION98.82
2.81-3.210.36621090.28822456X-RAY DIFFRACTION98.88
3.21-4.050.25981310.21642486X-RAY DIFFRACTION98.98
4.05-29.350.22061490.17882587X-RAY DIFFRACTION99.27
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)
18.809429590372.132214860320.05360379223525.00975676269-0.9176040927947.434004909060.1142759196530.1628295261730.381675503570.03455802997080.02340238965460.123133409674-0.4030384809580.0636827930206-0.09613282189350.4231376708110.04877811205320.05671732416610.3891029375990.05017791599120.315253329784-16.649831858249.217729862798.420258894
28.625393169332.10973867983-4.977627312541.77742496109-0.1823635241293.733574157290.247622904318-0.273969244139-0.2764767239380.0902832184259-0.0264999375691-0.02796441915310.431214313647-0.436765653434-0.2062372953640.792773286404-0.03366557967230.02552787702460.5375225641220.02662690287590.432499263495-1.9479830513250.088974163481.4957971964
38.925119757032.19748496407-1.713731422653.03765384827-0.6968165093155.210159400870.00495754186279-0.05109878960340.8198772789240.1125155284240.1806200555730.117776826271-1.275153403770.179857748491-0.1322454127360.89851627911-0.02062541921430.1329638479410.5092117633190.03062791149670.44697910134-7.5129032197759.150046264991.2541237998
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 69 )
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 117 )
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 176 )

+
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