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- PDB-8jzc: Crystal structure of Geobacillus stearothermophilus NarJ -

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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 / metallochaperone activity / nitrate assimilation / chaperone-mediated protein complex assembly / unfolded protein binding / oxidoreductase activity
Similarity search - Function
Nitrate reductase chaperone, NarJ / DMSO/Nitrate reductase chaperone / TorD-like superfamily / Nitrate reductase delta subunit
Similarity search - Domain/homology
Respiratory nitrate reductase delta chain
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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 )

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