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- PDB-8jzd: Crystal structure of Escherichia coli NarJ in complex with the si... -

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Basic information

Entry
Database: PDB / ID: 8jzd
TitleCrystal structure of Escherichia coli NarJ in complex with the signal peptide of E. coli NarG
Components
  • Nitrate reductase molybdenum cofactor assembly chaperone NarJ
  • Respiratory nitrate reductase 1 alpha chain
KeywordsCHAPERONE / redox enzyme maturation protein / NarJ subfamily / signal peptide
Function / homology
Function and homology information


nitrate reductase (quinone) / NarGHI complex / nitrate metabolic process / metallochaperone activity / nitrate reductase activity / anaerobic electron transport chain / anaerobic respiration / molybdopterin cofactor binding / chaperone-mediated protein complex assembly / nitrate assimilation ...nitrate reductase (quinone) / NarGHI complex / nitrate metabolic process / metallochaperone activity / nitrate reductase activity / anaerobic electron transport chain / anaerobic respiration / molybdopterin cofactor binding / chaperone-mediated protein complex assembly / nitrate assimilation / unfolded protein binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane / metal ion binding / cytoplasm
Similarity search - Function
Nitrate reductase chaperone, NarJ / Nitrate reductase, alpha subunit / DMSO/Nitrate reductase chaperone / Nitrate reductase, alpha subunit, N-terminal / TorD-like superfamily / Nitrate reductase, alpha subunit, N-terminal domain superfamily / Nitrate reductase delta subunit / Respiratory nitrate reductase alpha N-terminal / Nitrate reductase alpha subunit-like, MopB domain / Prokaryotic molybdopterin oxidoreductases signature 2. ...Nitrate reductase chaperone, NarJ / Nitrate reductase, alpha subunit / DMSO/Nitrate reductase chaperone / Nitrate reductase, alpha subunit, N-terminal / TorD-like superfamily / Nitrate reductase, alpha subunit, N-terminal domain superfamily / Nitrate reductase delta subunit / Respiratory nitrate reductase alpha N-terminal / Nitrate reductase alpha subunit-like, MopB domain / Prokaryotic molybdopterin oxidoreductases signature 2. / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase
Similarity search - Domain/homology
Respiratory nitrate reductase 1 alpha chain / Nitrate reductase molybdenum cofactor assembly chaperone NarJ
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 NarJ
B: Respiratory nitrate reductase 1 alpha chain
C: Nitrate reductase molybdenum cofactor assembly chaperone NarJ
D: Respiratory nitrate reductase 1 alpha chain


Theoretical massNumber of molelcules
Total (without water)47,4764
Polymers47,4764
Non-polymers00
Water0
1
A: Nitrate reductase molybdenum cofactor assembly chaperone NarJ
B: Respiratory nitrate reductase 1 alpha chain


Theoretical massNumber of molelcules
Total (without water)23,7382
Polymers23,7382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-9 kcal/mol
Surface area8800 Å2
MethodPISA
2
C: Nitrate reductase molybdenum cofactor assembly chaperone NarJ
D: Respiratory nitrate reductase 1 alpha chain


Theoretical massNumber of molelcules
Total (without water)23,7382
Polymers23,7382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-10 kcal/mol
Surface area8470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.443, 185.443, 37.943
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 67 or (resid 68...
d_2ens_1(chain "C" and (resid 1 or (resid 2 and (name...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 1 - 166 / Label seq-ID: 1 - 166

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2CC

NCS oper: (Code: givenMatrix: (0.484383861145, 0.874280994641, 0.0317020105334), (-0.859790785871, 0.482426023097, -0.167406501579), (-0.161654197576, 0.0538319110657, 0.985378123239)Vector: -31. ...NCS oper: (Code: given
Matrix: (0.484383861145, 0.874280994641, 0.0317020105334), (-0.859790785871, 0.482426023097, -0.167406501579), (-0.161654197576, 0.0538319110657, 0.985378123239)
Vector: -31.8640970718, 59.8367076352, -6.87999998122)

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Components

#1: Protein Nitrate reductase molybdenum cofactor assembly chaperone NarJ / Redox enzyme maturation protein NarJ


Mass: 21781.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: narJ, b1226, JW1217 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AF26
#2: Protein/peptide Respiratory nitrate reductase 1 alpha chain / Nitrate reductase A subunit alpha / Quinol-nitrate oxidoreductase subunit alpha


Mass: 1956.337 Da / Num. of mol.: 2 / Fragment: signal peptide / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria) / References: UniProt: P09152, nitrate reductase (quinone)

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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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, 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: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 17555 / % possible obs: 98.1 % / Redundancy: 4.6 % / Biso Wilson estimate: 52.97 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 31.3
Reflection shellResolution: 2.45→2.49 Å / Rmerge(I) obs: 0.617 / Num. unique obs: 871

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model

Resolution: 2.45→28.88 Å / SU ML: 0.3492 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 36.6935
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2531 848 4.84 %
Rwork0.2081 16662 -
obs0.2103 17510 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.26 Å2
Refinement stepCycle: LAST / Resolution: 2.45→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 0 0 0 2719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742775
X-RAY DIFFRACTIONf_angle_d0.96963779
X-RAY DIFFRACTIONf_chiral_restr0.0499440
X-RAY DIFFRACTIONf_plane_restr0.0081490
X-RAY DIFFRACTIONf_dihedral_angle_d15.1883973
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.461118709957 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.60.36711450.33482754X-RAY DIFFRACTION97.84
2.6-2.80.35341300.28282804X-RAY DIFFRACTION98.89
2.8-3.090.3641330.29992848X-RAY DIFFRACTION98.77
3.09-3.530.30711480.23492760X-RAY DIFFRACTION98.01
3.53-4.450.22021390.1862781X-RAY DIFFRACTION97.95
4.45-28.880.19731530.15722715X-RAY DIFFRACTION96.08
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)
19.308359896750.9850805760940.2699147395964.69451955107-2.19762545723.468351321730.07548204801060.812797037217-0.0416175543564-0.1160235681360.136810006665-0.1378586468640.16727466123-0.296941065053-0.1758395078230.3571813878340.04837128095750.1351015906850.3866557856980.02643200434050.71283709623713.343960782373.715660530325.9951729668
28.55188270171-1.134601747891.825837449323.311299038560.9256436646424.06950193659-0.01234635627980.4142746410830.998855107412-0.231231663278-0.197948550880.192860351661-0.402374827732-0.3804369088830.2252626205280.4059920647760.0813501255270.08854601621630.5110622744740.06302950653090.737099038333-1.1692053008283.656204417426.3829022791
33.81133282882-1.820746859024.028906676971.68639713607-2.413074040874.547802406810.9018882507163.176306612770.0733981012281-1.84875831618-0.044140956876-0.0226854904819-0.00922325646564-1.10332019984-0.3818436309570.9622318862940.1634869428550.1855649008691.31209461160.03314501605930.49760709468110.291907748271.922153714713.2816973618
47.333773645180.1001482450413.258796815595.76460376738-0.7567885143772.96772857946-0.06060245981161.28086676742-0.1257127938110.611643059604-0.4076372871671.277913575710.1310315788890.2060793689450.3588151613780.6488602104690.1537526174010.1521212205381.045125950880.04136355919090.755043137684-0.40568707036874.003142414114.0829715172
55.644382970550.0995006224137-2.955055028164.99760327506-1.305298494342.869461343510.08902204403670.264797174016-0.0135445029205-0.293022011576-0.0657225187139-0.546250633804-0.1029344428920.0427137532028-0.0622749495340.5024674581850.0483527017120.1971787553860.4170948820460.02569620417870.99612400945439.892019897979.612876959820.46584902
63.27984277845-4.290775255810.2077110252069.317273836281.777960158862.86737890348-0.04254924664150.1412579805650.6875488428-0.51837681963-0.0410497471671-1.15997602315-0.6148143211340.02823667659360.02093655918030.608046584785-0.009171563207860.09460325896980.4933957007390.03868781954131.1993179600841.513678093596.68772109924.2857262354
75.72294884710.6043042756463.352558641233.348103389493.275522059914.582321926150.7649143471680.2796603657830.825332431641-2.74399871319-1.415227698560.774440720453-2.08310025488-0.9325434256290.2470176549161.027993584370.08340990932460.1220518184690.6908495524020.1924460606270.73406830018534.223114856688.928860702311.3535309335
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 65 )AA1 - 651 - 65
22chain 'A' and (resid 66 through 166 )AA66 - 16666 - 166
33chain 'B' and (resid 2 through 6 )BB2 - 61 - 5
44chain 'B' and (resid 7 through 14 )BB7 - 146 - 13
55chain 'C' and (resid 1 through 65 )CC1 - 651 - 65
66chain 'C' and (resid 66 through 166 )CC66 - 16666 - 166
77chain 'D' and (resid 3 through 12 )DD3 - 121 - 10

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