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- PDB-9i0f: Revisited AvNifEN crystal structure -

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Basic information

Entry
Database: PDB / ID: 9i0f
TitleRevisited AvNifEN crystal structure
Components(Nitrogenase iron-molybdenum cofactor biosynthesis protein ...) x 2
KeywordsMETAL BINDING PROTEIN / NITROGENASE COFACTOR MATURATION / PROTEIN BINDING / Metalloenzyme / Iron-Sulfur Cluster
Function / homology
Function and homology information


nitrogenase activity / 4 iron, 4 sulfur cluster binding / protein-containing complex assembly / metal ion binding
Similarity search - Function
Nitrogenase MoFe cofactor biosynthesis protein NifE / Nitrogenase molybdenum-iron cofactor biosynthesis protein / : / Nitrogenase component 1, conserved site / Nitrogenases component 1 alpha and beta subunits signature 2. / Nitrogenases component 1 alpha and beta subunits signature 1. / : / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / FeFe cofactor / IRON/SULFUR CLUSTER / Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE / Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
Similarity search - Component
Biological speciesAzotobacter vinelandii DJ (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPaya Tormo, L. / Nguyen, T.Q. / Fyfe, C. / Basbous, H. / Dobrzynska, K. / Echavarri-Erasun, C. / Martin, L. / Caserta, G. / Legrand, P. / Thorn, A. ...Paya Tormo, L. / Nguyen, T.Q. / Fyfe, C. / Basbous, H. / Dobrzynska, K. / Echavarri-Erasun, C. / Martin, L. / Caserta, G. / Legrand, P. / Thorn, A. / Amara, P. / Schoehn, G. / Cherrier, M.V. / Rubio, L.M. / Nicolet, Y.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-15-IDEX-02 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05-02 France
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)ANR-17-EURE-0003 France
CitationJournal: Science / Year: 2011
Title: Structure of precursor-bound NifEN: a nitrogenase FeMo cofactor maturase/insertase
Authors: Kaiser, J.T. / Hu, Y. / Wiig, J.A. / Rees, D.C. / Ribbe, M.W.
History
DepositionJan 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Remark 0THIS ENTRY 9I0F REFLECTS AN ALTERNATIVE MODELING OF THESTRUCTURAL DATA IN 3PDI, ORIGINAL DATA ...THIS ENTRY 9I0F REFLECTS AN ALTERNATIVE MODELING OF THESTRUCTURAL DATA IN 3PDI, ORIGINAL DATA DETERMINED BY AUTHOR: Kaiser JT, Hu Y, Wiig JA, Rees DC, Ribbe MW

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
B: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
C: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
D: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
E: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
F: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
G: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
H: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)426,205178
Polymers409,3948
Non-polymers16,811170
Water17,565975
1
A: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
B: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
C: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
D: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,356106
Polymers204,6974
Non-polymers9,659102
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
F: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
G: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
H: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,84972
Polymers204,6974
Non-polymers7,15268
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.070, 95.220, 149.980
Angle α, β, γ (deg.)90.00, 95.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Nitrogenase iron-molybdenum cofactor biosynthesis protein ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE


Mass: 53046.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303 / Gene: nifE, Avin_01450 / Production host: Azotobacter vinelandii (bacteria) / References: UniProt: C1DH03
#2: Protein
Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN


Mass: 49301.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303 / Gene: nifN, Avin_01470 / Production host: Azotobacter vinelandii (bacteria) / References: UniProt: C1DH04

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Non-polymers , 9 types, 1145 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-S5Q / FeFe cofactor


Mass: 747.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CFe8S9 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 118 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 975 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.54 Å3/Da / Density % sol: 51.5 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 3PDI
Crystal growTemperature: 297 K / Method: liquid diffusion / pH: 7.5
Details: 20% PEG 3350, 0.2M Magnersium Nitrate, pH 7.5, LIQUID DIFFUSION, temperature 297K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 25, 2008
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.4→39.83 Å / Num. obs: 139612 / % possible obs: 87.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.7
Reflection shellResolution: 2.4→2.43 Å / Rmerge(I) obs: 0.389 / Num. unique obs: 691

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (10-JUL-2024)refinement
XDSdata reduction
SCALAdata scaling
Blu-Icedata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→39.83 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.83 / SU R Cruickshank DPI: 0.7 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.72 / SU Rfree Blow DPI: 0.345 / SU Rfree Cruickshank DPI: 0.352
RfactorNum. reflection% reflectionSelection details
Rfree0.3045 13821 9.9 %RANDOM
Rwork0.2487 ---
obs0.2542 139612 87.2 %-
Displacement parametersBiso mean: 61.82 Å2
Baniso -1Baniso -2Baniso -3
1--5.7995 Å20 Å2-3.0255 Å2
2---6.8539 Å20 Å2
3---12.6534 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.4→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27916 0 911 975 29802
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00729285HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8639549HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d10141SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes4901HARMONIC5
X-RAY DIFFRACTIONt_it29285HARMONIC10
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion17.36
X-RAY DIFFRACTIONt_chiral_improper_torsion3689SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance24HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact23933SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.47 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.388 278 9.95 %
Rwork0.3058 2515 -
all0.314 2793 -
obs--22.02 %
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)
10.91350.1084-0.08730.9312-0.03610.0163-0.0187-0.36410.52920.18030.0626-0.05290.0435-0.0311-0.0440.10280.0864-0.1121-0.0013-0.0979-0.073652.86-1.645462.339
21.0260.07540.19330.87430.16260.12080.07340.22150.4038-0.0573-0.1011-0.46470.0471-0.14060.0277-0.15120.021-0.0247-0.19320.07950.377576.09360.348337.6476
31.1879-0.34120.1381.14060.25640.04980.21150.6331-0.6422-0.4084-0.1633-0.1429-0.02180.0683-0.04820.08090.1401-0.01360.0843-0.1673-0.058459.6175-43.217412.8434
41.376-0.57060.08021.08270.45860.31890.16730.0743-0.10320.0942-0.0094-0.49050.0617-0.0838-0.1579-0.27970.0763-0.0404-0.2749-0.03440.485982.57-36.980536.9231
51.12690.25850.27740.8650.10480.1287-0.1022-0.5943-0.92190.37120.06370.3059-0.10250.0870.0385-0.22820.10620.0985-0.2280.22880.56520.8767-49.675863.4444
61.8690.3534-0.03441.635-0.310.06660.07770.0863-0.5547-0.0873-0.18690.4206-0.15410.14910.1092-0.40970.0547-0.0343-0.3922-0.14510.6108-2.8428-52.328839.3286
71.2617-0.6865-0.27341.15870.05980.09580.3470.58960.4604-0.5299-0.30060.5552-0.14440.02-0.0464-0.0240.1851-0.2312-0.05660.05070.247212.9222-9.017613.0284
82.525-1.09170.29461.6649-0.87290.36920.18970.1662-0.05790.0022-0.07880.4902-0.04010.1366-0.1109-0.40970.0631-0.0465-0.3868-0.07810.6084-9.6463-14.66437.6606
90.26850.11810.05820.0273-0.08310.0456-0.0167-0.0736-0.047-0.00810.01750.15190.03850.1118-0.00080.10210.0390.0502-0.0223-0.01960.088341.0614-19.632941.9432
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

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