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- PDB-8q5x: MgADP-bound Fe protein of the molybdenum nitrogenase from Methano... -

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Basic information

Entry
Database: PDB / ID: 8q5x
TitleMgADP-bound Fe protein of the molybdenum nitrogenase from Methanococcus maripaludis
ComponentsNitrogenase iron protein
KeywordsELECTRON TRANSPORT / nitrogenase / electron donor / ATPase / [4Fe-4S]-cluster / electron transfer / conformational changes / methanogenic archaea / oxidoreductase / O2-sensitivity / N2-fixation
Function / homology
Function and homology information


: / nitrogenase / nitrogenase activity / nitrogen fixation / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase iron protein NifH / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / Nitrogenase iron protein
Similarity search - Component
Biological speciesMethanococcus maripaludis S2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMaslac, N. / Wagner, T.
Funding support Germany, Switzerland, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
Swiss National Science FoundationNCCR Catalysis 180544 Switzerland
CitationJournal: Febs J. / Year: 2024
Title: Structural comparison of (hyper-)thermophilic nitrogenase reductases from three marine Methanococcales.
Authors: Maslac, N. / Cadoux, C. / Bolte, P. / Murken, F. / Gu, W. / Milton, R.D. / Wagner, T.
History
DepositionAug 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrogenase iron protein
B: Nitrogenase iron protein
C: Nitrogenase iron protein
D: Nitrogenase iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,77834
Polymers127,0054
Non-polymers3,77330
Water24,0681336
1
A: Nitrogenase iron protein
C: Nitrogenase iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,41517
Polymers63,5032
Non-polymers1,91215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nitrogenase iron protein
D: Nitrogenase iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,36317
Polymers63,5032
Non-polymers1,86015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.546, 111.094, 78.820
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Nitrogenase iron protein


Mass: 31751.260 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: / / Source: (gene. exp.) Methanococcus maripaludis S2 (archaea) / Strain: S2 / Tissue: / / Cell: / / Cell line: / / Gene: nifH / Organ: / / Variant: / / Plasmid: WG35
Details (production host): pET21a vector carrying the nifH gene from M.?maripaludis with a C terminal 6 x HIS tag (cloned from M.?maripaludis Strain S2 derivative MM901) behind a T7 promoter
Cell (production host): / / Cell line (production host): / / Organ (production host): / / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Tissue (production host): / / Variant (production host): delta iscR / References: UniProt: P0CW57

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Non-polymers , 9 types, 1366 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1336 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 47.98 % / Description: Fragment from a thick brown plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The purified protein was crystallised at a final concentration of 13 mg/ml with 2 mM ATP and 2 mM MgCl2 by spotting 0.7 ul of crystallisation solution with 0.7 ul of protein sample. ...Details: The purified protein was crystallised at a final concentration of 13 mg/ml with 2 mM ATP and 2 mM MgCl2 by spotting 0.7 ul of crystallisation solution with 0.7 ul of protein sample. Crystallisation was done anaerobically in a Coy tent containing N2/H2 (97:3%) atmosphere. The screening was done at 20 degrees Celsius on 96-Well MRC 2-drop polystyrene (SWISSCI) plates containing 90 ul of crystallisation solution. The crystallisation solution in which crystals were obtained contained 20 % w/v polyethylene glycol 3000, 100 mM Tris pH 7.0 and 200 mM calcium acetate. The crystal was soaked in the crystallisation solution supplemented with 20% glycerol prior to freezing in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.7→78.82 Å / Num. obs: 94344 / % possible obs: 94.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 20.79 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.219 / Rpim(I) all: 0.09 / Rrim(I) all: 0.237 / Net I/σ(I): 7.5
Reflection shellResolution: 1.7→1.86 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.232 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4718 / CC1/2: 0.468 / Rpim(I) all: 0.511 / Rrim(I) all: 1.336 / % possible all: 57.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→46.89 Å / Cross valid method: FREE R-VALUE / σ(F): 36.09 / Phase error: 21.09 / Stereochemistry target values: TWIN_LSQ_F
Details: Translation-libration screw was used during refinement. The model was refined with riding hydrogens that were omitted in the final deposited model.
RfactorNum. reflection% reflection
Rfree0.1859 4771 5.06 %
Rwork0.1597 --
obs0.1618 94335 73.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.79 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8531 0 205 1343 10079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098931
X-RAY DIFFRACTIONf_angle_d0.91312055
X-RAY DIFFRACTIONf_dihedral_angle_d15.9873340
X-RAY DIFFRACTIONf_chiral_restr0.0621342
X-RAY DIFFRACTIONf_plane_restr0.0081567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.3647160.2566242X-RAY DIFFRACTION4
1.73-1.770.3594150.2588574X-RAY DIFFRACTION9
1.77-1.80.1694530.2428973X-RAY DIFFRACTION15
1.8-1.840.2459630.23561439X-RAY DIFFRACTION22
1.84-1.880.26111020.22612248X-RAY DIFFRACTION35
1.88-1.920.22581750.21693035X-RAY DIFFRACTION48
1.92-1.970.23522270.20683993X-RAY DIFFRACTION62
1.97-2.020.24252200.19964834X-RAY DIFFRACTION76
2.02-2.080.24742690.18545482X-RAY DIFFRACTION85
2.08-2.150.21142990.17935801X-RAY DIFFRACTION91
2.15-2.220.22232710.17346068X-RAY DIFFRACTION95
2.22-2.310.18683390.16796076X-RAY DIFFRACTION95
2.31-2.420.17763190.1596098X-RAY DIFFRACTION95
2.42-2.550.2113410.1596078X-RAY DIFFRACTION95
2.55-2.710.18293160.15046074X-RAY DIFFRACTION95
2.71-2.910.17762990.15456135X-RAY DIFFRACTION95
2.91-3.210.17993290.14896072X-RAY DIFFRACTION95
3.21-3.670.1653160.13826130X-RAY DIFFRACTION95
3.67-4.620.13653300.13026153X-RAY DIFFRACTION95
4.63-46.890.19263020.16896229X-RAY DIFFRACTION95
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)
10.81650.1191-0.12440.4981-0.01320.56470.0252-0.01080.0341-0.0137-0.0134-0.0311-0.02730.0215-0.01070.1207-0.0104-0.00270.1333-0.0060.111956.525264.5753.5461
25.53661.56161.40031.5720.93320.7776-0.012-0.18660.10350.0445-0.03970.1736-0.0602-0.03990.07920.1339-0.00380.04630.11660.00240.10242.844265.415663.9577
32.17970.1396-0.23171.7906-0.29891.9574-0.0739-0.28860.33930.22170.05530.1021-0.2694-0.0681-0.05180.13660.0252-0.01040.1037-0.03720.155169.508726.311777.5163
41.3812-0.18650.0320.4281-0.01980.8155-0.01740.13940.1007-0.03120.0139-0.0118-0.02790.02380.00780.0954-0.01270.00960.09770.02030.099967.748619.92464.0512
53.09050.0442-0.39781.0551-0.72471.72670.0148-0.1435-0.0543-0.00830.03010.0895-0.02970.0053-0.04160.08390.01440.01050.059-0.00570.072129.877744.932953.6852
68.8454-6.48130.25056.6125-1.09871.0789-0.0296-0.34410.33010.1227-0.1839-0.31350.1042-0.02160.20360.1842-0.0009-0.03130.1728-0.04270.12338.884941.305768.5209
77.5887-3.41164.30671.5421-1.93442.4426-0.1929-0.5203-0.29980.23630.3450.1494-0.143-0.3392-0.13550.16920.01720.00360.15680.02010.174736.794732.641568.2505
80.65870.11150.13220.7888-0.5430.80870.01860.0833-0.0843-0.0254-0.0111-0.03520.01070.0958-0.01480.11310.0125-0.00030.1094-0.01880.116138.65643.957947.3752
91.3824-0.3078-0.39561.13520.2271.6182-0.0131-0.05590.06280.00890.0570.0801-0.1045-0.0742-0.0530.08010.012-0.01150.09070.01870.089422.192153.505850.6542
101.50941.7196-0.20474.80970.65281.8324-0.1850.21230.1095-0.48660.2589-0.023-0.17920.177-0.0660.11340.0126-0.02820.15710.01330.104639.807856.799135.276
110.9673-0.70640.31931.5253-0.04640.95120.04940.0665-0.044-0.1023-0.03430.07020.07250.0383-0.01790.1075-0.0189-0.00330.0873-0.00410.07340.97635.047263.0614
123.6413-4.59261.00879.8597-1.30760.3639-0.03890.16350.1997-0.1109-0.10410.3976-0.0407-0.07290.11850.1928-0.0363-0.00560.12070.01770.148529.382213.90657.7056
130.9219-0.08680.50511.3715-0.27130.87880.0185-0.08120.01290.02940.00210.09280.0157-0.1179-0.01140.0864-0.0210.01160.0919-0.00180.072939.977110.942769.6526
140.84280.22760.05640.8320.61421.87610.0942-0.0235-0.1205-0.0123-0.0332-0.09570.18830.0321-0.06520.14340.0058-0.00220.08340.02710.127551.1978-2.348673.1633
154.09520.9315-0.81651.1806-0.32972.02120.0578-0.2431-0.32590.1027-0.0809-0.3326-0.01010.220.03810.1346-0.0056-0.03310.07490.02710.176260.24152.843481.9343
162.24360.40510.30991.7627-0.25642.33520.0020.1685-0.1607-0.23040.0394-0.20990.17220.188-0.03560.12510.00150.03290.1374-0.01490.093563.766561.430744.2703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 80 through 248 )
2X-RAY DIFFRACTION2chain 'C' and (resid 249 through 280 )
3X-RAY DIFFRACTION3chain 'D' and (resid 2 through 79 )
4X-RAY DIFFRACTION4chain 'D' and (resid 80 through 279 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2 through 49 )
6X-RAY DIFFRACTION6chain 'A' and (resid 50 through 65 )
7X-RAY DIFFRACTION7chain 'A' and (resid 66 through 79 )
8X-RAY DIFFRACTION8chain 'A' and (resid 80 through 203 )
9X-RAY DIFFRACTION9chain 'A' and (resid 204 through 248 )
10X-RAY DIFFRACTION10chain 'A' and (resid 249 through 281 )
11X-RAY DIFFRACTION11chain 'B' and (resid 2 through 65 )
12X-RAY DIFFRACTION12chain 'B' and (resid 66 through 79 )
13X-RAY DIFFRACTION13chain 'B' and (resid 80 through 154 )
14X-RAY DIFFRACTION14chain 'B' and (resid 155 through 248 )
15X-RAY DIFFRACTION15chain 'B' and (resid 249 through 281 )
16X-RAY DIFFRACTION16chain 'C' and (resid 2 through 79 )

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