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- PDB-8q50: Nitrogenase Fe protein from Methanothermococcus thermolithotrophi... -

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Basic information

Entry
Database: PDB / ID: 8q50
TitleNitrogenase Fe protein from Methanothermococcus thermolithotrophicus, tetragonal crystalline form at 1.91-A resolution
ComponentsNitrogenase iron protein 1
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 / FE2/S2 (INORGANIC) CLUSTER / Nitrogenase iron protein 1
Similarity search - Component
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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 7, 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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8498
Polymers31,2721
Non-polymers5777
Water2,270126
1
A: Nitrogenase iron protein 1
hetero molecules

A: Nitrogenase iron protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,69816
Polymers62,5442
Non-polymers1,15414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5810 Å2
ΔGint-75 kcal/mol
Surface area20940 Å2
Unit cell
Length a, b, c (Å)98.895, 98.895, 61.149
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

21A-512-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nitrogenase iron protein 1


Mass: 31271.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: SN-1 / Tissue: / / References: UniProt: P25767

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Non-polymers , 5 types, 133 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.39 Å3/Da / Density % sol: 48.55 %
Description: The crystal was in a shape of an orthorhombic rod and brown.
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: The purified protein was crystallised at a final concentration of 6 mg/ml by spotting 0.5 ul of crystallisation solution with 0.5 ul of protein sample. Crystallization was done anaerobically ...Details: The purified protein was crystallised at a final concentration of 6 mg/ml by spotting 0.5 ul of crystallisation solution with 0.5 ul of protein sample. Crystallization 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 crystallization solution. The crystallisation solution in which crystals were obtained contained 30 % v/v 2-methyl-2,4-pentanediol, 100 mM sodium acetate, pH 4.6 and 20 mM calcium chloride.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.74013 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74013 Å / Relative weight: 1
ReflectionResolution: 1.91→52.01 Å / Num. obs: 24200 / % possible obs: 100 % / Redundancy: 41.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.025 / Rrim(I) all: 0.161 / Net I/σ(I): 15.9
Reflection shellResolution: 1.91→1.94 Å / Redundancy: 23.9 % / Rmerge(I) obs: 3.12 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1183 / CC1/2: 0.616 / Rpim(I) all: 0.644 / Rrim(I) all: 3.19 / % possible all: 100

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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: 1.91→52.01 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.84 / Stereochemistry target values: ML
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
Rfree0.2305 1157 4.78 %
Rwork0.2019 --
obs0.2032 24197 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.31 Å2
Refinement stepCycle: LAST / Resolution: 1.91→52.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2123 0 29 126 2278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132177
X-RAY DIFFRACTIONf_angle_d1.4312925
X-RAY DIFFRACTIONf_dihedral_angle_d19.331825
X-RAY DIFFRACTIONf_chiral_restr0.305326
X-RAY DIFFRACTIONf_plane_restr0.012385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.990.34851430.30962798X-RAY DIFFRACTION100
1.99-2.10.2541600.24182806X-RAY DIFFRACTION100
2.1-2.230.26281340.24012848X-RAY DIFFRACTION100
2.23-2.40.27111330.242847X-RAY DIFFRACTION100
2.4-2.640.23121530.21282862X-RAY DIFFRACTION100
2.64-3.030.27911430.23232880X-RAY DIFFRACTION100
3.03-3.810.21981550.1932912X-RAY DIFFRACTION100
3.81-52.010.19291360.17073087X-RAY DIFFRACTION100
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)
14.9823-1.55411.69522.686-1.37447.6073-0.12280.48260.59180.26530.03530.172-0.91830.13690.19950.3042-0.0129-0.04040.33330.02890.2869-21.93-0.09-9.154
28.97492.46710.3244.89250.6862.2858-0.3350.4696-0.1755-0.42170.2613-0.0001-0.1039-0.2390.01630.3118-0.0763-0.02540.3711-0.01710.1678-23.577-9.737-15.517
30.6872-0.17581.04030.7526-0.94995.7418-0.90010.6941-1.2214-0.58710.4662-0.8355-0.2430.66280.04360.4791-0.22620.28050.5433-0.14060.5712-2.926-7.734-20.682
42.45982.0544-0.59552.4482-0.58653.8422-0.61661.1313-0.4733-0.76510.3363-0.30760.33220.08340.20510.4859-0.16090.05460.4995-0.04240.2596-13.837-7.93-18.552
57.3660.47390.322.9262-1.78613.3563-0.76520.95790.845-0.48530.346-0.2933-0.4521-0.09030.35980.4149-0.1132-0.00480.41940.07290.3393-12.7942.139-17.737
66.1540.94062.69415.387-1.04165.45430.1078-0.0706-0.0807-0.05420.082-0.18020.4095-0.1984-0.06090.2774-0.0089-0.02060.2821-0.00580.232-16.416-3.383-5.021
76.83172.2887-2.04266.1588-0.4585.0015-0.06650.33010.2634-0.08790.1550.0504-0.2365-0.0236-0.10050.27930.0202-0.00540.27520.00810.2208-20.1310.3-2.56
85.18062.024-2.0452.51650.91343.79390.2054-0.2470.22650.4305-0.1427-0.359-0.13920.2093-0.15360.33420.0088-0.01020.2815-0.00180.2672-18.520.5945.704
94.87783.2739-2.82687.8024-3.46614.62130.1321-0.05610.11170.2954-0.19870.56290.0933-0.2389-0.00010.29370.02580.03820.3133-0.02480.2948-31.011-5.9126.129
101.83520.246-0.26643.38415.09037.8561-0.24780.16-0.20120.55380.15140.21750.7949-0.19480.170.3253-0.0120.06580.46450.00810.4337-32.625-14.601-4.795
114.44981.7378-0.4582.69042.9515.3567-0.37890.4555-0.0122-0.0149-0.18920.60380.2842-0.76680.55490.2616-0.0617-0.03730.5210.02860.3773-35.565-11.492-12.925
123.55520.1107-0.3925.1211-1.7194.55540.0217-0.18690.15560.8777-0.22340.0156-0.20850.02450.19260.4967-0.02940.0860.2928-0.04220.2915-26.822-2.01612.077
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 6:23 )A6 - 23
2X-RAY DIFFRACTION2( CHAIN A AND RESID 24:66 )A24 - 66
3X-RAY DIFFRACTION3( CHAIN A AND RESID 67:80 )A67 - 80
4X-RAY DIFFRACTION4( CHAIN A AND RESID 81:106 )A81 - 106
5X-RAY DIFFRACTION5( CHAIN A AND RESID 107:129 )A107 - 129
6X-RAY DIFFRACTION6( CHAIN A AND RESID 130:145 )A130 - 145
7X-RAY DIFFRACTION7( CHAIN A AND RESID 146:163 )A146 - 163
8X-RAY DIFFRACTION8( CHAIN A AND RESID 164:184 )A164 - 184
9X-RAY DIFFRACTION9( CHAIN A AND RESID 185:212 )A185 - 212
10X-RAY DIFFRACTION10( CHAIN A AND RESID 213:231 )A213 - 231
11X-RAY DIFFRACTION11( CHAIN A AND RESID 232:258 )A232 - 258
12X-RAY DIFFRACTION12( CHAIN A AND RESID 259:281 )A259 - 281

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