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- PDB-8cnr: Hybrid Cluster Protein from the thermophilic methanogen Methanoth... -

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Basic information

Entry
Database: PDB / ID: 8cnr
TitleHybrid Cluster Protein from the thermophilic methanogen Methanothermococcus thermolithotrophicus as isolated in a reduced state at 1.45-A resolution
ComponentsHybrid cluster protein from the thermophilic methanogen Methanothermococcus thermolithotrophicus
KeywordsOXIDOREDUCTASE / Hybrid cluster / prismane protein / Hybrid cluster protein / methanogenic archaea / anaerobic biochemistry / thermophile / metallocluster / Nitric oxide reductase / hydroxylamine
Function / homologyRossmann fold - #2030 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ACETATE ION / 2-ETHOXYETHANOL / FORMIC ACID / FE4-S3 CLUSTER / IRON/SULFUR CLUSTER
Function and homology information
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsLemaire, O.N. / Wagner, T.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)Schwerpunktprogram 1927 Iron-sulfur for Life WA 4053/1-1 Germany
CitationJournal: Front Microbiol / Year: 2023
Title: Structural and biochemical elucidation of class I hybrid cluster protein natively extracted from a marine methanogenic archaeon.
Authors: Lemaire, O.N. / Belhamri, M. / Wagner, T.
History
DepositionFeb 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hybrid cluster protein from the thermophilic methanogen Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,84817
Polymers60,3361
Non-polymers1,51216
Water11,692649
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-62 kcal/mol
Surface area20440 Å2
Unit cell
Length a, b, c (Å)97.557, 102.454, 58.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1173-

HOH

21A-1224-

HOH

31A-1333-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hybrid cluster protein from the thermophilic methanogen Methanothermococcus thermolithotrophicus


Mass: 60335.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Compared to the automatic gene annotation, the sequence has 5 extra residues in N-terminal (MRPSK).
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: DSM 2095 / Tissue: / / References: hydroxylamine reductase

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Non-polymers , 10 types, 665 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#6: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: CH2O2
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#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-SF3 / FE4-S3 CLUSTER


Mass: 319.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S3 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 649 / 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: 2.44 Å3/Da / Density % sol: 49.55 %
Description: Brown orthorhombic rods, appeared after few weeks.
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: Crystallisation was performed anaerobically at 20 degree Celsius using the sitting drop method on 96-Well MRC 2-Drop polystyrene Crystallisation Plates (SWISSCI) in a Coy tent containing a ...Details: Crystallisation was performed anaerobically at 20 degree Celsius using the sitting drop method on 96-Well MRC 2-Drop polystyrene Crystallisation Plates (SWISSCI) in a Coy tent containing a N2/H2 (97:3%) atmosphere. The reservoir chamber was filled with 90 ul of crystallisation condition and the drop was formed by spotting 0.55 ul protein with 0.55 ul of 20% (w/v) PEG 3,350 and 200 mM Magnesium formate. The protein was crystallized at 9.9 mg/ml in 25 mM Tris/HCl pH 7.6, 2 mM dithiothreitol and 10% (v/v) glycerol. Densities in the electron density map suggest a contamination from another crystallisation condition spatially close and containing 30% (v/v) 2-Methyl-2,4-pentanediol, 20 mM Calcium chloride and 100 mM Sodium acetate, pH 4.6. Crystals were cryo-protected by soaking in 20% (w/v) PEG 3,350 and 200mM Magnesium formate supplemented with 20% v/v glycerol for a few seconds.
PH range: / / Temp details: /

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.23984 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23984 Å / Relative weight: 1
ReflectionResolution: 1.45→51.061 Å / Num. obs: 103697 / % possible obs: 98.8 % / Redundancy: 5.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.056 / Rrim(I) all: 0.132 / Net I/σ(I): 9.5
Reflection shellResolution: 1.451→1.476 Å / Rmerge(I) obs: 1.193 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4833 / CC1/2: 0.51 / Rpim(I) all: 0.642 / Rrim(I) all: 1.361 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
autoPROCdata reduction
autoPROCdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→51.06 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.8 / Stereochemistry target values: ML
Details: Last refinement steps were performed by refining with translation liberation screw (TLS) The model was refined with hydrogens in riding position. Hydrogens were omitted in the final deposited model.
RfactorNum. reflection% reflection
Rfree0.1524 5332 5.15 %
Rwork0.1331 --
obs0.1341 103571 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.51 Å2
Refinement stepCycle: LAST / Resolution: 1.45→51.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4236 0 68 649 4953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094492
X-RAY DIFFRACTIONf_angle_d1.2886108
X-RAY DIFFRACTIONf_dihedral_angle_d13.6391674
X-RAY DIFFRACTIONf_chiral_restr0.093701
X-RAY DIFFRACTIONf_plane_restr0.011789
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.22551360.26682968X-RAY DIFFRACTION89
1.47-1.480.26441400.24813146X-RAY DIFFRACTION95
1.48-1.50.24611770.22933142X-RAY DIFFRACTION95
1.5-1.520.26581620.21313162X-RAY DIFFRACTION97
1.52-1.540.23531630.19373190X-RAY DIFFRACTION97
1.54-1.560.17161440.18263249X-RAY DIFFRACTION97
1.56-1.590.20551890.17783181X-RAY DIFFRACTION98
1.59-1.610.17851940.17223199X-RAY DIFFRACTION98
1.61-1.630.1811990.16323232X-RAY DIFFRACTION99
1.63-1.660.1721870.15853252X-RAY DIFFRACTION99
1.66-1.690.16442140.15143231X-RAY DIFFRACTION99
1.69-1.720.19461820.1533247X-RAY DIFFRACTION99
1.72-1.750.17621750.15143278X-RAY DIFFRACTION99
1.75-1.790.161590.14673296X-RAY DIFFRACTION100
1.79-1.830.1721850.13143252X-RAY DIFFRACTION100
1.83-1.870.14891740.12763316X-RAY DIFFRACTION100
1.87-1.920.13751850.12413289X-RAY DIFFRACTION99
1.92-1.970.1351700.1193315X-RAY DIFFRACTION100
1.97-2.030.12831630.11543291X-RAY DIFFRACTION100
2.03-2.090.14191780.11723318X-RAY DIFFRACTION100
2.09-2.170.13271900.1173302X-RAY DIFFRACTION100
2.17-2.250.12871600.11323333X-RAY DIFFRACTION100
2.25-2.360.14232040.10733312X-RAY DIFFRACTION100
2.36-2.480.15241760.10973325X-RAY DIFFRACTION100
2.48-2.640.13681910.10993324X-RAY DIFFRACTION100
2.64-2.840.13022090.11563331X-RAY DIFFRACTION100
2.84-3.130.13482050.11713342X-RAY DIFFRACTION100
3.13-3.580.14691750.11713379X-RAY DIFFRACTION100
3.58-4.510.12011750.10533444X-RAY DIFFRACTION100
4.51-51.060.17031710.16213593X-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)
11.78760.036-0.52530.62960.05860.66560.010.1191-0.0334-0.0658-0.0081-0.03210.04590.0111-0.0130.08650.0027-0.00990.0729-0.00740.0879-6.975219.9446-38.8272
24.88971.8839-2.63182.83920.12462.029-0.02490.0872-0.4217-0.11640.037-0.2170.0814-0.0048-0.11160.15480.01270.02590.0769-0.04470.10781.69412.0796-47.5667
30.4476-0.016-0.00040.90130.17230.41690.0046-0.0084-0.01520.05290.0019-0.0680.04350.0221-0.0130.0711-0.0049-0.0040.05930.00620.0818-3.428725.8701-26.5672
40.9002-0.02340.08881.50310.09630.6220.00960.02880.0958-0.0477-0.04280.1279-0.054-0.03130.03410.06550.0086-0.00570.06020.00450.0981-18.294641.8383-31.798
52.1659-0.14490.66471.0928-0.14962.35930.01840.26110.066-0.1198-0.00890.0766-0.0784-0.0099-0.00290.0835-0.0112-0.0130.0113-0.0020.1462-16.865346.1921-33.5252
61.26850.6021.08251.21160.9573.3820.0729-0.24520.02010.2599-0.058-0.01960.0075-0.0504-0.01560.13630.0104-0.00220.104-0.00790.0957-10.645735.9695-5.0657
70.88530.01140.07050.83640.06170.99580.0181-0.15630.00740.2139-0.03680.02480.0146-0.00730.01960.1257-0.01970.00030.0955-0.00070.0819-12.623130.7951-9.4553
82.2877-0.39720.04331.65330.50520.6761-0.052-0.2743-0.10240.33120.02390.08380.1423-0.01570.04350.2072-0.02390.01070.11860.04370.1077-14.232416.2292-9.0886
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 99 )
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 127 )
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 244 )
4X-RAY DIFFRACTION4chain 'A' and (resid 245 through 335 )
5X-RAY DIFFRACTION5chain 'A' and (resid 336 through 373 )
6X-RAY DIFFRACTION6chain 'A' and (resid 374 through 406 )
7X-RAY DIFFRACTION7chain 'A' and (resid 407 through 502 )
8X-RAY DIFFRACTION8chain 'A' and (resid 503 through 548 )

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