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- PDB-8qpm: Structure of methylene-tetrahydromethanopterin reductase from Met... -

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Basic information

Entry
Database: PDB / ID: 8qpm
TitleStructure of methylene-tetrahydromethanopterin reductase from Methanocaldococcus jannaschii
Components5,10-methylenetetrahydromethanopterin reductase
KeywordsOXIDOREDUCTASE / methylene-tetrahydropterin reductase
Function / homology
Function and homology information


5,10-methylenetetrahydromethanopterin reductase / coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase activity / methanogenesis, from carbon dioxide / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / one-carbon metabolic process / cytoplasm
Similarity search - Function
5,10-methylenetetrahydromethanopterin reductase / : / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily
Similarity search - Domain/homology
5,10-methylenetetrahydromethanopterin reductase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGehl, M. / Demmer, U. / Ermler, U. / Shima, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Protein Sci. / Year: 2024
Title: Mutational and structural studies of ( beta alpha ) 8 -barrel fold methylene-tetrahydropterin reductases utilizing a common catalytic mechanism.
Authors: Gehl, M. / Demmer, U. / Ermler, U. / Shima, S.
History
DepositionOct 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5,10-methylenetetrahydromethanopterin reductase
B: 5,10-methylenetetrahydromethanopterin reductase
C: 5,10-methylenetetrahydromethanopterin reductase
D: 5,10-methylenetetrahydromethanopterin reductase


Theoretical massNumber of molelcules
Total (without water)143,3474
Polymers143,3474
Non-polymers00
Water11,836657
1
A: 5,10-methylenetetrahydromethanopterin reductase
B: 5,10-methylenetetrahydromethanopterin reductase


Theoretical massNumber of molelcules
Total (without water)71,6732
Polymers71,6732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-25 kcal/mol
Surface area25370 Å2
MethodPISA
2
C: 5,10-methylenetetrahydromethanopterin reductase
D: 5,10-methylenetetrahydromethanopterin reductase


Theoretical massNumber of molelcules
Total (without water)71,6732
Polymers71,6732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-26 kcal/mol
Surface area25500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.660, 96.280, 166.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
5,10-methylenetetrahydromethanopterin reductase / Coenzyme F420-dependent N(5) / N(10)-methylenetetrahydromethanopterin reductase / Methylene-H(4)MPT reductase


Mass: 35836.656 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: mer, HA335_01095 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A832SYB5, 5,10-methylenetetrahydromethanopterin reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 657 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 35% (v/v) 2-methyl-2,4-pentanediol, 100 mM sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.33 Å / Num. obs: 144127 / % possible obs: 99.84 % / Redundancy: 3.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.3
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 0.822 / Num. unique obs: 14203 / CC1/2: 0.503

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.33 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2016 --
Rwork0.1805 --
obs-144111 99.84 %
Refinement stepCycle: LAST / Resolution: 1.8→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9831 0 0 657 10488

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