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- PDB-8qq8: Crystal Structure of F420-dependent Methylene-Tetrahydromethanopt... -

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Basic information

Entry
Database: PDB / ID: 8qq8
TitleCrystal Structure of F420-dependent Methylene-Tetrahydromethanopterin Reductase Mutant E6Q from Methanocaldococcus Jannaschii
Components5,10-methylenetetrahydromethanopterin reductase
KeywordsOXIDOREDUCTASE / F420-dependent methylene-tetrahydromethanopterin 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: 2 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 4, 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

Downloads & links

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Assembly

Deposited unit
A: 5,10-methylenetetrahydromethanopterin reductase


Theoretical massNumber of molelcules
Total (without water)35,3931
Polymers35,3931
Non-polymers00
Water4,504250
1
A: 5,10-methylenetetrahydromethanopterin reductase

A: 5,10-methylenetetrahydromethanopterin reductase


Theoretical massNumber of molelcules
Total (without water)70,7862
Polymers70,7862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,x,-z1
Buried area3100 Å2
ΔGint-26 kcal/mol
Surface area25550 Å2
Unit cell
Length a, b, c (Å)98.000, 98.000, 200.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-455-

HOH

21A-583-

HOH

31A-588-

HOH

41A-621-

HOH

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Components

#1: Protein 5,10-methylenetetrahydromethanopterin reductase


Mass: 35393.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: mer / Production host: Escherichia coli (E. coli) / References: UniProt: A0A832SYB5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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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: 3.41 Å3/Da / Density % sol: 63.88 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 15 % w/v Polyethylene glycol 4,000 200 mM Ammonium sulfate 2 mM F420 2 mM CH3-H4MPT 20 mg/ml jMer_E6Q

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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 EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40.65 Å / Num. obs: 33460 / % possible obs: 99.2 % / Redundancy: 4.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.23
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 1.9 / Num. unique obs: 4452 / CC1/2: 0.491

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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: 2→40.65 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 1999 6.03 %
Rwork0.1929 --
obs0.1954 33125 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→40.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 0 250 2729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.903
X-RAY DIFFRACTIONf_dihedral_angle_d6.196348
X-RAY DIFFRACTIONf_chiral_restr0.052396
X-RAY DIFFRACTIONf_plane_restr0.008440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.45141410.41182182X-RAY DIFFRACTION99
2.05-2.110.38141410.35932177X-RAY DIFFRACTION99
2.11-2.170.32211400.31962188X-RAY DIFFRACTION99
2.17-2.240.33041410.29862190X-RAY DIFFRACTION100
2.24-2.320.27581400.26292197X-RAY DIFFRACTION99
2.32-2.410.33731430.24212211X-RAY DIFFRACTION100
2.41-2.520.28221410.22722207X-RAY DIFFRACTION99
2.52-2.650.26471440.20872228X-RAY DIFFRACTION100
2.65-2.820.27521400.20882202X-RAY DIFFRACTION100
2.82-3.040.27621450.19182243X-RAY DIFFRACTION100
3.04-3.340.23781430.19582230X-RAY DIFFRACTION99
3.34-3.830.22471430.17922231X-RAY DIFFRACTION98
3.83-4.820.17471460.1492282X-RAY DIFFRACTION99
4.82-40.650.2041510.17142358X-RAY DIFFRACTION97
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)
11.32160.1481-0.13711.4980.10151.72890.0942-0.14280.01290.03850.0140.06560.0179-0.1484-00.45550.01010.00090.4970.04570.431-15.3879-5.35287.0167
20.24330.48540.02431.0089-0.15570.72010.1038-0.2135-0.19470.5042-0.0222-0.0560.5891-0.0438-0.00030.5878-0.0344-0.02390.47460.09120.4216-17.1817-25.136113.3413
30.0783-0.0577-0.25050.7548-0.23641.0351-0.0272-0.1587-0.55410.28560.01630.10030.2942-0.0518-0.00030.6518-0.0514-0.00030.64280.07760.5664-17.8829-14.410618.194
41.68160.6027-0.15881.08910.32450.91760.1753-0.21980.30390.40670.06850.442-0.1047-0.12380.00040.71060.01580.10040.70790.04780.6302-25.123-3.372823.3992
52.02980.19060.04882.4821-0.72790.40050.04910.21240.71410.18980.26751.1691-0.1385-0.780.00180.63780.03240.10030.9980.22671.04-33.94977.615413.253
60.25410.06570.51850.3217-0.09921.92160.064-0.46760.77620.35260.12370.2633-1.3846-0.3014-0.02330.51290.0050.15210.513-0.06450.5861-14.926413.437317.7031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 109 )
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 143 )
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 171 )
4X-RAY DIFFRACTION4chain 'A' and (resid 172 through 219 )
5X-RAY DIFFRACTION5chain 'A' and (resid 220 through 313 )
6X-RAY DIFFRACTION6chain 'A' and (resid 314 through 331 )

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