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- PDB-8qpj: FAD-independent Methylene-Tetrahydrofolate Reductase Mutant E9Q f... -

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Basic information

Entry
Database: PDB / ID: 8qpj
TitleFAD-independent Methylene-Tetrahydrofolate Reductase Mutant E9Q from Mycobacterium hassiacum
ComponentsMethylenetetrahydrofolate reductase (NAD(P)H)
KeywordsOXIDOREDUCTASE / Methylenetetrahydrofolate reductase / methylene-tetrahydrofolate reductase
Function / homology: / Mycobacterial methylenetetrahydrofolate reductase / Uncharacterized protein
Function and homology information
Biological speciesMycolicibacterium hassiacum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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
Revision 1.1Jun 12, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Methylenetetrahydrofolate reductase (NAD(P)H)
B: Methylenetetrahydrofolate reductase (NAD(P)H)


Theoretical massNumber of molelcules
Total (without water)65,6732
Polymers65,6732
Non-polymers00
Water5,693316
1
A: Methylenetetrahydrofolate reductase (NAD(P)H)


Theoretical massNumber of molelcules
Total (without water)32,8371
Polymers32,8371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methylenetetrahydrofolate reductase (NAD(P)H)


Theoretical massNumber of molelcules
Total (without water)32,8371
Polymers32,8371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.800, 45.800, 254.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Methylenetetrahydrofolate reductase (NAD(P)H)


Mass: 32836.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium hassiacum (bacteria) / Gene: C731_4202 / Production host: Escherichia coli (E. coli) / References: UniProt: K5BDY6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.03 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 25 % PEG MME 5000 10 mg/ml Mfr_E9Q 2 mM NAD+ 2 mM CH3-H4F

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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: 1.75→45.8 Å / Num. obs: 51871 / % possible obs: 98.7 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.17
Reflection shellResolution: 1.75→1.813 Å / Rmerge(I) obs: 1.05 / Num. unique obs: 5183 / CC1/2: 0.431

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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: 1.75→45.8 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2315 --
Rwork0.1997 --
obs-51862 98.91 %
Refinement stepCycle: LAST / Resolution: 1.75→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4510 0 0 316 4826

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