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- PDB-8bgr: FAD-independent Methylene-Tetrahydrofolate Reductase from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 8bgr
TitleFAD-independent Methylene-Tetrahydrofolate Reductase from Mycobacterium hassiacum
ComponentsMethylenetetrahydrofolate reductase
KeywordsOXIDOREDUCTASE / FAD-independent / NADH-dependent / Methylene-Tetrahydrofolate Reductase
Function / homologyMycobacterial methylenetetrahydrofolate reductase / Methylenetetrahydrofolate reductase (NAD(P)H)
Function and homology information
Biological speciesMycolicibacterium hassiacum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGehl, M. / Ermler, U. / Shima, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Proteins / Year: 2023
Title: Crystal structure of FAD-independent methylene-tetrahydrofolate reductase from Mycobacterium hassiacum.
Authors: Gehl, M. / Demmer, U. / Ermler, U. / Shima, S.
History
DepositionOct 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methylenetetrahydrofolate reductase


Theoretical massNumber of molelcules
Total (without water)32,8381
Polymers32,8381
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.790, 45.790, 257.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Methylenetetrahydrofolate reductase


Mass: 32837.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium hassiacum (bacteria) / Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: C731_4202, MHAS_04356 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K5BDY6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 6000

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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: Jul 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 26845 / % possible obs: 94.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 25.93 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.104 / Rsym value: 0.093 / Net I/σ(I): 9
Reflection shellResolution: 1.8→1.9 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 3422 / CC1/2: 0.851 / Rrim(I) all: 1.3 / Rsym value: 1.11

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold Model

Resolution: 1.8→37.31 Å / SU ML: 0.2736 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.7791
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2494 1216 4.79 %
Rwork0.2322 24157 -
obs0.2331 25373 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.38 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 0 206 2452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272333
X-RAY DIFFRACTIONf_angle_d0.5973172
X-RAY DIFFRACTIONf_chiral_restr0.0431351
X-RAY DIFFRACTIONf_plane_restr0.0038423
X-RAY DIFFRACTIONf_dihedral_angle_d12.3688883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.39321260.34732380X-RAY DIFFRACTION87.81
1.87-1.960.29831330.32272464X-RAY DIFFRACTION89.58
1.96-2.060.35111120.2952564X-RAY DIFFRACTION92.4
2.06-2.190.30741250.27262636X-RAY DIFFRACTION94.04
2.19-2.360.29241410.2742662X-RAY DIFFRACTION96.42
2.36-2.60.30991480.26172751X-RAY DIFFRACTION98.17
2.6-2.970.30641490.252792X-RAY DIFFRACTION98.72
2.97-3.740.2611240.21012864X-RAY DIFFRACTION98.48
3.74-37.310.16421580.18773044X-RAY DIFFRACTION98.25

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