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- PDB-5zf1: Molecular structure of a novel 5,10-methylenetetrahydrofolate deh... -

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Basic information

Entry
Database: PDB / ID: 5zf1
TitleMolecular structure of a novel 5,10-methylenetetrahydrofolate dehydrogenase from the silkworm, Bombyx mori
Components5,10-methylenetetrahydrofolate dehydrogenase
KeywordsOXIDOREDUCTASE / Lepidoptera / 5 / 10-methylenetetrahydrofolate dehydrogenase / NADP+ / Serine
Function / homologyLeucine Dehydrogenase, chain A, domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsHaque, R. / Higashiura, A. / Nakagawa, A. / Yamamoto, K.
CitationJournal: FEBS Open Bio / Year: 2019
Title: Molecular structure of a 5,10-methylenetetrahydrofolate dehydrogenase from the silkwormBombyx mori.
Authors: Haque, M.R. / Higashiura, A. / Nakagawa, A. / Hirowatari, A. / Furuya, S. / Yamamoto, K.
History
DepositionMar 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / 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
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5,10-methylenetetrahydrofolate dehydrogenase
B: 5,10-methylenetetrahydrofolate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0949
Polymers65,5242
Non-polymers5707
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-69 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.789, 89.789, 127.306
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 5,10-methylenetetrahydrofolate dehydrogenase


Mass: 32761.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: LOC101741628 / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 3.91 Å3/Da / Density % sol: 68.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1 M sodium cacodylate trihydrate, 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: AGILENT EOS CCD / Detector: CCD / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.75→38.3 Å / Num. obs: 100729 / % possible obs: 99.3 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 52.3
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.487

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.75→38.295 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.75
RfactorNum. reflection% reflection
Rfree0.2409 4958 4.93 %
Rwork0.2112 --
obs0.2127 100664 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→38.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4351 0 32 315 4698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074578
X-RAY DIFFRACTIONf_angle_d0.8696233
X-RAY DIFFRACTIONf_dihedral_angle_d6.2733867
X-RAY DIFFRACTIONf_chiral_restr0.057752
X-RAY DIFFRACTIONf_plane_restr0.006807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7492-1.76910.26561480.25283195X-RAY DIFFRACTION99
1.7691-1.78990.30571710.25313229X-RAY DIFFRACTION100
1.7899-1.81170.27561570.24343208X-RAY DIFFRACTION100
1.8117-1.83460.27781950.24643162X-RAY DIFFRACTION100
1.8346-1.85880.2591550.24433194X-RAY DIFFRACTION100
1.8588-1.88420.28731780.23953179X-RAY DIFFRACTION100
1.8842-1.91110.27921980.23283230X-RAY DIFFRACTION100
1.9111-1.93970.24871500.22073164X-RAY DIFFRACTION100
1.9397-1.970.23271480.22253248X-RAY DIFFRACTION100
1.97-2.00230.26311580.2283220X-RAY DIFFRACTION100
2.0023-2.03680.27511680.22623213X-RAY DIFFRACTION100
2.0368-2.07380.25051840.22273173X-RAY DIFFRACTION100
2.0738-2.11370.25031480.22473222X-RAY DIFFRACTION100
2.1137-2.15690.2451550.21663218X-RAY DIFFRACTION100
2.1569-2.20380.22841970.21813195X-RAY DIFFRACTION100
2.2038-2.2550.23891590.2123233X-RAY DIFFRACTION100
2.255-2.31140.23911770.21733195X-RAY DIFFRACTION100
2.3114-2.37390.2411390.2073202X-RAY DIFFRACTION100
2.3739-2.44370.23331790.21623207X-RAY DIFFRACTION100
2.4437-2.52260.23041710.21093206X-RAY DIFFRACTION100
2.5226-2.61270.23641530.20893245X-RAY DIFFRACTION100
2.6127-2.71730.22641860.21483203X-RAY DIFFRACTION100
2.7173-2.84090.26071750.22143199X-RAY DIFFRACTION100
2.8409-2.99070.27741570.22033243X-RAY DIFFRACTION100
2.9907-3.1780.24241590.22243215X-RAY DIFFRACTION100
3.178-3.42320.2431690.20973222X-RAY DIFFRACTION100
3.4232-3.76740.22071750.19433221X-RAY DIFFRACTION100
3.7674-4.31190.22861390.18593225X-RAY DIFFRACTION99
4.3119-5.43010.21511720.19013147X-RAY DIFFRACTION97
5.4301-38.30420.24611380.2162693X-RAY DIFFRACTION82

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